@article{aktar_serrano_ghiladi_franzen_2023, title={Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B}, volume={247}, ISSN={["1873-3344"]}, DOI={10.1016/j.jinorgbio.2023.112332}, abstractNote={The dehaloperoxidase-hemoglobin (DHP), first isolated from the coelom of a marine terebellid polychaete, Amphitrite ornata, is an example of a multi-functional heme enzyme. Long known for its reversible oxygen (O2) binding, further studies have established DHP activity as a peroxidase, oxidase, oxygenase, and peroxygenase. The specific reactivity depends on substrate binding at various internal and external binding sites. This study focuses on comparison of the binding and reactivity of the substrate 2,4-dichlorophenol (DCP) in the isoforms DHPA and B. There is strong interest in the degradation of DCP because of its wide use in the chemical industry, presence in waste streams, and particular reactivity to form dioxins, some of the most toxic compounds known. The catalytic efficiency is 3.5 times higher for DCP oxidation in DHPB than DHPA by a peroxidase mechanism. However, DHPA and B both show self-inhibition even at modest concentrations of DCP. This phenomenon is analogous to the self-inhibition of 2,4,6-trichlorophenol (TCP) at higher concentration. The activation energies of the electron transfer steps in DCP in DHPA and DHPB are 19.3 ± 2.5 and 24.3 ± 3.2 kJ/mol, respectively, compared to 37.2 ± 6.5 kJ/mol in horseradish peroxidase (HRP), which may be a result of the more facile electron transfer of an internally bound substrate in DHPA. The x-ray crystal structure of DHPA bound with DCP determined at 1.48 Å resolution, shows tight substrate binding inside the heme pocket of DHPA (PDB 8EJN). This research contributes to the studies of DHP as a naturally occurring bioremediation enzyme capable of oxidizing a wide range of environmental pollutants.}, journal={JOURNAL OF INORGANIC BIOCHEMISTRY}, author={Aktar, Mst Sharmin and Serrano, Vesna and Ghiladi, Reza and Franzen, Stefan}, year={2023}, month={Oct} }
 @article{madhuresh_nguyen_franzen_2023, title={The divergent pH dependence of substrate turnover in dehaloperoxidases A and B}, volume={238}, ISSN={["1873-3344"]}, DOI={10.1016/j.jinorgbio.2022.112029}, abstractNote={The pH-dependent peroxidase activity in both dehaloperoxidases A and B was studied by a kinetic assay, stopped flow spectroscopy, resonance Raman spectroscopy, and high-performance liquid chromatography at pH 5.0, 6.0, and 7.0. At pH 7.0, both isozymes follow the peroxidase ping-pong kinetic model derived from the three-step reaction scheme using the steady-state approximation. However, deviation from standard saturation behavior is observed at pH < 6.0 and [TCP] > 0.7 mM, owing to multiple processes: a) self-inhibition of TCP by internal binding; b) oxidation of the product by a pH- and concentration-dependent secondary reaction; and c) formation of an inactive species known as compound RH in the absence of oxidizable substrate. Although DHP-A and DHP-B differ by only 5 amino acids, they show a complete trend reversal in their observed peroxidase kinetics and product yields. Although at pH 7.0 DHP-B had higher TCP oxidation activity than DHP-A as reported previously, as pH was lowered, DHP-A appeared to have a higher peroxidase activity than DHP-B. This is an unprecedented result. However, the fact that there are multiple processes contributing to both kinetics and yield of TCP oxidation complicates interpretation of these data. Deactivation via compound RH and self-inhibition are pH dependent reactions that compete with substrate oxidation. Compound RH formation was observed to be rapid at low pH. A complete set of control experiments were conducted to differentiate the various contributions to the observed enzyme kinetics.}, journal={JOURNAL OF INORGANIC BIOCHEMISTRY}, author={Madhuresh, Nikhila Kashyap Dhanvantari and Nguyen, Hilbert and Franzen, Stefan}, year={2023}, month={Jan} }
 @article{gao_aspnes_franzen_2022, title={Classical Model of Surface Enhanced Infrared Absorption (SEIRA) Spectroscopy}, volume={1}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.1c08463}, abstractNote={The molecule-plasmon interaction is the key to the mechanisms of surface enhanced infrared absorption (SEIRA) and surface enhanced Raman scattering (SERS). Since plasmons are well described by Maxwell's equations, one fundamental treatment involves the classical interpretation of infrared absorption and resonance Raman spectroscopies. We can understand the molecule-plasmon interaction using electromagnetic theory if the classical field effect on a transition dipole moment or transition polarizability is properly described. In previous work, we derived the Raman excitation profile of a model molecule using a classical driven spring attached to a charged mass with a perturbative force constant due to vibrational oscillations. In this study we generalize the interactions of plasmons with molecules by considering the N2O asymmetric stretch SEIRA signal on a Dy doped CdO (CdO:Dy) film. This semiconductor has tunable plasmon dispersion curves throughout the near-and mid-infrared that can interact directly with vibrational absorption transitions. We have demonstrated this using the Kretschmann configuration with a CaF2 prism and a MgO substrate. The model predicts the phase behavior of SEIRA. The calculated enhancement factor relative to an Au control is 6.2, in good agreement with the value of 6.8 ± 0.5 measured under the same conditions.}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Gao, Yuan and Aspnes, D. E. and Franzen, Stefan}, year={2022}, month={Jan} }
 @article{thompson_shay_serrano_dumarieh_ghiladi_franzen_2021, title={A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study}, volume={25}, ISSN={["1099-1409"]}, DOI={10.1142/S1088424621500826}, abstractNote={As multifunctional catalytic hemoglobins, dehaloperoxidase isoenzymes A and B (DHP A and B) are among the most versatile hemoproteins in terms of activities displayed. The ability of DHP to bind over twenty different substrates in the distal pocket might appear to resemble the promiscuousness of monooxygenase enzymes, yet there are identifiable substrate-specific interactions that can steer the type of oxidation (O-atom vs. electron transfer) that occurs inside the DHP distal pocket. Here, we have investigated the DHP A(V59W) mutant in order to probe the limits of conformational flexibility in the distal pocket as it relates to the genesis of this substrate-dependent activity differentiation. The X-ray crystal structure of the metaquo DHP A(V59W) mutant (PDB 3K3U) and the V59W mutant in complex with fluoride [denoted as DHP A(V59W-F)] (PDB 7MNH) show significant mobility of the tryptophan in the distal pocket, with two parallel conformations having W59-N[Formula: see text] H-bonded to a heme-bound ligand (H 2 O or F[Formula: see text], and another conformation [observed only in DHP A(V59W-F)] that brings W59 sufficiently close to the heme as to preclude axial ligand binding. UV-vis and resonance Raman spectroscopic studies show that DHP A(V59W) is 5-coordinate high spin (5cHS) at pH 5 and 6-coordinate high spin (6cHS) at pH 7, whereas DHP A(V59W-F) is 6cHS from pH 5 to 7. Enzyme assays confirm robust peroxidase activity at pH 5, but complete loss of activity at pH 7. We find no evidence that tryptophan plays a role in the oxidation mechanism ([Formula: see text]. radical formation). Instead, the data reveal a new mechanism of DHP inhibition, namely a shift towards a non-reactive form by OH[Formula: see text] ligation to the heme-Fe that is strongly stabilized (presumably through H-bonding interactions) by the presence of W59 in the distal cavity.}, number={7-8}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Thompson, Matthew K. and Shay, Madeline R. and Serrano, Vesna and Dumarieh, Rania and Ghiladi, Reza A. and Franzen, Stefan}, year={2021}, month={Jul}, pages={756–771} }
 @article{gao_aspnes_franzen_2020, title={Classical Correlation Model of Resonance Raman Spectroscopy}, volume={124}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.0c04401}, abstractNote={A classical correlation model (CCM), based on forces instead of potentials, is developed and applied to resonance Raman scattering to provide a foundation for further advances in understanding the effects of fields and vibronic perturbations on the optical properties of materials by a simple, yet versatile, description. The model consists of a charge connected by a classical spring to a surface and driven by an external electric field. The spring represents the charge cloud of the electrons and the transition strength, and the surface represents the nucleus or molecule. Molecular vibrations are assumed to be many-body effects that change the configuration and hence modify the spring constant directly, as opposed to all previous classical models of Raman scattering, and opposed to the anisotropic bond model (ABM) of nonlinear optics, by adding anharmonic terms to the potential. The resulting expression agrees exactly with quantum mechanical models of resonance Raman scattering in the limit of weak electron-phonon coupling, and it agrees well when the coupling becomes strong. The result is a classical derivation of Kramers-Heisenberg-Dirac scattering theory. We show that the difference between classical and quantum approaches lies only in the interpretation of the prefactor. In particular, the Raman excitation profile shows excellent agreement with all other methods of calculation. By comparing complementary classical and quantum solutions of the same complex system, understanding of both is enhanced.}, number={44}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Gao, Y. and Aspnes, D. E. and Franzen, S.}, year={2020}, month={Nov}, pages={9177–9186} }
 @article{sachet_aspnes_maria_franzen_2020, title={Critical Test of the Interaction of Surface Plasmon Resonances with Molecular Vibrational Transitions}, volume={124}, ISSN={["1520-5215"]}, DOI={10.1021/acs.jpca.9b10835}, abstractNote={We determine the infrared absorption spectra of a gas due to evanescent plasmonic electromagnetic fields in a system where surface interactions (physisorption and chemisorption) are demonstrably negligible. The plasmonic host material, the degenerate semiconductor CdO:Dy, has high mobility (366–450 cm2/(V s)) and carrier density ((0.6–3.5) × 1020 cm–3), and therefore supports low-loss surface plasmon resonances in the mid-IR. This high-mobility layer gives the highest resolution observed in a plasmonic conducting material in the infrared, higher than that of gold and rivaling that of silver. The high resolution permits a new understanding of the nature of the interaction of emerging fields with molecular transitions. Using different carrier concentrations, the resonance condition of the surface plasmon polariton (SPP) frequency (ωSPP) and N2O vibrational absorption spectral frequency (ωN2O) can be controlled, thereby allowing a critical test of field–molecule interactions. Experiment and theory both indicate a dispersive N2O line shape for ωSPP < ωN2O, an absorptive line shape for ωSPP < ωN2O, and an abrupt change between the two when the resonance condition ωSPP < ωN2O is reached. A first-order expansion of the Airy equation describes this behavior analytically. The SPP surface enhancement is 6.8 ± 0.5 on-resonance, lower than enhancements observed in other systems, but in agreement with recent quantitative reports of surface enhanced infrared reflection absorption spectroscopy (SEIRA). Our results show that interactions of infrared SPPs with molecular vibrations are in the weak coupling limit, and that enhancements comparable those reported for noble metals can be achieved.}, number={9}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Sachet, Edward and Aspnes, D. E. and Maria, J-P and Franzen, Stefan}, year={2020}, month={Mar}, pages={1744–1753} }
 @misc{khamh_sachet_kelly_maria_franzen_2018, title={As good as gold and better: conducting metal oxide materials for mid-infrared plasmonic applications}, volume={6}, ISSN={["2050-7534"]}, DOI={10.1039/c7tc05760a}, abstractNote={Review of material properties of conducting metal oxides that make them suitable for mid-infrared surface plasmon resonance applications.}, number={31}, journal={JOURNAL OF MATERIALS CHEMISTRY C}, author={Khamh, Hniang and Sachet, Edward and Kelly, Kyle and Maria, Jon-Paul and Franzen, Stefan}, year={2018}, month={Aug}, pages={8326–8342} }
 @article{zhao_xue_gudanis_gracz_findenegg_gdaniec_franzen_2018, title={Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation}, volume={181}, ISSN={["1873-3344"]}, DOI={10.1016/j.jinorgbio.2018.01.006}, abstractNote={Dehaloperoxidase-hemoglobin is the first hemoglobin identified with biologically-relevant oxidative functions, which include peroxidase, peroxygenase and oxidase activities. Herein we report a study of the protein backbone dynamics of DHP using heteronuclear NMR relaxation methods and molecular dynamics (MD) simulations to address the role of protein dynamics in switching from one function to another. The results show that DHP's backbone helical regions and turns have average order parameters of S2 = 0.87 ± 0.03 and S2 = 0.76 ± 0.08, respectively. Furthermore, DHP is primarily a monomer in solution based on the overall tumbling correlation time τm is 9.49 ± 1.65 ns calculated using the prolate diffusion tensor model in the program relax. A number of amino acid residues have significant Rex using the Lipari-Szabo model-free formalism. These include Lys3, Ile6, Leu13, Gln18, Arg32, Ser48, Met49, Thr56, Phe60, Arg69, Thr71 Cys73, Ala77, Asn81, Gly95, Arg109, Phe115, Leu127 and Met136, which may experience slow conformational motions on the microseconds-milliseconds time scale according to the model. Caution should be used when the model contains >4 fitting parameters. The program caver3.0 was used to identify tunnels inside DHP obtained from MD simulation snapshots that are consistent with the importance of the Xe binding site, which is located at the central intersection of the tunnels. These tunnels provide diffusion pathways for small ligands such as O2, H2O and H2O2 to enter the distal pocket independently of the trajectory of substrates and inhibitors, both of which are aromatic molecules.}, journal={JOURNAL OF INORGANIC BIOCHEMISTRY}, author={Zhao, Jing and Xue, Mengjun and Gudanis, Dorota and Gracz, Hanna and Findenegg, Gerhard H. and Gdaniec, Zofia and Franzen, Stefan}, year={2018}, month={Apr}, pages={65–73} }
 @article{wu_zhao_franzen_tsai_2017, title={Bindings of NO, CO, and O-2 to multifunctional globin type dehaloperoxidase follow the 'sliding scale rule'}, volume={474}, journal={Biochemical Journal (London, England : 1984)}, author={Wu, G. and Zhao, J. and Franzen, S. and Tsai, A. L.}, year={2017}, pages={3485–3498} }
 @article{wu_zhao_franzen_tsai_2017, title={Bindings of NO, CO, and O2 to multifunctional globin type dehaloperoxidase follow the ‘sliding scale rule’}, volume={474}, ISSN={0264-6021 1470-8728}, url={http://dx.doi.org/10.1042/BCJ20170515}, DOI={10.1042/BCJ20170515}, abstractNote={Dehaloperoxidase–hemoglobin (DHP), a multifunctional globin protein, not only functions as an oxygen carrier as typical globins such as myoglobin and hemoglobin, but also as a peroxidase, a mono- and dioxygenase, peroxygenase, and an oxidase. Kinetics of DHP binding to NO, CO, and O2 were characterized for wild-type DHP A and B and the H55D and H55V DHP A mutants using stopped-flow methods. All three gaseous ligands bind to DHP significantly more weakly than sperm whale myoglobin (SWMb). Both CO and NO bind to DHP in a one-step process to form a stable six-coordinate complex. Multiple-step NO binding is not observed in DHP, which is similar to observations in SWMb, but in contrast with many heme sensor proteins. The weak affinity of DHP for O2 is mainly due to a fast O2 dissociation rate, in accordance with a longer εN–Fe distance between the heme iron and distal histidine in DHP than that in Mb, and an open-distal pocket that permits ligand escape. Binding affinities in DHP show the same 3–4 orders separation between the pairs NO/CO and CO/O2, consistent with the ‘sliding scale rule’ hypothesis. Strong gaseous ligand discrimination by DHP is very different from that observed in typical peroxidases, which show poor gaseous ligand selectivity, correlating with a neutral proximal imidazole ligand rather than an imidazolate. The present study provides useful insights into the rationale for DHP to function both as mono-oxygenase and oxidase, and is the first example of a globin peroxidase shown to follow the ‘sliding scale rule’ hypothesis in gaseous ligand discrimination.}, number={20}, journal={Biochemical Journal}, publisher={Portland Press Ltd.}, author={Wu, Gang and Zhao, Jing and Franzen, Stefan and Tsai, Ah-Lim}, year={2017}, month={Oct}, pages={3485–3498} }
 @article{mccombs_moreno-chicano_carey_franzen_hough_ghiladi_2017, title={Interaction of Azole-Based Environmental Pollutants with the Coelomic Hemoglobin from Amphitrite ornata: A Molecular Basis for Toxicity}, volume={56}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/acs.biochem.7b00041}, DOI={10.1021/acs.biochem.7b00041}, abstractNote={The toxicities of azole pollutants that have widespread agricultural and industrial uses are either poorly understood or unknown, particularly with respect to how infaunal organisms are impacted by this class of persistent organic pollutant. To identify a molecular basis by which azole compounds may have unforeseen toxicity on marine annelids, we examine here their impact on the multifunctional dehaloperoxidase (DHP) hemoglobin from the terebellid polychaete Amphitrite ornata. Ultraviolet-visible and resonance Raman spectroscopic studies showed an increase in the six-coordinate low-spin heme population in DHP isoenzyme B upon binding of imidazole, benzotriazole, and benzimidazole (Kd values of 52, 82, and 110 μM, respectively), suggestive of their direct binding to the heme-Fe. Accordingly, atomic-resolution X-ray crystal structures, supported by computational studies, of the DHP B complexes of benzotriazole (1.14 Å), benzimidazole (1.08 Å), imidazole (1.08 Å), and indazole (1.12 Å) revealed two ligand binding motifs, one with direct ligand binding to the heme-Fe, and another in which the ligand binds in the hydrophobic distal pocket without coordinating the heme-Fe. Taken together, the results demonstrate a new mechanism by which azole pollutants can potentially disrupt hemoglobin function, thereby improving our understanding of their impact on infaunal organisms in marine and aquatic environments.}, number={17}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={McCombs, Nikolette L. and Moreno-Chicano, Tadeo and Carey, Leiah M. and Franzen, Stefan and Hough, Michael A. and Ghiladi, Reza A.}, year={2017}, month={Apr}, pages={2294–2303} }
 @article{thompson_lamb_delley_franzen_2017, title={Vibrational spectroscopy of the double complex salt Pd(NH3)4(ReO4)2, a bimetallic catalyst precursor}, volume={173}, ISSN={1386-1425}, url={http://dx.doi.org/10.1016/J.SAA.2016.10.011}, DOI={10.1016/J.SAA.2016.10.011}, abstractNote={Tetraamminepalladium(II) perrhenate, a double complex salt, has significant utility in PdRe catalyst preparation; however, the vibrational spectra of this readily prepared compound have not been described in the literature. Herein, we present the infrared (IR) and Raman spectra of tetraamminepalladium(II) perrhenate and several related compounds. The experimental spectra are complemented by an analysis of normal vibrational modes that compares the experimentally obtained spectra with spectra calculated using DFT (DMol3). The spectra are dominated by features due to the ammine groups and the ReO stretch in Td ReO4-; lattice vibrations due to the D4h Pd(NH3)42+ are also observed in the Raman spectrum. Generally, we observe good agreement between ab initio calculations and experimental spectra. The calculated IR spectrum closely matches experimental results for peak positions and their relative intensities. The methods for calculating resonance Raman intensities are implemented using the time correlator formalism using two methods to obtain the excited state displacements and electron-vibration coupling constants, which are the needed inputs in addition to the normal mode wave numbers. Calculated excited state energy surfaces of Raman-active modes correctly predict relative intensities of the peaks and Franck-Condon activity; however, the position of Raman bands are predicted at lower frequencies than observed. Factor group splitting of Raman peaks observed in spectra of pure compounds is not predicted by DFT.}, journal={Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy}, publisher={Elsevier BV}, author={Thompson, Simon T. and Lamb, H. Henry and Delley, Bernard and Franzen, Stefan}, year={2017}, month={Feb}, pages={618–624} }
 @article{franzen_ghiladi_lebioda_dawson_2016, title={Multi-functional hemoglobin dehaloperoxidases}, number={4}, journal={Heme peroxidases}, author={Franzen, S. and Ghiladi, R. A. and Lebioda, L. and Dawson, J.}, year={2016}, pages={218–244} }
 @article{kang_losego_sachet_maria_franzen_2016, title={Near-Infrared Optical Extinction of Indium Tin Oxide Structures Prepared by Nanosphere Lithography}, volume={3}, ISSN={["2330-4022"]}, DOI={10.1021/acsphotonics.6b00649}, abstractNote={Indium tin oxide (ITO) has been the most widely studied conducting metal oxide and serves as the best candidate for proof-of-concept experiments in the field of surface plasmon resonance and studies of electric field confinement and manipulation. ITO is chemically stable and relatively easy to sputter. In this report, arrays of ITO nanostructures were produced using nanosphere lithography, which was originally developed for plasmonic applications involving noble metals. However, the experiments presented here show that patterned ITO with similar size and shape to noble metals has an observed extinction that corresponds to the epsilon-near-zero mode. The carrier density of ITO nanostructure can be controlled by the postdeposition annealing process. Thus, one can prove that the optical signals on the surface are those of the ITO nanostructure by reversible on/off switching of the capacitive plasmon resonance by annealing the surfaces successively in forming gas (N2/H2) and in air. Thus, using conducting metal oxides confident of the electric field is possible not only along the z-axis perpendicular to the thin film but within the plane of the film as well.}, number={10}, journal={ACS PHOTONICS}, author={Kang, Misun and Losego, Mark and Sachet, Edward and Maria, Jon-Paul and Franzen, Stefan}, year={2016}, month={Oct}, pages={1993–1999} }
 @article{zhang_santos_zhou_liang_wang_wu_franzen_2016, title={Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin}, volume={211}, ISSN={["1873-4200"]}, DOI={10.1016/j.bpc.2016.01.003}, abstractNote={The binding free energy of 4-bromophenol (4-BP), an inhibitor that binds in the internal binding site in dehaloperoxidase-hemoglobin (DHP) was calculated using Molecular Dynamics (MD) methods combined with pulling or umbrella sampling. The effects of systematic changes in the pulling speed, pulling force constant and restraint force constant on the calculated potential of mean force (PMF) are presented in this study. The PMFs calculated using steered molecular dynamics (SMD) were validated by umbrella sampling (US) in the strongly restrained regime. A series of restraint force constants ranging from 1000 down to 5 kJ/(mol nm(2)) were used in SMD simulations. This range was validated using US, however noting that weaker restraints give rise to a broader sampling of configurations. This comparison was further tested by a pulling simulation conducted without any restraints, which was observed to have a value closest to the experimentally measured free energy for binding of 4-BP to DHP based on ultraviolet-visible (UV-vis) and resonance Raman spectroscopies. The protein-inhibitor system is well suited for fundamental study of free energy calculations because the DHP protein is relatively small and the inhibitor is quite rigid. Simulation configuration structures are compared to the X-ray crystallography structures of the binding site of 4-BP in the distal pocket above the heme.}, journal={BIOPHYSICAL CHEMISTRY}, author={Zhang, Zhisen and Santos, Andrew P. and Zhou, Qing and Liang, Lijun and Wang, Qi and Wu, Tao and Franzen, Stefan}, year={2016}, month={Apr}, pages={28–38} }
 @article{franzen_cochran_weng_bartolotti_delley_2016, title={The quadrapolar character of the Markovnikov reaction transition state}, volume={464}, ISSN={["1873-4421"]}, DOI={10.1016/j.chemphys.2015.11.001}, abstractNote={The properties of the transition states for the electrophilic addition reactions of four molecules of the type HX (X = Br, Cl, F and OH) to 1-propene form 2-X propane by the Markovnikov mechanism have been calculated using density functional theory (DFT). A comparative study of the transition state along the reaction path for both M and AM addition was studied in order to understand the origins of regioselectivity of H2O. The quadrapolar nature of the transition state is arises because of a sequential mechanism, in which the addition across the π-bond occurs in two steps, first H+ and then X−. The M reaction mechanism is consistent with a H+X− dipole which induces an oppositely polarized C1−C2+ dipole in the transition state, resulting in a quadrupole. The C1−C2+ dipole in the M mechanism is consistently larger than the C1+C2− dipole of the AM transition state for all species studied.}, journal={CHEMICAL PHYSICS}, author={Franzen, Stefan and Cochran, Kristin H. and Weng, James and Bartolotti, Libero and Delley, Bernard}, year={2016}, month={Jan}, pages={46–54} }
 @article{burns_huang_weare_bartolotti_wang_yao_li_franzen_2015, title={Aerobic oxidation of beta-isophorone by tetraphenylporphYrin catalysts in pyridine solution}, volume={410}, ISSN={["1873-314X"]}, DOI={10.1016/j.molcata.2015.09.015}, abstractNote={A kinetic study was conducted using five metallo-tetraphenylporphyrins (MTPPs) as catalysts for the aerobic oxidation reaction of β-isophorone (β-IP) to ketoisophorone (KIP). The oxidation reaction catalyzed by MTPPs (M = Cr, Mn, Fe, Co and Cu) was observed over a seven hour period under a range of experimental conditions. Changes in the specificity of conversion of reactant to the product, KIP, and the main side-product, α-isophorone (α-IP), were observed at temperatures ranging from 60 °C to 75 °C, in solvents with varying compositions of pyridine and β-IP, with different MTPP catalysts, oxygen gas flow rates, and solution agitation frequencies. Control experiments show that MTPP catalysts modestly increase the rate of KIP formation, but significantly improve specificity through the apparent suppression of α-IP formation. Analysis revealed that MnTPP (CH3COO−) produced the highest product specificity ratio [KIP]/[α-IP]. Given that all of the metals were in the 3+ oxidation state in this study and there was no observed binding by O2 to any of the MTPP catalysts, the catalytic mechanism is suggested to involve the binding of β-IP to the MTPP metal center. Binding of β-IP is most favorable when pyridine is the trans ligand, but β-IP is also observed to weakly bind when trans to acetate in the MnTPP adduct. This conclusion is supported by electronic absorption spectroscopy, resonance Raman spectroscopy and density functional theory (DFT) calculations. The role played by the catalyst appears to be the activation of hydrogen abstraction following the substrate's ligation to the metal, rather than the more traditional role of MTPPs as O2 activation catalysts by ligation of diatomic O2. β-IP oxidation is an example of a case where the catalyst appears to have a more important role for improving the specificity of the reaction (through decreasing side-product formation) rather than increasing the rate of product formation.}, journal={JOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL}, author={Burns, Eric and Huang, Tao and Weare, Walter W. and Bartolotti, Libero and Wang, Xinyu and Yao, Jia and Li, Haoran and Franzen, Stefan}, year={2015}, month={Dec}, pages={110–120} }
 @article{zhao_lu_franzen_2015, title={Distinct Enzyme-Substrate Interactions Revealed by Two Dimensional Kinetic Comparison between Dehaloperoxidase-Hemoglobin and Horseradish Peroxidase}, volume={119}, ISSN={["1520-6106"]}, DOI={10.1021/acs.jpcb.5b07126}, abstractNote={The time-resolved kinetics of substrate oxidation and cosubstrate H2O2 reduction by dehaloperoxidase-hemoglobin (DHP) on a seconds-to-minutes time scale was analyzed for peroxidase substrates 2,4,6-tribromophenol (2,4,6-TBP), 2,4,6-trichlorophenol (2,4,6-TCP), and ABTS. Substrates 2,4,6-TBP and 2,4,6-TCP show substrate inhibition at high concentration due to the internal binding at the distal pocket of DHP, whereas ABTS does not show substrate inhibition at any concentration. The data are consistent with an external binding site for the substrates with an internal substrate inhibitor binding site for 2,4,6-TBP and 2,4,6-TCP. We have also compared the kinetic behavior of horseradish peroxidase (HRP) in terms of kcat, Km(AH2) and Km(H2O2) using the same kinetic scheme. Unlike DHP, HRP does not exhibit any measurable substrate inhibition, consistent with substrate binding at the edge of heme near the protein surface at all substrate concentrations. The binding of substrates and their interactions with the heme iron were further compared between DHP and HRP using a competitive fluoride binding experiment, which provides a method for quantitative measurement of internal association constants associated with substrate inhibition. These experiments show the regulatory role of an internal substrate binding site in DHP from both a kinetic and competitive ligand binding perspective. The interaction of DHP with substrates as a result of internal binding actually stabilizes that protein and permits DHP to function under conditions that denature HRP. As a consequence, DHP is a tortoise, a slow but steady enzyme that wins the evolutionary race against the HRP-type of peroxidase, which is a hare, initially rapid, but flawed for this application because of the protein denaturation under the conditions of the experiment.}, number={40}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Zhao, Jing and Lu, Chang and Franzen, Stefan}, year={2015}, month={Oct}, pages={12828–12837} }
 @article{sachet_shelton_harris_gaddy_irving_curtarolo_donovan_hopkins_sharma_sharma_et al._2015, title={Dysprosium-doped cadmium oxide as a gateway material for mid-infrared plasmonics}, volume={14}, ISSN={1476-1122 1476-4660}, url={http://dx.doi.org/10.1038/NMAT4203}, DOI={10.1038/NMAT4203}, abstractNote={The interest in plasmonic technologies surrounds many emergent optoelectronic applications, such as plasmon lasers, transistors, sensors and information storage. Although plasmonic materials for ultraviolet-visible and near-infrared wavelengths have been found, the mid-infrared range remains a challenge to address: few known systems can achieve subwavelength optical confinement with low loss in this range. With a combination of experiments and ab initio modelling, here we demonstrate an extreme peak of electron mobility in Dy-doped CdO that is achieved through accurate 'defect equilibrium engineering'. In so doing, we create a tunable plasmon host that satisfies the criteria for mid-infrared spectrum plasmonics, and overcomes the losses seen in conventional plasmonic materials. In particular, extrinsic doping pins the CdO Fermi level above the conduction band minimum and it increases the formation energy of native oxygen vacancies, thus reducing their populations by several orders of magnitude. The substitutional lattice strain induced by Dy doping is sufficiently small, allowing mobility values around 500 cm(2) V(-1) s(-1) for carrier densities above 10(20) cm(-3). Our work shows that CdO:Dy is a model system for intrinsic and extrinsic manipulation of defects affecting electrical, optical and thermal properties, that oxide conductors are ideal candidates for plasmonic devices and that the defect engineering approach for property optimization is generally applicable to other conducting metal oxides.}, number={4}, journal={Nature Materials}, publisher={Springer Science and Business Media LLC}, author={Sachet, Edward and Shelton, Christopher T. and Harris, Joshua S. and Gaddy, Benjamin E. and Irving, Douglas L. and Curtarolo, Stefano and Donovan, Brian F. and Hopkins, Patrick E. and Sharma, Peter A. and Sharma, Ana Lima and et al.}, year={2015}, month={Feb}, pages={414–420} }
 @article{zhao_moretto_le_franzen_2015, title={Measurement of Internal Substrate Binding in Dehaloperoxidase-Hemoglobin by Competition with the Heme-Fluoride Binding Equilibrium}, volume={119}, ISSN={["1520-5207"]}, DOI={10.1021/jp512996v}, abstractNote={The application of fluoride anion as a probe for investigating the internal substrate binding has been developed and applied to dehaloperoxidase-hemoglobin (DHP) from Amphitrite ornata. By applying the fluoride titration strategy using UV-vis spectroscopy, we have studied series of halogenated phenols, other substituted phenols, halogenated indoles, and several natural amino acids that bind internally (and noncovalently) in the distal binding pocket of the heme. This approach has identified 2,4-dibromophenol (2,4-DBP) as the tightest binding substrate discovered thus far, with approximately 20-fold tighter binding affinity than that of 4-bromophenol (4-BP), a known internally binding inhibitor in DHP. Combined with resonance Raman spectroscopy, we have confirmed that competitive binding equilibria exist between fluoride anion and internally bound molecules. We have further investigated the hydrogen bonding network of the active site of DHP that stabilizes the exogenous fluoride ligand. These measurements demonstrate a general method for determination of differences in substrate binding affinity based on detection of a competitive fluoride binding equilibrium. The significance of the binding that 2,4-dibromophenol binds more tightly than any other substrate is evident when the structural and mechanistic data are taken into consideration.}, number={7}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Zhao, Jing and Moretto, Justin and Le, Peter and Franzen, Stefan}, year={2015}, month={Feb}, pages={2827–2838} }
 @article{zhao_serrano_franzen_2014, title={A Model for the Flexibility of the Distal Histidine in Dehaloperoxidase-Hemoglobin A Based on X-ray Crystal Structures of the Carbon Monoxide Adduct}, volume={53}, ISSN={["0006-2960"]}, DOI={10.1021/bi5001905}, abstractNote={Dehaloperoxidase hemoglobin A (DHP A) is a multifunctional hemoglobin that appears to have evolved oxidative pathways for the degradation of xenobiotics as a protective function that complements the oxygen transport function. DHP A possesses at least two internal binding sites, one for substrates and one for inhibitors, which include various halogenated phenols and indoles. Herein, we report the X-ray crystallographic structure of the carbonmonoxy complex (DHPCO). Unlike other DHP structures with 6-coordinated heme, the conformation of the distal histidine (H55) in DHPCO is primarily external or solvent exposed, despite the fact that the heme Fe is 6-coordinated. As observed generally in globins, DHP exhibits two distal histidine conformations (one internal and one external). In previous structural studies, we have shown that the distribution of H55 conformations is weighted strongly toward the external position when the DHP heme Fe is 5-coordinated. The large population of the external conformation of the distal histidine observed in DHPCO crystals at pH 6.0 indicates that some structural factor in DHP must account for the difference from other globins, which exhibit a significant external conformation only when pH < 4.5. While the original hypothesis suggested that interaction with a heme-Fe-bound ligand was the determinant of H55 conformation, the current study forces a refinement of that hypothesis. The external or open conformation of H55 is observed to have interactions with two propionate groups in heme, at distances of 3.82 and 2.73 Å, respectively. A relatively weak hydrogen bonding interaction between H55 and CO, combined with strong interactions with heme propionate (position 6), is hypothesized to strengthen the external conformation of H55. Density function theory (DFT) calculations were conducted to test whether there is a weaker hydrogen bond interaction between H55 and heme bonded CO or O2. Molecular dynamics simulations were conducted to examine how the tautomeric forms of H55 affect the dynamic motions of the distal histidine that govern the switching between open and closed conformations. The calculations support the modified hypothesis suggesting a competition between the strength of interactions with heme ligand and the heme propionates as the factors that determine the conformation of the distal histidine.}, number={15}, journal={BIOCHEMISTRY}, author={Zhao, Junjie and Serrano, Vesna and Franzen, Stefan}, year={2014}, month={Apr}, pages={2474–2482} }
 @article{guo_franzen_ye_gu_yu_2014, title={Controlling enantioselectivity of esterase in asymmetric hydrolysis of aryl prochiral diesters by introducing aromatic interactions}, volume={111}, ISSN={0006-3592}, url={http://dx.doi.org/10.1002/BIT.25249}, DOI={10.1002/BIT.25249}, abstractNote={Aromatic interactions specific to aryl radicals were introduced into two esterases, BioH from Escherichia coli and RspE from Rhodobacter sphaeroides to control their enantioselectivity in the asymmetric hydrolysis of prochiral aryl glutaric acid diesters. As a result, the enantiomeric excess (ee) of the S-product of dimethyl 3-phenylglutarate was increased from 25% (BioH wild type) to 96% (B_L83F/L86F) and from 13% (RspE wild type) to >99% (R_Y27R), respectively, while another variant of RspE R_M121F gave a reversed ee of 50% (R-product). Similar enhancement or reversion of enantioselectivity were also observed in the hydrolysis of three other prochiral aryl diesters (dimethyl 3-(4-flouro)-phenylglutarate, dimethyl 3-(4-cholo)-phenylglutarate and dimethyl 3-(3,4-dicholo)-phenylglutarate). Especially, the mutant R_Y27R was shown to be an excellent S-selective hydrolase for prochiral aryl diesters, with ee of all S-products >99%. In the mutants with altered enantioselectivity, the successful introduction of designed aromatic interactions was confirmed by molecular dynamics simulations and binding free energy analysis. These results demonstrate that aromatic interaction is one of the origins of enzyme enantioselectivity, the tuning of which leads to dramatic change in enantioselectivity. Besides, the successful engineering of the enantioselectivity in two different proteins toward four different substrates suggests that the introduction of aromatic interactions is a generally applicable strategy in the control of enantioselectivity toward aryl substrates. Biotechnol. Bioeng. 2014;111: 1729–1739. © 2014 Wiley Periodicals, Inc.}, number={9}, journal={Biotechnology and Bioengineering}, publisher={Wiley}, author={Guo, Fei and Franzen, Stefan and Ye, Lidan and Gu, Jiali and Yu, Hongwei}, year={2014}, month={Apr}, pages={1729–1739} }
 @article{le_zhao_franzen_2014, title={Correlation of Heme Binding Affinity and Enzyme Kinetics of Dehaloperoxidase}, volume={53}, ISSN={["0006-2960"]}, DOI={10.1021/bi5005975}, abstractNote={Chemical and thermal denaturation of dehaloperoxidase-hemoglobin (DHP) was investigated to test the relative stability of isoforms DHP A and DHP B and the H55V mutant of DHP A with respect to heme loss. In thermal denaturation experiments, heme loss was observed at temperatures of 54, 46, and 61 °C in DHP A, DHP B, and H55V, respectively. Guanidinium hydrochloride (GdnHCl)- and urea-induced denaturation was observed at respective concentrations of 1.15 ± 0.01 M DHP A and 1.09 ± 0.02 M DHP B, and 5.19 ± 0.05 M DHP A and 4.12 ± 0.14 M DHP B, respectively. The binding affinity of heme appears to be significantly smaller in both isoforms of DHP than in myoglobins. This observation was corroborated by heme transfer experiments, in which heme was observed to transfer for DHP A and B to horse skeletal muscle myoglobin (HSMb). GdnHCl-induced denaturation suggests a threshold of 1 mM for stabilization by binding of the inhibitor 4-bromophenol (4-BP). Concentrations of 4-BP greater than 1 mM caused destabilization. Urea-induced denaturation showed only destabilizing effects from phenolic ligand binding. Heme transfer experiments from DHP to HSMb further support the hypothesis that the binding of halophenols to DHP facilitates the removal of the heme. Thermal denaturation assessed via UV–visible spectroscopy and that assessed by differential scanning calorimetry (DSC) are both in agreement with chemical denaturation experiments and show that the denaturing abilities of the halophenols improve with the size of the para halogen atom in 4-XP, where X = iodo, bromo, chloro, or fluoro (4-IP > 4-BP > 4-CP > 4-FP), and the number of halo substituents as in 2,4,6-tribromophenol (2,4,6-TBP > 4-BP). DHP B, which differs in five amino acids, is less stable than DHP A with ΔHcal and Tm values of 165.1 kJ/mol and 47.5 °C compared to values of 183.3 kJ/mol and 50.4 °C for DHP B and DHP A, respectively. Kinetic studies verified that DHP B has a catalytic efficiency (kcat/Km) ∼5–6 times greater than that of DHP A but showed an increased level of substrate inhibition in DHP B for both 2,4,6-TCP and 2,4,6-TBP. An inverse correlation between protein stability with respect to heme loss and catalytic efficiency is suggested on the basis of the fact that the heme in DHP B has a stability lower than that of DHP A but a catalytic efficiency higher than that of DHP A.}, number={44}, journal={BIOCHEMISTRY}, author={Le, Peter and Zhao, Jing and Franzen, Stefan}, year={2014}, month={Nov}, pages={6863–6877} }
 @article{franzen_zhao_gracz_2014, title={Dynamics of Multifunctional Dehaloperoxidase Hemoglobin}, volume={106}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/J.BPJ.2013.11.3665}, DOI={10.1016/J.BPJ.2013.11.3665}, abstractNote={Multi-functional dehaloperoxidase-hemoglobin (DHP) is a versatile protein that functions as an oxygen transporter, but also has functions related to detoxification of a range of substrates including brominated phenols and indoles. It is ironic that the inhibitor binding site has been known for 15 years, but the substrate binding sites remain elusive. Two recent X-ray crystallographic studies reveal internal substrate binding sites. However, since there are at least three binding sites for 2,4,6-trihalophenols alone, the functional location of substrate binding remains unresolved. Moreover, recent kinetic data show that a number of indoles are excellent substrates for DHP and the isotope data indicate that some of these are oxidized directly by bound H2O2 (peroxygenase function) or O2 (monooxygenase function). Clearly the internal binding requires a large binding cavity and protein dynamics that permit the entrance of these large molecules into the distal pocket. Time-resolved X-ray crystallography reveals ballistic motion of carbon monoxide to the only internal Xe-binding site and rapid escape from the protein, both features that are consistent with the open architecture of the distal pocket. Preliminary NMR dynamic studies show that this method can be used to complement X-ray crystallography to provide information on the location of substrate binding. Resonance Raman studies complement these methods as well providing a means to study how ligand binding to the heme Fe interacts with the internally bound inhibitors and substrates. This combination of methods has the potential to reveal functional differences in the binding of different substrates and the role played by protein dynamics in controlling the functional switching of DHP.}, number={2}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Franzen, Stefan and Zhao, Jing and Gracz, Hanna}, year={2014}, month={Jan}, pages={662a} }
 @article{nowak-karnowska_chebib_milecki_franzen_skalski_2014, title={Highly Efficient Fluorescent Interstrand Photo-crosslinking of DNA Duplexes Labeled with 5-Fluoro-4-thio-2 '-O-methyluridine}, volume={15}, ISSN={["1439-7633"]}, DOI={10.1002/cbic.201402182}, abstractNote={The formation of a fluorescent photoadduct between 5-fluoro-4-thiouridine (FSU), in the sequence context 5′-AFSUA-3′ and incorporated into a synthetic oligonucleotide either at its 3′- or 5′-end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo-crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo-crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo-crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.}, number={14}, journal={CHEMBIOCHEM}, author={Nowak-Karnowska, Joanna and Chebib, Ziad and Milecki, Jan and Franzen, Stefan and Skalski, Bohdan}, year={2014}, month={Sep}, pages={2045–2049} }
 @article{barrios_d’antonio_mccombs_zhao_franzen_schmidt_sombers_ghiladi_2014, title={Peroxygenase and Oxidase Activities of Dehaloperoxidase-Hemoglobin from Amphitrite ornata}, volume={136}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja500293c}, DOI={10.1021/ja500293c}, abstractNote={The marine globin dehaloperoxidase-hemoglobin (DHP) from Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of monohaloindoles, a previously unknown class of substrate for DHP. Using 5-Br-indole as a representative substrate, the major monooxygenated products were found to be 5-Br-2-oxindole and 5-Br-3-oxindolenine. Isotope labeling studies confirmed that the oxygen atom incorporated was derived exclusively from H2O2, indicative of a previously unreported peroxygenase activity for DHP. Peroxygenase activity could be initiated from either the ferric or oxyferrous states with equivalent substrate conversion and product distribution. It was found that 5-Br-3-oxindole, a precursor of the product 5-Br-3-oxindolenine, readily reduced the ferric enzyme to the oxyferrous state, demonstrating an unusual product-driven reduction of the enzyme. As such, DHP returns to the globin-active oxyferrous form after peroxygenase activity ceases. Reactivity with 5-Br-3-oxindole in the absence of H2O2 also yielded 5,5'-Br2-indigo above the expected reaction stoichiometry under aerobic conditions, and O2-concentration studies demonstrated dioxygen consumption. Nonenzymatic and anaerobic controls both confirmed the requirements for DHP and molecular oxygen in the catalytic generation of 5,5'-Br2-indigo, and together suggest a newly identified oxidase activity for DHP.}, number={22}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Barrios, David A. and D’Antonio, Jennifer and McCombs, Nikolette L. and Zhao, Jing and Franzen, Stefan and Schmidt, Andreas C. and Sombers, Leslie A. and Ghiladi, Reza A.}, year={2014}, month={May}, pages={7914–7925} }
 @article{komodzinski_lepczynska_gdaniec_bartolotti_delley_franzen_skalski_2014, title={Photochemistry of 6-amino-2-azido, 2-amino-6-azido and 2,6-diazido analogues of purine ribonucleosides in aqueous solutions}, volume={13}, ISSN={["1474-9092"]}, DOI={10.1039/c3pp50385b}, abstractNote={The photochemistry of 6-amino-2-azidopurine, 2-amino-6-azidopurine and 2,6-diazidopurine ribonucleosides has been investigated in aqueous solutions under aerobic and anaerobic conditions. Near UV irradiation of 6-amino-2-azido-9-(2′,3′,5′-tri-O-acetyl-β-d-ribofuranosyl)purine and 2-amino-6-azido-9-(2′,3′,5′-tri-O-acetyl-β-d-ribofuranosyl)purine in the presence of oxygen leads to efficient formation of 6-amino-2-nitro-9-(2′,3′,5′-tri-O-acetyl-β-d-ribofuranosyl)purine and 2-amino-6-nitro-9-(2′,3′,5′-tri-O-acetyl-β-d-ribofuranosyl)purine. Under anaerobic conditions, both azidopurine ribonucleosides preferentially undergo photoreduction to 2,6-diamino-9-(2′,3′,5′-tri-O-acetyl-β-d-ribofuranosyl)purine. The structures of the photoproducts formed were confirmed by UV, NMR and HR ESI-TOF MS spectral data. The photoproducts observed in this study for the aminoazidopurines are distinctly different from those observed previously for 6-azidopurine. When no amino group is present, the photochemistry of 6-azidopurine leads to the formation of a 1,3,5-triazepinone nucleoside. The energetics of the 6-nitreno moiety along both oxidation and ring expansion pathways was calculated using the nudged elastic band (NEB) method based on density functional theory (DFT) using DMol3. The role of the 2-amino group in regulating the competition between these pathways was elucidated in order to explain how the striking difference in reactivity under irradiation arises from the greater spin density on the 6-nitreno-9-methyl-9H-purin-2-amine, which essentially eliminates the barrier to oxidation observed in 6-nitreno-9-methyl-9H-purine. Finally, the importance of tetrazolyl intermediates for the photochemical activation of azide bond cleavage to release N2 and form the 6-nitreno group was also corroborated using the DFT methods.}, number={3}, journal={PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES}, author={Komodzinski, Krzysztof and Lepczynska, Jolanta and Gdaniec, Zofia and Bartolotti, Libero and Delley, Bernard and Franzen, Stefan and Skalski, Bohdan}, year={2014}, pages={563–573} }
 @article{zhao_xue_gracz_franzen_2014, title={Self-Assembley of Dehaloperoxidase-Hemoglobin Probed by Backbone Dynamics using NMR Relaxation Experiments and Molecular Dynamics Simulation}, volume={106}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/J.BPJ.2013.11.2638}, DOI={10.1016/J.BPJ.2013.11.2638}, abstractNote={Dehaloperoxidase-hemoglobin (DHP) is a multi-functional protein isolated from the annelid marine worm Amphitrite ornata. It has been shown to function as an oxygen transporter, peroxidase, peroxygenase, oxidase and hydrogen sulfide oxidase with substrates that include a range of phenols and indoles. DHP primarily exists as a monomer in the solution (∼90%), while is observed as a dimer in the X-ray crystal structure. The dimer-monomer equilibrium in solution has shown to be able to change the redox state of the protein which further regulates the multiple enzyme functions of DHP. The self-assembly behavior of DHP has been studied by NMR and MD simulations in terms of backbone dynamics. The R1, R2 and {1H} −15N NOE of the backbone amide N-H bonds have been measured using NMR relaxation experiments at multiple magnetic fields. The squared generalize order parameter S2 that describe the spatial restriction of the internal motions of amide N-H bond was extracted using the model-free analysis for each residue. S2 were also theoretically calculated from correlation functions based on MD simulations. The dynamic pattern of DHP monomer shows that the μs-ms slow motions experiencing by residues in the dimer interface are primarily responsible for association between each monomers. Moreover, the disulfide bond is formed between the only cysteine in DHP during the dimerization process which leads to the unique autoreduction phenomenon in DHP. While most heme proteins autooxidize, DHP will actually autoreduce if prepared in the ferric form because of its very high reduction potential (the highest known for a monomeric hemoglobin) and reduction by surface cysteines that form disulfide bonds during the dimerization process.}, number={2}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Zhao, Jing and Xue, Mengjun and Gracz, Hanna and Franzen, Stefan}, year={2014}, month={Jan}, pages={466a} }
 @article{franzen_skalski_bartolotti_delley_2014, title={The coupling of tautomerization to hydration in the transition state on the pyrimidine photohydration reaction path}, volume={16}, ISSN={["1463-9084"]}, DOI={10.1039/c4cp02160f}, abstractNote={The ground state reaction path for formation of the pyrimidine hydrates was calculated using a nudged elastic band (NEB) approach, combined with a calculation of the transition state, and implemented using a numerical basis set in the density functional theory (DFT) code DMol3. The model systems used for study consist of 1-methyl pyrimidines with a H2O molecule as the reactant, and the corresponding C5-hydro-C6-hydroxypyrimidine as the product. The barrier to addition of water across the C5–C6 π-bond ranges from 43–48 kcal mol−1 in the 1-methylpyrimidines (1-MP) studied. Similar but slightly smaller barriers of 34–45 kcal mol−1 were found for the tautomers of the 1-MPs, i.e. the enols of uridine and thymine and imine of cytosine. Comparison of these calculations with previous computational and experimental work suggests that a hot ground state formed by the rapid internal conversion of pyrimidines has sufficient energy to permit crossover from the common form to the tautomeric form of the pyrimidine at the transition state. The hot ground state mechanism can account for the experimentally observed yield and thermal reversion of pyrimidine photohydrates, while simultaneously explaining the effect of photohydrates on the mutation rate.}, number={37}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Franzen, S. and Skalski, B. and Bartolotti, L. and Delley, B.}, year={2014}, pages={20164–20174} }
 @article{schkolnik_utesch_zhao_jiang_thompson_mroginski_hildebrandt_franzen_2013, title={Catalytic efficiency of dehaloperoxidase A is controlled by electrostatics - application of the vibrational Stark effect to understand enzyme kinetics}, volume={430}, ISSN={["1090-2104"]}, DOI={10.1016/j.bbrc.2012.12.047}, abstractNote={The vibrational Stark effect is gaining popularity as a method for probing electric fields in proteins. In this work, we employ it to explain the effect of single charge mutations in dehaloperoxidase-hemoglobin A (DHP A) on the kinetics of the enzyme. In a previous communication published in this journal (BBRC 2012, 420, 733-737) it has been shown that an increase in the overall negative charge of DHP A through mutation causes a decrease in its catalytic efficiency. Here, by labeling the protein with 4-mercaptobenzonitrile (MBN), a Stark probe molecule, we provide further evidence that the diffusion control of the catalytic process arises from the electrostatic repulsion between the enzyme and the negatively charged substrate. The linear correlation observed between the nitrile stretching frequency of the protein-bound MBN and the catalytic efficiency of the single-site mutants of the enzyme indicates that electrostatic interactions play a dominant role in determining the catalytic efficiency of DHP A.}, number={3}, journal={BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS}, author={Schkolnik, Gal and Utesch, Tillmann and Zhao, Junjie and Jiang, Shu and Thompson, Matthew K. and Mroginski, Maria-Andrea and Hildebrandt, Peter and Franzen, Stefan}, year={2013}, month={Jan}, pages={1011–1015} }
 @article{franzen_2013, title={Comment on 'Cooperativity between two selected RNA Pdases in the synthesis of Pd nanoparticles' by J. L. Rouge et al., J. Mater. Chem., 2010, 20, 8394-8398}, volume={1}, ISSN={["2050-7518"]}, DOI={10.1039/c3tb20820f}, number={45}, journal={JOURNAL OF MATERIALS CHEMISTRY B}, author={Franzen, Stefan}, year={2013}, pages={6339–6341} }
 @article{chung_leonard_altoe_aloni_de yoreo_franzen_2013, title={Crystals: The Formation of Pd Nanocrystals from Pd2(dba)3Microcrystals (Part. Part. Syst. Charact. 3/2013)}, volume={30}, ISSN={0934-0866}, url={http://dx.doi.org/10.1002/PPSC.201370010}, DOI={10.1002/PPSC.201370010}, number={3}, journal={Particle & Particle Systems Characterization}, publisher={Wiley}, author={Chung, Sungwook and Leonard, Donovan N. and Altoe, Virginia and Aloni, Shaul and De Yoreo, James J. and Franzen, Stefan}, year={2013}, month={Mar}, pages={298–298} }
 @article{zhao_srajer_franzen_2013, title={Functional Consequences of the Open Distal Pocket of Dehaloperoxidase-Hemoglobin Observed by Time-Resolved X-ray Crystallography}, volume={52}, ISSN={["0006-2960"]}, DOI={10.1021/bi401118q}, abstractNote={Using time-resolved X-ray crystallography, we contrast a bifunctional dehaloperoxidase-hemoglobin (DHP) with previously studied examples of myoglobin and hemoglobin to understand the functional role of the distal pocket of globins. One key functional difference between DHP and other globins is the requirement that H2O2 enter the distal pocket of oxyferrous DHP to displace O2 from the heme Fe atom and thereby activate the heme for the peroxidase function. The open architecture of DHP permits more than one molecule to simultaneously enter the distal pocket of the protein above the heme to facilitate the unique peroxidase cycle starting from the oxyferrous state. The time-resolved X-ray data show that the distal pocket of DHP lacks a protein valve found in the two other globins that have been studied previously. The photolyzed CO ligand trajectory in DHP does not have a docking site; rather, the CO moves immediately to the Xe-binding site. From there, CO can escape but can also recombine an order of magnitude more rapidly than in other globins. The contrast with DHP dynamics and function more precisely defines the functional role of the multiple conformational states of myoglobin. Taken together with the high reduction potential of DHP, the open distal site helps to explain how a globin can also function as a peroxidase.}, number={45}, journal={BIOCHEMISTRY}, author={Zhao, Junjie and Srajer, Vukica and Franzen, Stefan}, year={2013}, month={Nov}, pages={7943–7950} }
 @article{zhao_franzen_2013, title={Kinetic Study of the Inhibition Mechanism of Dehaloperoxidase-Hemoglobin A by 4-Bromophenol}, volume={117}, ISSN={["1520-6106"]}, DOI={10.1021/jp3116353}, abstractNote={The mechanism of dehaloperoxidase-hemoglobin (DHP) inhibition by 4-bromophenol (4-BP) was investigated using Michealis-Menten and transient-state kinetic analyses. Transient-state kinetics using the stopped-flow technique to mix DHP and H2O2 in the presence of inhibitor concentrations less than 10-fold greater than the enzyme concentration show that 4-BP does not fully impede H2O2 entering the distal pocket to activate DHP. It is not clear whether an oxoferryl intermediate is formed under these conditions and there may be alternative pathways for H2O2 reaction in the 4-BP bound form of DHP. Two new species have been identified during the reaction of 4-BP bound form of DHP in the transient-state kinetic experiment by using Singular Value Decomposition (SVD) and global-fitting analysis. Rather than forming Compound ES in the unbound form, an inhibitor bound intermediate that possesses blue-shifted Soret band and a double peaked Q-band is observed. This intermediate is subsequently converted to the end-point species that is distinguished from Compound RH formed in the uninhibited enzyme. Bench-top mixing kinetics of DHP were conducted in order to determine the inhibitor binding constant and to understand the enzyme inhibition mechanism from a thermodynamic perspective. It was found that the inhibition constant, Ki, decreased from 2.56 mM to 0.15 mM over the temperature range from 283 to 298 K, which permits determination of the enthalpy and entropy for inhibitor binding as -135.5 ± 20.9 kJ/mol and 526.1 ± 71.9 J/(mol·K), respectively, leading to the conclusion that inhibitor binding is entropically driven.}, number={28}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Zhao, Jing and Franzen, Stefan}, year={2013}, month={Jul}, pages={8301–8309} }
 @article{sachet_losego_guske_franzen_maria_2013, title={Mid-infrared surface plasmon resonance in zinc oxide semiconductor thin films}, volume={102}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.4791700}, DOI={10.1063/1.4791700}, abstractNote={Surface plasmon resonance (SPR) in semiconducting materials at mid-infrared (mid-IR) energies offers the potential for new plasmonic functionalities and integration schemes. Mainstream semiconductors are transparent to mid-IR energies, thus a tightly integrated monolithic package for SPR sensing becomes feasible. We report mid-IR surface plasmon resonance in zinc oxide as a model material for semiconductors with 4 × 1019 to 8 × 1019 cm−3 carriers. The surface plasmon modes were characterized using spectroscopic IR-ellipsometry and compared to a reflectivity simulation. The data confirm the feasibility of mid-IR SPR, show a generic ability for plasmon tuning, and demonstrate the predictive power of the reflectivity model.}, number={5}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Sachet, Edward and Losego, Mark D. and Guske, Joshua and Franzen, Stefan and Maria, Jon-Paul}, year={2013}, month={Feb}, pages={051111} }
 @article{plummer_thompson_franzen_2013, title={Role of Polarity of the Distal Pocket in the Control of Inhibitor Binding in Dehaloperoxidase-Hemoglobin}, volume={52}, ISSN={["0006-2960"]}, DOI={10.1021/bi301509r}, abstractNote={Dehaloperoxidase (DHP A), a unique multifunctional enzyme, from the marine annelid Amphitrite ornata dehalogenates 2,4,6-tribromophenol to form 2,6-dibromo-1,4-benzoquinone. The catalytic cycle of DHP is similar to that of horseradish peroxidase (HRP), involving a high-valent ferryl heme and two single-electron transfers from the aromatic substrate to the enzyme. Like HRP, DHP has been investigated as a potential bioremediation enzyme. However, DHP fails as a bioremediation enzyme because, unlike HRP, it has an internal binding cavity on the distal side of the heme capable of accommodating p-bromophenols, which act as an inhibitor of peroxidase function. Blocking internal binding in DHP may be the key to allowing the enzyme to function effectively as a peroxidase on the full range of halogenated phenols. The distal cavity of DHP is surrounded by several hydrophobic amino acids that stabilize internal binding of the monohalogenated phenols, including a leucine residue near the back edge of the heme (L100). We have expressed the L100F, L100Q, L100T, and L100V mutants of DHP in an effort to prevent internal binding and thereby convert the inhibitors into substrates. Kinetic assays and resonance Raman indicate that the peroxidase activity of the L100T and L100F mutants is increased compared to that of native DHP in the presence of 4-bromophenol (4-BP), suggesting a reduction in the inhibitor binding constant. In addition, the X-ray crystal structure of L100F clearly indicates a reduced occupancy of the 4-BP inhibitor in the distal cavity of DHP. However, at the same time, the L100F structure reveals that steric interference alone is insufficient to exclude the inhibitor. Instead, the comparison of L100T and isosteric L100V reveals that an increase in polarity plays a decisive role in excluding the inhibitor from the distal binding pocket.}, number={13}, journal={BIOCHEMISTRY}, author={Plummer, Ashlee and Thompson, Matthew K. and Franzen, Stefan}, year={2013}, month={Apr}, pages={2218–2227} }
 @article{zhao_serrano_zhao_le_franzen_2013, title={Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata}, volume={52}, ISSN={["0006-2960"]}, DOI={10.1021/bi301307f}, abstractNote={X-ray crystal structures of dehaloperoxidase-hemoglobin A (DHP A) from Amphitrite ornata soaked with substrate, 2,4,6-tribromophenol (2,4,6-TBP), in buffer solvent with added methanol (MeOH), 2-propanol (2-PrOH), and dimethyl sulfoxide (DMSO) reveal an internal substrate binding site deep in the distal pocket above the α-edge of the heme that is distinct from the previously determined internal inhibitor binding site. The peroxidase function of DHP A has most often been studied using 2,4,6-trichlorophenol (2,4,6-TCP) as a substrate analogue because of the low solubility of 2,4,6-TBP in an aqueous buffer solution. Previous studies at low substrate concentrations pointed to the binding of substrate 2,4,6-TCP at an external site near the exterior heme β- or δ-edge as observed in the class of heme peroxidases. Here we report that the turnover frequencies of both substrates 2,4,6-TCP and 2,4,6-TBP deviate from Michaelis-Menten kinetics at high concentrations. The turnover frequency reaches a maximum in the range of 1400-1700 μM, with a decrease in rate at higher concentrations that is both substrate- and solvent-dependent. The X-ray crystal structure is consistent with the presence of an internal active site above the heme α-edge, in which the substrate would be oxidized in two consecutive steps inside the enzyme, followed by attack by H2O via a water channel in the protein. The physiological role of the internal site may involve interactions with any of a number of aromatic toxins found in benthic ecosystems where A. ornata resides.}, number={14}, journal={BIOCHEMISTRY}, author={Zhao, Jing and Serrano, Vesna and Zhao, Junjie and Le, Peter and Franzen, Stefan}, year={2013}, month={Apr}, pages={2427–2439} }
 @article{chung_leonard_altoe_aloni_de yoreo_franzen_2013, title={The Formation of Pd Nanocrystals from Pd2(dba)3Microcrystals}, volume={30}, ISSN={0934-0866}, url={http://dx.doi.org/10.1002/ppsc.201200114}, DOI={10.1002/ppsc.201200114}, abstractNote={As-grown platelets formed from tris-(dibenzylideneacetone) dipalladium(0) [Pd2(dba)3] precursor in the presence of Pd17 RNA are investigated before and after thermal annealing. Results show that as-grown platelets are disordered crystals of Pd2(dba)3 containing 1−2 nm Pd clusters and platelets grown in the absence of RNA are morphologically and structurally similar to those formed with RNA. The initially formed crystals are so sensitive to environmental variables that the degree of crystallinity can not be determined accurately by electron diffraction. X-ray crystallography on as-grown platelets gives a crystal structure consistent with Pd2(dba)3, but reveals a composition of ≈Pd1.07(dba)3, indicating one Pd atom in Pd2(dba)3 is lost from the structure. Both electron beam and thermally induced decomposition of as-grown Pd2(dba)3 platelets having a hexagonal habit on the micrometer scale produces elemental Pd platelets having a hexagonal habit on the nanometer scale. These hexagonal platelets are composed of a partially sparse form of Pd2(dba)3 that is initially crystalline but rapidly degrades due to the loss of Pd atoms from organic ligand cages. Once released, Pd atoms aggregate to form Pd clusters, which grow and transform into well-formed Pd nanocrystals under electron-beam irradiation or through thermal annealing.}, number={3}, journal={Particle & Particle Systems Characterization}, publisher={Wiley}, author={Chung, Sungwook and Leonard, Donovan N. and Altoe, Virginia and Aloni, Shaul and De Yoreo, James J. and Franzen, Stefan}, year={2013}, month={Feb}, pages={280–286} }
 @article{zhao_zhao_franzen_2013, title={The Regulatory Implications of Hydroquinone for the Multifunctional Enzyme Dehaloperoxidase-Hemoglobin from Amphitrite ornata}, volume={117}, ISSN={["1520-6106"]}, DOI={10.1021/jp407663n}, abstractNote={Hydroquinone (H2Q) has been observed to compete with the oxidation of substrates 2,4,6-tribromophenol (2,4,6-TBP) and 2,4,6-trichlorophenol (2,4,6-TCP) catalyzed by the dehaloperoxidase-hemoglobin (DHP) from Amphitrite ornata in the presence of H2O2. This competition is observed as a lag phase during which H2Q is preferentially oxidized to 1,4-benzoquinone (1,4-BQ) while totally inhibiting either 2,4,6-TBP or 2,4,6-TCP oxidation. The inhibition by H2Q is distinct from that of the native competitive inhibitor 4-bromophenol (4-BP) since H2Q is itself oxidized and its product 1,4-BQ is not an inhibitor. Thus, once H2Q is completely consumed, the inhibition is removed, and normal substrate turnover is initiated, which explains the lag phase. To probe the mechanism of lag phase, the reactions between H2Q and DHP were both studied both in the presence and in the absence of H2O2. The reversible reactions between ferric/oxyferrous DHP A and H2Q/1,4-BQ are shown to involve a proton-coupled electron transfer (PCET) mechanism, where the distal histidine His55 serves as the proton acceptor. The pKa of the distal histidine His55 has been determined by resonance Raman spectroscopy in order to corroborate its involvement in this mechanism. Consistent with the proposed mechanism, kinetic assays have shown that H2Q serves as a substrate for DHP that follows the Michaelis–Menten kinetics. Unlike H2Q, the product 1,4-BQ has a relatively large Ki value and therefore has negligible inhibition. This study sheds light on understanding the difference between substrate and inhibitor binding sites and regulatory implication for the peroxidase and oxygen-transporter functions in DHP. It also provides information on PCET in DHP, which is important for resolving the switching between the ferric peroxidase catalytic function and the ferrous oxygen transport function.}, number={47}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Zhao, Jing and Zhao, Junjie and Franzen, Stefan}, year={2013}, month={Nov}, pages={14615–14624} }
 @article{jiang_wright_swartz_franzen_2013, title={The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata}, volume={1834}, ISSN={["1878-1454"]}, DOI={10.1016/j.bbapap.2013.06.005}, abstractNote={The activation of dehaloperoxidase-hemoglobin (DHP) to form a ferryl intermediate requires the distal histidine, H55, to act as an acid base catalyst. The lack of ancillary amino acids in the distal pocket to assist in this process makes H55 even more important to the formation of active intermediates than in conventional peroxidases. Therefore, one can infer that the precise conformation H55 may greatly affect the enzymatic activity. Using site-direct mutagenesis at position T56, immediately adjacent to H55, we have confirmed that subtle changes in the conformation of H55 affect the catalytic efficiency of DHP. Mutating T56 to a smaller amino acid appears to permit H55 to rotate with relatively low barriers between conformations in the distal pocket, which may lead to an increase in catalytic activity. On the other hand, larger amino acids in the neighboring site appear to restrict the rotation of H55 due to the steric hindrance. In the case of T56V, which is an isosteric mutation, H55 appears less mobile, but forced to be closer to the heme iron than in wild type. Both proximity to the heme iron and flexibility of motion in some of the mutants can result in an increased catalytic rate, but can also lead to protein inactivation due to ligation of H55 to the heme iron, which is known as hemichrome formation. A balance of enzymatic rate and protein stability with respect to hemichrome formation appears to be optimum in wild type DHP (WT-DHP).}, number={10}, journal={BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS}, author={Jiang, Shu and Wright, Iain and Swartz, Paul and Franzen, Stefan}, year={2013}, month={Oct}, pages={2020–2029} }
 @article{franzen_brown_gaff_delley_2012, title={A Resonance Raman Enhancement Mechanism for Axial Vibrational Modes in the Pyridine Adduct of Myoglobin Proximal Cavity Mutant (H93G)}, volume={116}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp302049p}, DOI={10.1021/jp302049p}, abstractNote={The proximal cavity mutant of myoglobin consists of a mutation of the proximal histidine to glycine (H93G), which permits exogenous ligands to bind to the heme iron. A non-native pyridine ligand can ligate to the heme to yield a five-coordinate adduct, H93G(Pyr), that cannot be formed freely in solution since the six-coordinate bis-pyridine adduct is more stable than the five-coordinate adduct. We have used resonance Raman spectroscopy in the Soret band region of the heme to study the enhancement of axial vibrations of bound pyridine in the H93G(Pyr) adduct. The observation that the pyridine ring breathing mode (ν(1)) and the symmetric ring stretching (ν(3)) modes are enhanced under these conditions is explained by a computational approach that shows that coupling of the π-system of the heme with the p-orbitals of the pyridine is analogous to π-backbonding in diatomic ligand adducts of heme proteins. The result has the broader significance that it suggests that the resonance enhancement of pyridine modes could be an important aspect of Raman scattering of pyridine on conducting surfaces such as those studied in surface enhanced Raman scattering experiments.}, number={35}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Franzen, Stefan and Brown, Derek and Gaff, John and Delley, B.}, year={2012}, month={Jun}, pages={10514–10521} }
 @article{guske_brown_welsh_franzen_2012, title={Infrared surface plasmon resonance of AZO-Ag-AZO sandwich thin films}, volume={20}, ISSN={["1094-4087"]}, DOI={10.1364/oe.20.023215}, abstractNote={Near-infrared surface plasmon resonance (SPR) spectra were collected of thin multilayer films of aluminum-doped zinc oxide (AZO) / silver (Ag) / AZO on BK-7 glass in the Kretschmann configuration in air, with the silver layer thickness varying from 5 nm to 50 nm. The SPR results were interpreted by modeling the reflectance with a five-layer transfer-matrix method, with the aid of a simplex algorithm. The model indicated that the Ag plasma frequency was significantly higher than the bulk value, possibly due to Schottky effect charge transfer from the AZO to the Ag layer. Continuous silver films were made as thin as 10 nm, indicating an inhibition of metal island formation for Ag deposited on AZO.}, number={21}, journal={OPTICS EXPRESS}, author={Guske, Joshua T. and Brown, Jeff and Welsh, Alex and Franzen, Stefan}, year={2012}, month={Oct}, pages={23215–23226} }
 @article{franzen_sasan_sturgeon_lyon_battenburg_gracz_dumariah_ghiladi_2012, title={Nonphotochemical Base-Catalyzed Hydroxylation of 2,6-Dichloroquinone by H2O2Occurs by a Radical Mechanism}, volume={116}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp208536x}, DOI={10.1021/jp208536x}, abstractNote={Kinetic and structural studies have shown that peroxidases are capable of the oxidation of 2,4,6-trichlorophenol (2,4,6-TCP) to 2,6-dichloro-1,4-benzoquinone (2,6-DCQ). Further reactions of 2,6-DCQ in the presence of H2O2 and OH– yield 2,6-dichloro-3-hydroxy-1,4-benzoquinone (2,6-DCQOH). The reactions of 2,6-DCQ have been monitored spectroscopically [UV–visible and electron spin resonance (ESR)] and chromatographically. The hydroxylation product, 2,6-DCQOH, has been observed by UV–visible and characterized structurally by 1H and 13C NMR spectroscopy. The results are consistent with a nonphotochemical base-catalyzed oxidation of 2,6-DCQ at pH > 7. Because H2O2 is present in peroxidase reaction mixtures, there is also a potential role for the hydrogen peroxide anion (HOO–). However, in agreement with previous work, we observe that the nonphotochemical epoxidation by H2O2 at pH < 7 is immeasurably slow. Both room-temperature ESR and rapid-freeze-quench ESR methods were used to establish that the dominant nonphotochemical mechanism involves formation of a semiquinone radical (base -catalyzed pathway), rather than epoxidation (direct attack by H2O2 at low pH). Analysis of the kinetics using an Arrhenius model permits determination of the activation energy of hydroxylation (Ea = 36 kJ/mol), which is significantly lower than the activation energy of the peroxidase-catalyzed oxidation of 2,4,6-TCP (Ea = 56 kJ/mol). However, the reaction is second order in both 2,6-DCQ and OH– so that its rate becomes significant above 25 °C due to the increased rate of formation of 2,6-DCQ that feeds the second-order process. The peroxidase used in this study is the dehaloperoxidase-hemoglobin (DHP A) from Amphitrite ornata, which is used to study the effect of a catalyst on the reactions. The control experiments and precedents in studies of other peroxidases lead to the conclusion that hydroxylation will be observed following any process that leads to the formation of the 2,6-DCQ at pH > 7, regardless of the catalyst used in the 2,4,6-TCP oxidation reaction.}, number={5}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Franzen, Stefan and Sasan, Koroush and Sturgeon, Bradley E. and Lyon, Blake J. and Battenburg, Benjamin J. and Gracz, Hanna and Dumariah, Rania and Ghiladi, Reza}, year={2012}, month={Jan}, pages={1666–1676} }
 @article{lepczynska_komodzinski_milecki_kierzek_gdaniec_franzen_skalski_2012, title={Photoaddition of 5-Bromouracil to Uracil in Oligonucleotides Leading to 5,5 '-Bipyrimidine-Type Adducts: Mechanism of the Photoreaction}, volume={77}, ISSN={["1520-6904"]}, DOI={10.1021/jo3021067}, abstractNote={5-Bromouracil (BrU) modified di- and hexanucleotides having BrU flanked on the 5′ or the 3′ side by uracil (U) have been synthesized, and their photochemical reactivity was examined under the conditions of irradiation with near UV light. The results indicate that the primary photochemical process in all of these compounds involves the formation of an intermediate cyclobutane phodoadduct composed of BrU and U, which undergoes further photochemically and thermally induced transformations to 5,5′-bipyrimidine type adducts.}, number={24}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Lepczynska, Jolanta and Komodzinski, Krzysztof and Milecki, Jan and Kierzek, Ryszard and Gdaniec, Zofia and Franzen, Stefan and Skalski, Bohdan}, year={2012}, month={Dec}, pages={11362–11367} }
 @article{gaff_franzen_2012, title={Resonance Raman enhancement of pyridine on Ag clusters}, volume={397}, ISSN={0301-0104}, url={http://dx.doi.org/10.1016/j.chemphys.2011.12.005}, DOI={10.1016/j.chemphys.2011.12.005}, abstractNote={Abstract Calculation of the dimensionless excited state displacements (ESD) using density functional theory (DFT) was used to estimate the resonance Raman cross sections of pyridine on Ag clusters using the time-correlator formalism. The model systems studied are supermolecules consisting of Ag clusters with bound pyridine, Pyr(Ag) n ( n  = 2, 4, 8, 14 and 20). It was found that structural changes in pyridine observed in the ESD for all five Pyr(Ag) n supermolecular clusters were essentially equivalent, and similar to those observed for the strongly allowed 168 nm transition of free pyridine. Enhancements of ∼10 3 –10 6 , were calculated for all Pyr(Ag) n , which is comparable to the overall surface enhanced Raman spectroscopy (SERS) effect in studies of pyridine on Ag, suggesting that resonance Raman may be a significant contributor to the effect.}, number={1}, journal={Chemical Physics}, publisher={Elsevier BV}, author={Gaff, John and Franzen, Stefan}, year={2012}, month={Mar}, pages={34–41} }
 @article{zhao_rowe_franzen_he_franzen_2012, title={Study of the electrostatic effects of mutations on the surface of dehaloperoxidase-hemoglobin A}, volume={420}, ISSN={["0006-291X"]}, DOI={10.1016/j.bbrc.2012.03.053}, abstractNote={Point mutations of dehaloperoxidase-hemoglobin A (DHP A) that affect the surface charge have been prepared to study the interaction between DHP A with its substrate 2,4,6-trichlorophenol (TCP). Kinetic studies of these surface mutations showed a correlation, in which the more positively charged mutants have increased catalytic efficiency compared with wild type DHP A. As a result, the hypothesis of this study is that there is a global electrostatic interaction between DHP A and TCP. The electrostatic nature of substrate binding was further confirmed by the result that kinetic assays of DHP A were affected by ionic strength. Furthermore, isoelectric focusing (IEF) gel study showed that the pI − 6.8 for DHP A, which indicates that DHP A has a slight negative charge pH 7, consistent with the kinetic observations.}, number={4}, journal={BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS}, author={Zhao, Junjie and Rowe, Jennifer and Franzen, Jocelyn and He, Chi and Franzen, Stefan}, year={2012}, month={Apr}, pages={733–737} }
 @article{zhao_de serrano_dumarieh_thompson_ghiladi_franzen_2012, title={The Role of the Distal Histidine in H2O2 Activation and Heme Protection in both Peroxidase and Globin Functions}, volume={116}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp300014b}, DOI={10.1021/jp300014b}, abstractNote={The distal histidine mutations of dehaloperoxidase-hemoglobin A (DHP A) to aspartate (H55D) and asparagine (H55N) have been prepared to study the role played by the distal histidine in both activation and protection against oxidation by radicals in heme proteins. The H55D and H55N mutants of DHP A have ∼6-fold and ∼11-fold lower peroxidase activities than wild type enzyme toward the oxidation of 2,4,6-trichlorophenol (TCP) to yield 2,6-dichloroquinone (DCQ) in the presence of H2O2. The origin of the lower rate constants may be the solvent-exposed conformations of distal D55 and N55, which would have the dual effect of destabilizing the binding of H2O2 to the heme iron, and of removing the acid–base catalyst necessary for the heterolytic O–O bond cleavage of heme-bound H2O2 (i.e., compound 0). The partial peroxidase activity of H55D can be explained if one considers that there are two conformations of the distal aspartate (open and closed) by analogy with the distal histidine. We hypothesize that the distal aspartate has an active conformation in the distal pocket (closed). Although the open form is observed in the low-temperature X-ray crystal structure of ferric H55D, the closed form is observed in the FTIR spectrum of the carbonmonoxy form of the H55D mutant. Consistent with this model, the H55D mutant also shows inhibition of TCP oxidation by 4-bromophenol (4-BP). Consistent with the protection hypothesis, compound ES, the tyrosyl radical-containing ferryl intermediate observed in WT DHP A, was not observed in H55D.}, number={40}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Zhao, Junjie and de Serrano, Vesna and Dumarieh, Rania and Thompson, Matt and Ghiladi, Reza A. and Franzen, Stefan}, year={2012}, month={Sep}, pages={12065–12077} }
 @article{franzen_thompson_ghiladi_2012, title={The dehaloperoxidase paradox}, volume={1824}, ISSN={1570-9639}, url={http://dx.doi.org/10.1016/j.bbapap.2011.12.008}, DOI={10.1016/j.bbapap.2011.12.008}, abstractNote={The dual functions of the dehaloperoxidase-hemoglobin of Amphitrite ornata leads to a paradox. Peroxidase and hemoglobin functions require ferric and ferrous resting states, respectively. Assuming that hemoglobin function is the dominant function, the starting point for peroxidase activation would be the oxyferrous state. Activation of that state leads to the ferryl intermediate, followed by one-electron oxidation of the substrate, which results in the ferric state. Since no exogenous reductant is known, there is no return to the ferrous form or hemoglobin function. The observation that an internal binding site for 4-bromophenol leads to inhibition leads to a further paradox that the enzyme would be inhibited immediately upon activation under ambient conditions in benthic ecosystems where the inhibitor, 4-bromophenol is present in greater concentration than the substrate, 2,4,6-tribromophenol. In this review, we explore the unresolved aspects of the reaction scheme that leads to the apparent paradox. Recent data showing activation of the oxyferrous state, an extremely high reduction potential and exogenous reduction by the 2,6-dibromoquinone product present a potential resolution of the paradox. These aspects are discussed in the context of control of reactivity radical pathways and reactivity by the motion of the distal histidine, H55, which in turn is coupled to the binding of substrate and inhibitor.}, number={4}, journal={Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics}, publisher={Elsevier BV}, author={Franzen, Stefan and Thompson, Matthew K. and Ghiladi, Reza A.}, year={2012}, month={Apr}, pages={578–588} }
 @article{edward l. d'antonio_bowden_franzen_2012, title={Thin-layer spectroelectrochemistry of the Fe(III)/Fe(II) redox reaction of dehaloperoxidase-hemoglobin}, volume={668}, ISSN={["1873-2569"]}, DOI={10.1016/j.jelechem.2011.12.015}, abstractNote={Dehaloperoxidase-hemoglobin (DHP A; isoenzyme A) is a globin from the annelid Amphitrite ornata that displays enhanced peroxidase activity compared to other myoglobins and hemoglobins. In this study, anaerobic thin-layer spectroelectrochemistry was used to measure formal reduction potentials (E°′) for the Fe(III)/Fe(II) redox couple of DHP A from pH 5.0 to pH 7.0. The value of E°′ determined at pH 7.0 (100 mM potassium phosphate buffer under ambient temperature), +0.202 ± 0.006 V vs SHE, gives DHP A the most positive Fe(III)/Fe(II) reduction potential among known intracellular globins (approximately 150 mV and 50 mV higher than typical myoglobins and hemoglobins, respectively). This finding is particularly distinctive in light of DHP A’s enhanced peroxidase activity, a function that is commonly carried out from the Fe(III) state, which is favored by more negative reduction potentials. For example, horseradish peroxidase has a formal potential that falls 0.47 V negative of the DHP A value. Using available crystal structures, two major energetic factors involving the distal histidine (H55) have been identified that appear to account for the unusually positive DHP A reduction potential. First, H55, which is positioned ∼1 Å further away from the heme iron than distal histidines in hemoglobin and myoglobin, displays a diminished capacity to serve as the hydrogen bond acceptor for a ligated water molecule, resulting in destabilization of the Fe(III) state relative to a common globin. The more distant positioning of H55 from the heme iron also imparts to it a conformational flexibility, which is linked to the electron transfer reaction. In its internal (closed) conformation, H55 hydrogen bonds with and stabilizes an iron-ligated H2O molecule, whereas in its external (open) conformation, H55 hydrogen bonds to a heme propionate resulting in a 5-coordinate heme iron. A thermodynamic cycle that links the conformational change to electron transfer is shown to be consistent with a positive shift in reduction potential if the open conformation is differentially favored by the Fe(II) state, a proposal that is supported by the available crystallographic data.}, journal={JOURNAL OF ELECTROANALYTICAL CHEMISTRY}, author={Edward L. D'Antonio and Bowden, Edmond F. and Franzen, Stefan}, year={2012}, month={Mar}, pages={37–43} }
 @article{schkolnik_salewski_millo_zebger_franzen_hildebrandt_2012, title={Vibrational Stark Effect of the Electric-Field Reporter 4-Mercaptobenzonitrile as a Tool for Investigating Electrostatics at Electrode/SAM/Solution Interfaces}, volume={13}, ISSN={["1422-0067"]}, DOI={10.3390/ijms13067466}, abstractNote={4-mercaptobenzonitrile (MBN) in self-assembled monolayers (SAMs) on Au and Ag electrodes was studied by surface enhanced infrared absorption and Raman spectroscopy, to correlate the nitrile stretching frequency with the local electric field exploiting the vibrational Stark effect (VSE). Using MBN SAMs in different metal/SAM interfaces, we sorted out the main factors controlling the nitrile stretching frequency, which comprise, in addition to external electric fields, the metal-MBN bond, the surface potential, and hydrogen bond interactions. On the basis of the linear relationships between the nitrile stretching and the electrode potential, an electrostatic description of the interfacial potential distribution is presented that allows for determining the electric field strengths on the SAM surface, as well as the effective potential of zero-charge of the SAM-coated metal. Comparing this latter quantity with calculated values derived from literature data, we note a very good agreement for Au/MBN but distinct deviations for Ag/MBN which may reflect either the approximations and simplifications of the model or the uncertainty in reported structural parameters for Ag/MBN. The present electrostatic model consistently explains the electric field strengths for MBN SAMs on Ag and Au as well as for thiophenol and mercaptohexanoic acid SAMs with MBN incorporated as a VSE reporter.}, number={6}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Schkolnik, Gal and Salewski, Johannes and Millo, Diego and Zebger, Ingo and Franzen, Stefan and Hildebrandt, Peter}, year={2012}, month={Jun}, pages={7466–7482} }
 @article{milecki_nowak_skalski_franzen_2011, title={5-Fluoro-4-thiouridine phosphoramidite: New synthon for introducing photoaffinity label into oligodeovnucleotides}, volume={19}, ISSN={["0968-0896"]}, DOI={10.1016/j.bmc.2011.08.035}, abstractNote={The synthesis of phosphoramidite of 5-fluoro-4-thio-2′-O-methyluridine is described. An appropriate set of protecting groups was optimized including the 4-thio function introduced via 4-triazolyl as the 4-(2-cyanoethyl)thio derivative, and the t-butyldimethyl silyl for 2′ and 3′ hydroxyl protection, enabling efficient synthesis of the phosphoramidite. These protecting groups prevented unwanted side reactions during oligonucleotide synthesis. The utility of the proposed synthetic route was proven by the preparation of several oligonucleotides via automated synthesis. Photochemical experiments confirmed the utility of the synthon.}, number={20}, journal={BIOORGANIC & MEDICINAL CHEMISTRY}, author={Milecki, Jan and Nowak, Joanna and Skalski, Bohdan and Franzen, Stefan}, year={2011}, month={Oct}, pages={6098–6106} }
 @misc{franzen_2011, title={A comparison of peptide and folate receptor targeting of cancer cells: from single agent to nanoparticle}, volume={8}, ISSN={["1744-7593"]}, DOI={10.1517/17425247.2011.554816}, abstractNote={Introduction: There is broad interest in a targeted strategy that delivers a concentrated therapeutic payload to tumor cells, because of the significant potential for improvements in therapeutic outcomes and reduction of side effects if therapeutics can be delivered only to diseased tissue. Areas covered: This review describes how the coupling chemistry and surface charge effects of peptide labeling in nanoparticle drug delivery strategies have proved difficult to control, resulting in many studies that use folate instead. However, the successful peptide targeting of structural, hormonal, cytokine and endocrine receptors in the delivery of therapeutic and diagnostic radionuclides provides a strong indication that it is worth finding methods to synthesize peptide-targeted nanoparticles. Expert opinion: Chemical conjugation to peptides reduces colloidal stability, which is a limiting factor in the development of targeting nanoparticles. Mechanistic studies are needed in order to develop peptide targeting for nanoparticles to rival the selectivity that has been achieved with the small molecule folate. Although most of the work so far has been done using gold nanoparticles, biological and polymer nanoparticles are more colloidally stable and present enormous opportunities for coupling to peptides.}, number={3}, journal={EXPERT OPINION ON DRUG DELIVERY}, author={Franzen, Stefan}, year={2011}, month={Mar}, pages={281–298} }
 @article{franzen_leonard_2011, title={Analysis of RNA-Mediated Materials Synthesis Using Magnetic Selection}, volume={115}, ISSN={["1932-7447"]}, DOI={10.1021/jp108689v}, abstractNote={The products that result from the mediation of imidazole-modified RNA (imRNA) using FeCl2, CoCl2, NaCl, and KCl as starting materials for nanoparticle synthesis are studied using high resolution transmission electron microscopy (HRTEM), electron energy loss spectroscopy (EELS), X-ray photoelectron spectroscopy (XPS), and superconducting quantum interference device (SQUID) magnetometry. The combination of analytical methods shows that, although elemental Fe and O may be present in some samples, the majority of the samples consist of NaCl and KCl, which can form nanoparticle structures under the conditions of the experiment. The observed result is consistent with the formation of diamagnetic particles or formation of magnetic material at a concentration below the limit of detection by any of the analytical methods used. We find no evidence for iron oxide nanoparticle formation under the conditions of the selection. On the basis of the analysis, it appears that 32P radiolabeled imRNA was detected in previously presented assays only because imRNA binds to salt particles or possibly to iron oxide particles, which are not observed directly because their quantity is below the detection limit of EELS, XPS, or SQUID measurements. The role of magnetic field selection is examined critically on the basis of the physical measurements as part of the set of conditions required to prove imRNA-mediation.}, number={19}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Franzen, Stefan and Leonard, Donovan N.}, year={2011}, month={May}, pages={9335–9343} }
 @article{losego_guske_efremenko_maria_franzen_2011, title={Characterizing the Molecular Order of Phosphonic Acid Self-Assembled Monolayers on Indium Tin Oxide Surfaces}, volume={27}, ISSN={["0743-7463"]}, DOI={10.1021/la201161q}, abstractNote={Self-assembled monolayers (SAMs) of alkanephosphonic acids with chain lengths between 8 and 18 carbon units were formed on thin films of indium tin oxide (ITO) sputter-deposited on silicon substrates with 400 nm thermally grown SiO2. The silicon substrates, while not intended for use in near-IR or visible optics applications, do provide smooth surfaces that permit systematic engineering of grain size and surface roughness as a function of the sputter pressure. Argon sputter pressures from 4 to 20 mTorr show systematic changes in surface morphology ranging from smooth, micrometer-sized grain structures to <50 nm grains with 3× higher surface roughness. Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy experiments are conducted for alkanephosphonic acids deposited on these wide range of ITO surfaces to evaluate the effects of these morphological features on monolayer ordering. Results indicate that long-chain SAMs are more highly ordered, and have a smaller tilt angle, than short-chain SAMs. Surprisingly, the 1-octadecyl phosphonic acids maintain their order as the lateral grain dimensions of the ITO surface shrink to ∼50 nm. It is only when the ITO surface roughness becomes greater than the SAM chain length (∼15 Å) that SAMs are observed to become relatively disordered.}, number={19}, journal={LANGMUIR}, author={Losego, Mark D. and Guske, Joshua T. and Efremenko, Alina and Maria, Jon-Paul and Franzen, Stefan}, year={2011}, month={Oct}, pages={11883–11888} }
 @article{thompson_franzen_ghiladi_reeder_svistunenko_2011, title={Decay of Compound ES in Dehaloperoxidase-Hemoglobin}, volume={100}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2010.12.1275}, DOI={10.1016/j.bpj.2010.12.1275}, abstractNote={Dehaloperoxidase (DHP) is a respiratory hemoglobin (Hb) that catalyzes the conversion of trihalophenols to dihaloquinones in the presence of hydrogen peroxide. Ferric heme states of the resting DHP and the free radical intermediates formed under H2O2 treatment were studied by low temperature EPR spectroscopy in the range of reaction time of 50 ms - 2 min at three different pH values. Two high spin ferric heme forms were identified in the resting enzyme and assigned to the open and closed conformations of the distal histidine, His55. Two free radicals were found in DHP activated by H2O2: the radical associated with Compound ES has been assigned to Tyr34, the other radical - to Tyr38. The Tyr34 radical is formed with a very high relative yield (almost 100% of heme), atypical of other globins. The HPLC analysis of the reaction products showed a pH dependent formation of covalent heme-to-protein cross-links. The stable DHP Compound RH formed under H2O2 in the absence of substrates is proposed to be a state with the ferric heme covalently cross-linked to Tyr34. A kinetic model of the experimental data suggests that formation of Compound RH or the Tyr38 radical are two alternative routes of Compound ES decay. Which route is taken depends on the conformation of His55: in the less populated closed conformation, the Tyr38 radical is formed, but in the major open conformation, Compound ES decays yielding Compound RH, a product of safe termination of the two oxidizing equivalents of H2O2 when no substrate is available.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Thompson, Matthew K. and Franzen, Stefan and Ghiladi, Reza A. and Reeder, Brandon J. and Svistunenko, Dimitri A.}, year={2011}, month={Feb}, pages={194a} }
 @article{nicoletti_thompson_franzen_smulevich_2011, title={Degradation of sulfide by dehaloperoxidase-hemoglobin from Amphitrite ornata}, volume={16}, ISSN={["0949-8257"]}, DOI={10.1007/s00775-011-0762-2}, number={4}, journal={JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY}, author={Nicoletti, Francesco P. and Thompson, Matthew K. and Franzen, Stefan and Smulevich, Giulietta}, year={2011}, month={Apr}, pages={611–619} }
 @article{thompson_franzen_davis_oliver_krueger_2011, title={Dehaloperoxidase-Hemoglobin from Amphitrite ornata Is Primarily a Monomer in Solution}, volume={115}, ISSN={["1520-6106"]}, DOI={10.1021/jp201156r}, abstractNote={The crystal structures of the dehaloperoxidase-hemoglobin from A. ornata (DHP A) each report a crystallographic dimer in the unit cell. Yet, the largest dimer interface observed is 450 Å2, an area significantly smaller than the typical value of 1200−2000 Å2 and in contrast to the extensive interface region of other known dimeric hemoglobins. To examine the oligomerization state of DHP A in solution, we used gel permeation by fast protein liquid chromatography and small-angle X-ray scattering (SAXS). Gel permeation experiments demonstrate that DHP A elutes as a monomer (15.5 kDa) and can be separated from green fluorescent protein, which has a molar mass of 27 kDa, near the 31 kDa expected for the DHP A dimer. By SAXS, we found that DHP A is primarily monomeric in solution, but with a detectable level of dimer (∼10%), under all conditions studied up to a protein concentration of 3.0 mM. These concentrations are likely 10−100-fold lower than the Kd for dimer formation. Additionally, there was no significant effect either on the overall conformation of DHP A or its monomer−dimer equilibrium upon addition of the DHP A inhibitor, 4-iodophenol.}, number={14}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Thompson, Matthew K. and Franzen, Stefan and Davis, Michael F. and Oliver, Ryan C. and Krueger, Joanna K.}, year={2011}, month={Apr}, pages={4266–4272} }
 @article{franzen_2011, title={Determination of the Solubility Limit of Tris(dibenzylideneacetone) dipalladium(0) in Tetrahydrofuran/Water Mixtures}, volume={88}, ISSN={["1938-1328"]}, DOI={10.1021/ed100123d}, abstractNote={Determination of the solubility limit of a strongly colored organometallic reagent in a mixed-solvent system provides an example of quantitative solubility measurement appropriate to understand polymer, nanoparticle, and other macromolecular aggregation processes. The specific example chosen involves a solution of tris(dibenzylideneacetone) dipalladium(0), Pd2(dba)3, in THF/H2O mixtures, which has the desired properties of high absorption in the visible range (λmax = 528 nm) and significant difference in solubility in the two solvents THF and H2O. Pd2(dba)3 is readily available, safe, and commonly used in nanoparticle syntheses. The application of Flory−Huggins theory permits the fit of a quantitative model to data obtained from a straightforward laboratory experiment that can be conducted in less than 3 h. The absorbance of this compound is easily measured by UV−vis absorption spectroscopy. The application of the Beer−Lambert law to the data in this experiment is a useful exercise for students because the absorbances span three orders of magnitude.}, number={5}, journal={JOURNAL OF CHEMICAL EDUCATION}, author={Franzen, Stefan}, year={2011}, month={May}, pages={619–623} }
 @article{thompson_franzen_2011, title={Distal Histidine Flexibility as the Key to the Reactivity of Dehaloperoxidase-Hemoglobin}, volume={100}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2010.12.1426}, DOI={10.1016/j.bpj.2010.12.1426}, abstractNote={The enzymes dehaloperoxidase A and B (DHP A&B) from the marine worm Amphitrite ornata are unique hemoglobins that function as peroxidases, capable of converting 2,4,6-trihalo- phenols into the corresponding 2,6-dihalogenated quinones. It is difficult to explain the peroxidase activity of DHPs A&B since they are clearly both hemolgobins. Our recent discovery of an internal inhibitor binding site, in the distal pocket, clearly establishes the peroxidase function and suggests that the distal histidine (H55) plays the central role in both function switching and activation of DHPs A&B. Similar to many myoglobins, H55 of DHP A is observed in two conformations, open and closed. However, in DHP A, H55 has been shown to exist in the open conformation to a much greater extent than in any known myoglobin. This results in an open exit channel for bound diatomic ligands, which leads to rapid escape. However, the open conformation may also permit the entry of hydrogen peroxide and even the native inhibitor, 4-bromophenol. We also have structural and spectroscopic evidence that external binding of substrate pushes H55 more deeply into the protein. This may serve to aid in the activation of bound hydrogen peroxide as part of the peroxidase mechanism. Thus, in DHP A, the closed and open states are inactive and active, respectively, for peroxidase chemistry. We have systematically probed this hypothesis using a variety of methods and site-directed mutants to determine the role played by the distal cavity in the stabilization of the inhibitor and the flexibility of the distal histidine. Based on the binding of the series of 4-halophenols in X-ray crystal structures, it is evident that there is a protein cavity deep inside DHP A. The functional relevance of this cavity will be elucidated.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Thompson, Matt and Franzen, Stefan}, year={2011}, month={Feb}, pages={222a} }
 @article{zhao_de serrano_dumarieh_thompson_franzen_2011, title={Effect of H55D Mutation on Kinetics and Structure of Dehaloperoxidase-Hemoglobin A}, volume={100}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2010.12.1421}, DOI={10.1016/j.bpj.2010.12.1421}, abstractNote={The H55D mutant of dehaloperoxidase-hemoglobin A (DHP A) has been prepared to mimic the H64D mutant of Sperm Whale myoglobin (SWMb), which has the highest peroxidase activity of any myoglobin mutant studied to date. The high peroxidase activity has been attributed to the rapid formation as well as the prolonged lifetime of compound I following addition of H2O2. However, unlike H64D SWMb, the H55D mutant of DHP A has ∼13-fold lower peroxidase activity towards oxidation of 2,4,6-trichlorophenol (TCP) into 2,6-dichloroquinone (DCQ) in the presence of H2O2. The origin of the lower rate constant may be the solvent-exposed conformation of D55, which has the effect of removing the acid-base catalyst necessary for heterolytic cleavage O-O bond in Fe-bound H2O2. These observations further support the hypothesis that the flexibility of distal histidine in wild-type DHP A, plays a crucial role in enzyme function. Remarkably, the H55D mutant also shows inhibition by 4-bromophenol (4-BP) in the oxidation of TCP, which is substantiated by the X-ray crystal structure of 4-BP bound to the internal inhibitor binding site observed in wild type DHP A and B. The inhibitor complex is an unusual internally bound molecule, completely surrounded by the protein. Compound ES, a tyrosine radical species associated with the oxoferryl intermediate detected in DHP A, is not observed in H55D. Thus, the H55D mutant is a key test case for the role of electron transfer in the DHP A mechanism.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Zhao, Junjie and de Serrano, Vesna and Dumarieh, Rania and Thompson, Matt and Franzen, Stefan}, year={2011}, month={Feb}, pages={221a} }
 @article{d’antonio_d’antonio_de serrano_gracz_thompson_ghiladi_bowden_franzen_2011, title={Functional Consequences of the Creation of an Asp-His-Fe Triad in a 3/3 Globin}, volume={50}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi201368u}, DOI={10.1021/bi201368u}, abstractNote={The proximal side of dehaloperoxidase-hemoglobin A (DHP A) from Amphitrite ornata has been modified via site-directed mutagenesis of methionine 86 into aspartate (M86D) to introduce an Asp-His-Fe triad charge relay. X-ray crystallographic structure determination of the metcyano forms of M86D [Protein Data Bank (PDB) entry 3MYN] and M86E (PDB entry 3MYM) mutants reveal the structural origins of a stable catalytic triad in DHP A. A decrease in the rate of H2O2 activation as well as a lowered reduction potential versus that of the wild-type enzyme was observed in M86D. One possible explanation for the significantly lower activity is an increased affinity for the distal histidine in binding to the heme Fe to form a bis-histidine adduct. Resonance Raman spectroscopy demonstrates a pH-dependent ligation by the distal histidine in M86D, which is indicative of an increased trans effect. At pH 5.0, the heme Fe is five-coordinate, and this structure resembles the wild-type DHP A resting state. However, at pH 7.0, the distal histidine appears to form a six-coordinate ferric bis-histidine (hemichrome) adduct. These observations can be explained by the effect of the increased positive charge on the heme Fe on the formation of a six-coordinate low-spin adduct, which inhibits the ligation and activation of H2O2 as required for peroxidase activity. The results suggest that the proximal charge relay in peroxidases regulate the redox potential of the heme Fe but that the trans effect is a carefully balanced property that can both activate H2O2 and attract ligation by the distal histidine. To understand the balance of forces that modulate peroxidase reactivity, we studied three M86 mutants, M86A, M86D, and M86E, by spectroelectrochemistry and nuclear magnetic resonance spectroscopy of 13C- and 15N-labeled cyanide adducts as probes of the redox potential and of the trans effect in the heme Fe, both of which can be correlated with the proximity of negative charge to the Nδ hydrogen of the proximal histidine, consistent with an Asp-His-Fe charge relay observed in heme peroxidases.}, number={44}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={D’Antonio, Edward L. and D’Antonio, Jennifer and de Serrano, Vesna and Gracz, Hanna and Thompson, Matthew K. and Ghiladi, Reza A. and Bowden, Edmond F. and Franzen, Stefan}, year={2011}, month={Nov}, pages={9664–9680} }
 @article{plummer_thompson_franzen_2011, title={Making Substrates Out of Inhibitors: Distal Cavity Mutations in Dehaloperoxidase from Amphitrite Ornata}, volume={100}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2010.12.1424}, DOI={10.1016/j.bpj.2010.12.1424}, abstractNote={Dehaloperoxidase (DHP A), a unique multi-function enzyme, from the marine worm Amphitrite ornate dehalogenates 2,4,6-trihalophenols to form the corresponding 2,6-dihalogenated quinone product. The catalytic cycle of DHP is similar to horseradish peroxidase (HRP), involving a high-valent oxoferryl heme and two one electron transfers from the aromatic substrate to the enzyme. However, unlike HRP, DHP has an internal binding cavity on the distal side of the heme capable of accommodating monohalogenated phenols. Internal binding of monohalogenated phenols in the distal cavity of DHP inhibits peroxidase function. Therefore, even though the peroxidase mechanism of DHP is similar to HRP, DHP is not capable of oxidizing the same range of halogenated substrates. Blocking internal binding in DHP may be the key to effectively enable DHP to function as a peroxidase on the full range of halogenated phenols. The distal cavity of DHP is surrounded by several hydrophobic amino acids that stabilize internal binding of the monohalogenated phenols: several phenylalanine residues (F21, F24, and F35), a valine residue (V59), and a leucine residue near the back edge of the heme (L100). We have recently expressed the L100F, L100Q, L100T, and L100N mutants of DHP in an effort to prevent internal binding and turn the inhibitors into substrates. These mutants are being characterized by UV-vis spectroscopy, resonance Raman spectroscopy, X-ray crystallography, and molecular dynamics simulations. Kinetic assays indicate that the peroxidase activity of the L100 mutants is reduced compared to native DHP, and although we believe it to be possible theoretically, none of the L100 mutations have caused the switch from inhibitor to substrate up to the present.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Plummer, Ashlee M. and Thompson, Matthew K. and Franzen, Stefan}, year={2011}, month={Feb}, pages={222a} }
 @article{wang_lockney_goshe_franzen_2011, title={Mass Spectrometric Detection of Targeting Peptide Bioconjugation to Red clover necrotic mosaic virus}, volume={22}, ISSN={["1520-4812"]}, DOI={10.1021/bc2001769}, abstractNote={Plant virus nanoparticle (PVN) formulations constructed from Red clover necrotic mosaic virus by drug infusion and targeting peptide conjugation can be employed as drug delivery tools. In this investigation, we studied the cross-linked structures formed by application of sulfosuccinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (sSMCC) and succinimidyl-[(N-maleimidopropionamido)-hexaethylene glycol] ester (SMPEG) as heterobifunctional linkers in the bioconjugation process. The plant virus formulations using several targeting peptides cross-linked to the plant virus capsid were characterized by LC/MSE analysis, which produced at least 69% sequence coverage using trypsin and chymotrypsin digestion. The results showed evidence for several types of modification located in three domains of the capsid protein. Extensive linker modifications on lysines or cysteines were detected in all the domains, including both intended peptide–capsid cross-links and unintended intracapsid cross-links. Surprisingly, the most extensive peptide modification was observed in the R domain, which is thought to be quite inaccessible to peptides and cross-linking reagents in solution, since it is on the interior of the virus. These results show that heterobifunctional linkers may not be the most efficient method for attachment of peptides to plant virus capsids. As an alternative conjugation strategy, maleimide peptides were used to conjugate with the virus in a one-step reaction. Analysis by LC/MSE showed that these one-step maleimide coupling reactions were more specific, such as modifications of C154 and to a lesser extent C267, and provide a means for achieving more effective PVN formulations.}, number={10}, journal={BIOCONJUGATE CHEMISTRY}, author={Wang, Ruqi and Lockney, Dustin M. and Goshe, Michael B. and Franzen, Stefan}, year={2011}, month={Oct}, pages={1970–1982} }
 @article{sasan_franzen_2011, title={Molecular Activation by Peroxidases}, volume={100}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2010.12.1418}, DOI={10.1016/j.bpj.2010.12.1418}, abstractNote={The peroxidase class of enzymes has been known to activate substrates for electron transfer from nearly a century. The precise consequences of that electron transfer have been in less detail than the initial even. Herein, we examine the kinetic and structural studies indicate that peroxidase enzymes are capable of oxidation of 2,4,6-trichlorophenol (2,4,6-TCP) to 2,6-dichloro-1,4-benzoquinone (2,6-DCQ). There are two dehaloperoxidase-hemoglobins of Amphitrite ornata, DHP A and B, that both have peroxidase activity superior to hemoglobins or myoglobins previously studied. One consequence of the further oxidation of 2,6-DCQ is the formation 2,6-dichloro-3-hydroxy-1,4-benzoquinone 2,6-DCQOH. The secondary product, 2,6-DCQOH, has been observed by UV-vis spectrophotometry and 1H-13C NMR. The results are consistent with the spontaneous of oxidation of 2,6-DCQ in the of hydrogen peroxide anion (HO2-). Based Arrhenius analysis of the kinetics, the activation energy of spontaneous hydroxylation (Ea = 32.4 kJ/mol) is significantly lower than the activation energy of oxidation 2,4,6-TCP (Ea = 56.3 kJ/mol). 2,6-DCQOH Density functional theory (DFT) calculations were employed to differentiate between two possible hydroxylation mechanisms, leading to different products, 1.) 2,6,-DCQOH and 2.) 2,3-dihydroxy-6-cloro-1,4-benzoquinone. The formation rate of the 2,6-DCQ product appears to affect the secondary hydroxylation rate. We have probed the effect of alternative activation using peroxy acids, such as meta-chloroperoxybenzoic acid, to test the role played by activation and electron transfer in the formation of products by the dual function hemoglobin-dehaloperoxidase. These effects are modeled structurally using a variety of methods including docking, and structural studies of interaction of the substrate with the protein.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Sasan, Koroush and Franzen, Stefan}, year={2011}, month={Feb}, pages={221a} }
 @article{jiang_franzen_2011, title={Mutagenesis Study on the Conformation of Distal Histidine in Dehaloperoxidase-Hemoglobin}, volume={100}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2010.12.1420}, DOI={10.1016/j.bpj.2010.12.1420}, abstractNote={Dehaloperoxidase-hemoglobin (DHP A), found in terebellid polychaete Amphitrite ornata, acts as a bi-functional protein. It has the globin fold and acts as an oxygen carrier, but it can also act as the peroxidase, which can oxidatively dehalogenate halophenols found in benthic ecosystems to the corresponding quinones. The distal histidine His55 is the only residue that determines the substrate and heme ligand binding function. His55 also plays a key role in peroxidase catalysis. His55 has two conformations, open conformation and closed conformation, which is related to inhibitor and substrate binding respectively. In myoglobin, Phe46 and Arg45 have been suggested the critical residues effect the C alpha - C beta rotation of distal His64. Moreover, in myoglobin the residue adjacent to His 64 (the distal histidine) is a glycine (Gly65). Although this is a conserved feature in many globins, DHP A has a threonine in this position. To understand the role of the amino acid in this position the mutants T56G, T56A, T56S and T56V were prepared. Kinetic assay results show that all of these mutants have higher activity than wild-type DHP A. Molecular dynamics simulations, Resonance Raman spectroscopy, X-ray crystallography and other methods will be presented to understand how a change in the Thr56 position affects the both the conformation of His55 and peroxidase activity. The inhibitor in DHP A binds in an unusual internal binding site. We will determine the inhibitor binding constants and measure the enzyme inhibition in kinetic assays to understand the role played by the distal histidine conformation inhibition as well.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Jiang, Shu and Franzen, Stefan}, year={2011}, month={Feb}, pages={221a} }
 @article{szatkowski_thompson_kaminski_franzen_dybala-defratyka_2011, title={Oxidative dechlorination of halogenated phenols catalyzed by two distinct enzymes: Horseradish peroxidase and dehaloperoxidase}, volume={505}, ISSN={["1096-0384"]}, DOI={10.1016/j.abb.2010.09.018}, abstractNote={The mechanism of the dehalogenation step catalyzed by dehaloperoxidase (DHP) from Amphitrite ornata, an unusual heme-containing protein with a globin fold and peroxidase activity, has remarkable similarity with that of the classical heme peroxidase, horseradish peroxidase (HRP). Based on quantum mechanical/molecular mechanical (QM/MM) modeling and experimentally determined chlorine kinetic isotope effects, we have concluded that two sequential one electron oxidations of the halogenated phenol substrate leads to a cationic intermediate that strongly resembles a Meisenheimer intermediate - a commonly formed reactive complex during nucleophilic aromatic substitution reactions especially in the case of arenes carrying electron withdrawing groups.}, number={1}, journal={ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS}, author={Szatkowski, Lukasz and Thompson, Matthew K. and Kaminski, Rafal and Franzen, Stefan and Dybala-Defratyka, Agnieszka}, year={2011}, month={Jan}, pages={22–32} }
 @article{sturgeon_battenburg_lyon_franzen_2011, title={Revisiting the Peroxidase Oxidation of 2,4,6-Trihalophenols: ESR Detection of Radical Intermediates}, volume={24}, ISSN={["1520-5010"]}, DOI={10.1021/tx200215r}, abstractNote={The peroxidase oxidation of 2,4,6-trichlorophenol (TCP) has been clearly shown to result in 2,6-dichloro-1,4-benzoquinone (DCQ). DCQ is a 2-electron oxidation product of TCP that has undergone para dechlorination. Many peroxidases show similar oxidation of the substrate, TCP, to yield the quinone, DCQ. Depending on the substrate, peroxidases are thought to carry out both 1- and 2-electron oxidations; the mechanism can be confirmed by the detection of both enzyme and substrate intermediates. This article presents ESR evidence for the transient 2,4,6-trichlorophenoxyl radical intermediate (TCP•), which exists free in solution, i.e., is not enzyme associated. These data are best explained as a 1-electron peroxidase oxidation of TCP to form TCP•, followed by enzyme-independent radical reactions leading to the 2-electron oxidized product. Also presented are data for the peroxidase oxidation of 2,4,6-trifluorophenol and 2,6-dichloro-4-fluorophenol.}, number={11}, journal={CHEMICAL RESEARCH IN TOXICOLOGY}, author={Sturgeon, Bradley E. and Battenburg, Benjamin J. and Lyon, Blake J. and Franzen, Stefan}, year={2011}, month={Nov}, pages={1862–1868} }
 @article{de serrano_franzen_2011, title={Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata}, volume={98}, ISSN={0006-3525}, url={http://dx.doi.org/10.1002/bip.21674}, DOI={10.1002/bip.21674}, abstractNote={A functional role for a protein cavity that stabilizes inhibitor binding has been established based on a comparison of Xe-derivatized and inhibitor-bound X-ray crystal structures in dehaloperoxidase-hemoglobin (DHP A) of Amphitrite ornata. The internal binding affinity of four different inhibitors, 4-fluorophenol, 4-chlorophenol, 4-bromophenol, and 4-iodophenol in the distal pocket has been shown previously to increase proportional to the radius of the para-halogen atom. Inhibition of oxidation of the native substrate, 2,4,6-tribromophenol, has been shown to follow the trend in inhibitor binding strength, because of a two-site competitive inhibition mechanism that involves displacement of the substrate by the inhibitor in a gated mechanism involving the distal histidine of DHP A. In this study, it is shown that the origin of the stronger binding by a larger para-halogen substituent coincides structurally with a Xe-binding cavity (Xe1) characterized structurally by X-ray crystallography. The Xe1 site is surrounded by amino acid resides L100, F21, F24, F35, F60, and V59 in the distal pocket, located 4.8 Å from the heme iron, in a position that is coincident with the para-bromine atom of the inhibitor 4-bromophenol. 4-bromophenol is prevalent in benthic ecosystems where A. ornata resides. A second, less well-defined, binding site in DHP A, labeled as Xe2, is located near the surface of the protein in the vicinity of amino acid residues L62, R69, D79, T82, and L83, which may be related to substrate docking on the surface of DHP A.}, number={1}, journal={Biopolymers}, publisher={Wiley}, author={de Serrano, Vesna and Franzen, Stefan}, year={2011}, month={May}, pages={27–35} }
 @article{lockney_guenther_loo_overton_antonelli_clark_hu_luft_lommel_franzen_2011, title={The Red clover necrotic mosaic virus Capsid as a Multifunctional Cell Targeting Plant Viral Nanoparticle}, volume={22}, ISSN={["1520-4812"]}, DOI={10.1021/bc100361z}, abstractNote={Multifunctional nanoparticles hold promise as the next generation of therapeutic delivery and imaging agents. Nanoparticles comprising many types of materials are being tested for this purpose, including plant viral capsids. It has been found that Red clover necrotic mosaic virus (RCNMV) can be loaded with significant amounts of therapeutic molecules with molecular weights of 600 or even greater. Formulation of RCNMV into a plant viral nanoparticle (PVN) involves the loading of cargo and attachment of peptides. In this study, we show that targeting peptides (less than 16 amino acids) can be conjugated to the capsid using the heterobifunctional chemical linker sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (Sulfo-SMCC). The uptake of both native RCNMV capsids and peptide-conjugated RCNMV was tested in the HeLa cell line for peptides with and without fluorescent labels. Uptake of RCNMV conjugate with a CD46 targeting peptide was monitored by flow cytometry. When formulated PVNs loaded with doxorubicin and armed with a targeting peptide were delivered to HeLa cells, a cytotoxic effect was observed. The ability to modify RCNMV for specific cell targeting and cargo delivery offers a method for the intracellular delivery of reagents for research assays as well as diagnostic and therapeutic applications.}, number={1}, journal={BIOCONJUGATE CHEMISTRY}, author={Lockney, Dustin M. and Guenther, Richard N. and Loo, Lina and Overton, Wesley and Antonelli, Ray and Clark, Jennifer and Hu, Mei and Luft, Chris and Lommel, Steven A. and Franzen, Stefan}, year={2011}, month={Jan}, pages={67–73} }
 @article{gaff_franzen_delley_2010, title={Ab Initio Calculation of Resonance Raman Cross Sections Based on Excited State Geometry Optimization}, volume={114}, ISSN={["1089-5639"]}, DOI={10.1021/jp103321x}, abstractNote={A method for the calculation of resonance Raman cross sections is presented on the basis of calculation of structural differences between optimized ground and excited state geometries using density functional theory. A vibrational frequency calculation of the molecule is employed to obtain normal coordinate displacements for the modes of vibration. The excited state displacement relative to the ground state can be calculated in the normal coordinate basis by means of a linear transformation from a Cartesian basis to a normal coordinate one. The displacements in normal coordinates are then scaled by root-mean-square displacement of zero point motion to calculate dimensionless displacements for use in the two-time-correlator formalism for the calculation of resonance Raman spectra at an arbitrary temperature. The method is valid for Franck−Condon active modes within the harmonic approximation. The method was validated by calculation of resonance Raman cross sections and absorption spectra for chlorine dioxide, nitrate ion, trans-stilbene, 1,3,5-cycloheptatriene, and the aromatic amino acids. This method permits significant gains in the efficiency of calculating resonance Raman cross sections from first principles and, consequently, permits extension to large systems (>50 atoms).}, number={43}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Gaff, J. F. and Franzen, S. and Delley, B.}, year={2010}, month={Nov}, pages={11681–11690} }
 @article{thompson_parnell_franzen_2010, title={Block the Inhibitor Binding Site in the Interior of Dehaloperoxidase from Amphitrite Ornata}, volume={98}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2009.12.3513}, DOI={10.1016/j.bpj.2009.12.3513}, abstractNote={Dehaloperoxidase (DHP A) from the annelid Amphitrite ornata is a catalytically active hemoglobin-peroxidase that possesses an internal binding site in the distal pocket and an external binding site near the heme edge. We have recently demonstrated that DHP A has a unique two-site competitive binding mechanism, in which the internal and external binding sites communicate through two conformations of the distal histidine (H55). The native substrate is 2,4,6-tribromophenol, but DHP A is capable of oxidizing any 2,4,6-trihalophenol to the corresponding dihaloquinone and other products. While DHP A is very effective at oxidizing 2,4,6-trichlorophenol, assays of DHP A on 2,4-dichlorophenol and 4-chlorophenol show little to no activity. Binding of 4-halophenols in the internal site prevents oxidation of trihalogenated phenols at the external site, i.e. they are inhibitors. X-ray crystallography shows that when para-halogenated phenols (4-iodo-, 4-bromo-, 4-chlorophenol) bind internally, the halogen is accommodated by a hydrophobic cavity that is analogous to the Xenon 4 binding site in Sperm whale myoglobin. Using resonance Raman spectroscopy, we demonstrate that the apparent dissociation constants of the para-halogenated phenols mimic the trend observed in the X-ray crystal structures. The results suggest that a few amino acids (L100, V59, F21, F24, and F35) surrounding the hydrophobic cavity regulate internal binding of the inhibitor. Using site-directed mutagenesis, we have changed several of these amino acids to prevent internal binding, and thus to increase DHP A activity towards mono- and dichlorinated phenols. Mutation to tryptophan (F21W and V59W) gives rise to new radical intermediates which complicates the interpretation in terms of inhibitor binding. Alternatively, aliphatic amino acids and phenylalanine provide steric effects that can alter the oxidation of rates of 4-chloro-, and 2,4-dichlorophenol.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Thompson, Matthew K. and Parnell, Jonathon M. and Franzen, Stefan}, year={2010}, month={Jan}, pages={641a} }
 @article{thompson_franzen_ghiladi_reeder_svistunenko_2010, title={Compound ES of Dehaloperoxidase Decays via Two Alternative Pathways Depending on the Conformation of the Distal Histidine}, volume={132}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja106620q}, DOI={10.1021/ja106620q}, abstractNote={Dehaloperoxidase (DHP) is a respiratory hemoglobin (Hb) that has been shown to catalyze the conversion of trihalophenols to dihaloquinones in the presence of hydrogen peroxide. Ferric heme states of the resting DHP and the free radical intermediates formed under H2O2 treatment were studied by low-temperature electron paramagnetic resonance spectroscopy in the range of reaction times from 50 ms to 2 min at three different pH values. Two high-spin ferric heme forms were identified in the resting enzyme and assigned to the open and closed conformations of the distal histidine, His55. Two free radicals were found in DHP activated by H2O2: the radical associated with Compound ES (the enzyme with the heme in the oxoferryl state and a radical on the polypeptide chain) has been assigned to Tyr34, and the other radical has been assigned to Tyr38. The Tyr34 radical is formed with a very high relative yield (almost 100% of heme), atypical of other globins. High-performance liquid chromatography analysis of the reaction products showed a pH-dependent formation of covalent heme-to-protein cross-links. The stable DHP Compound RH, formed under H2O2 in the absence of the trihalophenol substrates, is proposed to be a state with the ferric heme covalently cross-linked to Tyr34. A kinetic model of the experimental data suggests that formation of Compound RH and formation of the Tyr38 radical are two alternative routes of Compound ES decay. Which route is taken depends on the conformation of His55: in the less populated closed conformation, the Tyr38 radical is formed, but in the major open conformation, Compound ES decays, yielding Compound RH, a product of safe termination of the two oxidizing equivalents of H2O2 when no substrate is available.}, number={49}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Thompson, Matthew K. and Franzen, Stefan and Ghiladi, Reza A. and Reeder, Brandon J. and Svistunenko, Dimitri A.}, year={2010}, month={Dec}, pages={17501–17510} }
 @article{davis_bobay_franzen_2010, title={Determination of Separate Inhibitor and Substrate Binding Sites in the Dehaloperoxidase−Hemoglobin fromAmphitrite ornata,}, volume={49}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi9018576}, DOI={10.1021/bi9018576}, abstractNote={Dehaloperoxidase−hemoglobin (DHP A) is a dual function protein found in the terrebellid polychaete Amphitrite ornata. A. ornata is an annelid, which inhabits estuary mudflats with other polychaetes that secrete a range of toxic brominated phenols. DHP A is capable of binding and oxidatively dehalogenating some of these compounds. DHP A possesses the ability to bind halophenols in a distinct, internal distal binding pocket. Since its discovery, the distal binding pocket has been reported as the sole binding location for halophenols; however, data herein suggest a distinction between inhibitor (monohalogenated phenol) and substrate (trihalogenated phenol) binding locations. Backbone 13Cα, 13Cβ, carbonyl 13C, amide 1H, and amide 15N resonance assignments have been made, and various halophenols were titrated into the protein. 1H−15N HSQC experiments were collected at stoichiometric intervals during each titration, and binding locations specific for mono- and trihalogenated phenols have been identified. Titration of monohalogenated phenol induced primary changes around the distal binding pocket, while introduction of trihalogenated phenols created alterations of the distal histidine and the local area surrounding W120, a structural region that corresponds to a possible dimer interface region recently observed in X-ray crystal structures of DHP A.}, number={6}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Davis, Michael F. and Bobay, Benjamin G. and Franzen, Stefan}, year={2010}, month={Feb}, pages={1199–1206} }
 @misc{franzen_2010, title={Expanding the catalytic repertoire of ribozymes and deoxyribozymes beyond RNA substrates}, volume={12}, number={2}, journal={Current Opinion in Molecular Therapeutics}, author={Franzen, S.}, year={2010}, pages={223–232} }
 @article{franzen_de serrano_oliver_krueger_2010, title={Experimental and Computational Study of the Monomer-Dimer Equilibrium in Dehaloperoxidase from Amphitrite Ornata}, volume={98}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2009.12.3506}, DOI={10.1016/j.bpj.2009.12.3506}, abstractNote={The enzyme dehaloperoxidase (DHP) from the annelid Amphitrite ornata is a unique hemoglobin that functions as a peroxidase, capable of converting 2,4,6-trihalophenols (TBP, TCP, and TFP) into dihalogenated quinones and other products. The DHP protein crystallizes as a dimer. Yet, it was originally characterized as a monomer in solution. We have conducted small angle X-ray scattering (SAXS) in order to probe the monomer-dimer equilibrium in solution. The interest in this area arises from the fact that many hemoglobins are multimers that play an essential role in the cooperativity of oxygen uptake and release. For example, A. ornata possesses a giant hemoglobin (erythrocruorin) like many other marine organisms. Since there are only two known hemoglobin genes (DHP A and DHP B) in A. ornata, it is logical that one or both of these proteins associate with other proteins to form the giant hemoglobin. On the other hand, coelomic DHP does not appear to have a high degree of cooperativity. Moreover, the dimer interface in the X-ray crystal structure of both DHP A and DHP B consists of only 3 amino acid residues. The SAXS data show that the equilibrium for DHP favors the monomer form up to the highest concentrations studied (∼ 200 micromolar). However, is there a small amount of the dimer in solution. Thus, it is of interest to apply the known interfaces from study of the X-ray crystal structure to determine which surfaces of DHP may be interacting weakly in solution. We studied the monomer-dimer interface using molecular dynamics (MD) simulations in order to ascertain the relative strength of these interfaces. These results are used to develop a systematic approach to characterization of monomer-multimer equilibria based SAXS and X-ray crystallography data.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Franzen, Stefan and de Serrano, Vesna and Oliver, Ryan C. and Krueger, Joanna}, year={2010}, month={Jan}, pages={640a} }
 @article{thompson_davis_serrano_nicoletti_howes_smulevich_franzen_2010, title={Internal Binding of Halogenated Phenols in Dehaloperoxidase-Hemoglobin Inhibits Peroxidase Function}, volume={99}, ISSN={["1542-0086"]}, DOI={10.1016/j.bpj.2010.05.041}, abstractNote={Dehaloperoxidase (DHP) from the annelid Amphitrite ornata is a catalytically active hemoglobin-peroxidase that possesses a unique internal binding cavity in the distal pocket above the heme. The previously published crystal structure of DHP shows 4-iodophenol bound internally. This led to the proposal that the internal binding site is the active site for phenol oxidation. However, the native substrate for DHP is 2,4,6-tribromophenol, and all attempts to bind 2,4,6-tribromophenol in the internal site under physiological conditions have failed. Herein, we show that the binding of 4-halophenols in the internal pocket inhibits enzymatic function. Furthermore, we demonstrate that DHP has a unique two-site competitive binding mechanism in which the internal and external binding sites communicate through two conformations of the distal histidine of the enzyme, resulting in nonclassical competitive inhibition. The same distal histidine conformations involved in DHP function regulate oxygen binding and release during transport and storage by hemoglobins and myoglobins. This work provides further support for the hypothesis that DHP possesses an external binding site for substrate oxidation, as is typical for the peroxidase family of enzymes.}, number={5}, journal={BIOPHYSICAL JOURNAL}, author={Thompson, Matthew K. and Davis, Michael F. and Serrano, Vesna and Nicoletti, Francesco P. and Howes, Barry D. and Smulevich, Giulietta and Franzen, Stefan}, year={2010}, month={Sep}, pages={1586–1595} }
 @article{ma_thompson_gaff_franzen_2010, title={Kinetic Analysis of a Naturally Occurring Bioremediation Enzyme: Dehaloperoxidase-Hemoglobin from Amphitrite ornata}, volume={114}, ISSN={["1520-6106"]}, DOI={10.1021/jp1014516}, abstractNote={The temperature dependence of the rate constant for substrate oxidation by the dehaloperoxidase-hemoglobin (DHP) of Amphitrite ornata has been measured from 278 to 308 K. The rate constant is observed to increase over this range by approximately a factor of 2 for each 10 °C temperature increment. An analysis of the initial rates using a phenomenological approach that expresses the peroxidase ping-pong mechanism in the form of the Michaelis−Menten equation leads to an interpretation of the effects in terms of the fundamental rate constants. The analysis of kinetic data considers a combination of diffusion rate constants for substrate and H2O2, elementary steps involving activation and heterolysis of the O−O bond of H2O2, and two electron transfers from the substrate to the iron. To complete the analysis from the perspective of turnover of substrate into product, density function theory (DFT) calculations were used to address the fate of phenoxy radical intermediates. The analysis suggests a dominant role for diffusion in the kinetics of DHP.}, number={43}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Ma, Huan and Thompson, Matthew K. and Gaff, John and Franzen, Stefan}, year={2010}, month={Nov}, pages={13823–13829} }
 @article{nicoletti_thompson_howes_franzen_smulevich_2010, title={New Insights into the Role of Distal Histidine Flexibility in Ligand Stabilization of Dehaloperoxidase-Hemoglobin from Amphitrite ornata}, volume={49}, ISSN={["0006-2960"]}, DOI={10.1021/bi9020567}, abstractNote={The present work highlights the important role played by the distal histidine in controlling the binding of heme ligands in dehaloperoxidase (DHP) as compared to myoglobin and peroxidases. In DHP the distal histidine is highly mobile and undergoes a conformational change that places it within hydrogen-bonding distance of anionic ligands and water, where strong hydrogen bonding can occur. The detailed resonance Raman (RR) analysis at room temperature shows the presence of an equilibrium between a 5-coordinate and a 6-coordinate (aquo) high-spin form. The equilibrium shifts toward the aquo form at 12 K. These two forms are consistent with the existing X-ray structures where a closed conformation, with His55 positioned in the distal pocket and H-bonded with the distal water molecule (6-coordinate), and an open solvent-exposed conformation, with the His55 displaced from the distal pocket (5-coordinate form), are in equilibrium. Moreover, the comparison between the Raman data at 298 and 12 K and the results obtained by EPR of DHP in the presence of 4-iodophenol highlights the formation of a pure 5-coordinate high-spin form (open conformation). The data reported herein support the role of His55 in facilitating the interaction of substrate and inhibitor in the regulation of enzyme function, as previously suggested. The two conformations of His55 in equilibrium at room temperature provide a level of control that permits the distal histidine to act as both the acid−base catalyst in the peroxidase mechanism and the stabilizing amino acid for exogenous heme-coordinated ligands.}, number={9}, journal={BIOCHEMISTRY}, author={Nicoletti, Francesco P. and Thompson, Matthew K. and Howes, Barry D. and Franzen, Stefan and Smulevich, Giulietta}, year={2010}, month={Mar}, pages={1903–1912} }
 @article{skalski_taras-goslinska_dembska_gdaniec_franzen_2010, title={Photoinduced Fluorescent Cross-Linking of 5-Chloro- and 5-Fluoro-4-thiouridines with Thymidine}, volume={75}, ISSN={["0022-3263"]}, DOI={10.1021/jo902136k}, abstractNote={Two highly fluorescent, thermally stable diastereomeric photoadducts, 3a,b, are formed when either 5-chloro-4-thiouridine, 1, or 5-fluoro-4-thiouridine, 2, are photoexcited with 366 nm UV light in the presence of thymidine (T). 5-Fluoro-4-thiouridine, 2, exhibits photoreactivity much higher than that of the 5-chloro derivative 1. In both cases the photoreaction is very clean, leading to highly eficient conversion of the 5-halogeno-4-thiouridine (1, 2) and T to photoadducts 3a,b. The identity and structure of 3a was confirmed using mass spectrometry and 2-D NMR. The epimeric relationship of 3a,b was established by UV circular dichroism spectroscopy. The geometry of the fluorescent photoadduct is consistent with formation of an interstrand cross-link in a DNA duplex if 1 or 2 is flanked by T in an opposite strand.}, number={3}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Skalski, Bohdan and Taras-Goslinska, Katarzyna and Dembska, Anna and Gdaniec, Zofia and Franzen, Stefan}, year={2010}, month={Feb}, pages={621–626} }
 @article{kruglik_yoo_franzen_vos_martin_negrerie_2010, title={Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins}, volume={107}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0912938107}, abstractNote={We investigated the ultrafast structural transitions of the heme induced by nitric oxide (NO) binding for several heme proteins by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We probed the heme iron motion by the evolution of the iron-histidine Raman band intensity after NO photolysis. Unexpectedly, we found that the heme response and iron motion do not follow the kinetics of NO rebinding. Whereas NO dissociation induces quasi-instantaneous iron motion and heme doming (<0.6 ps), the reverse process results in a much slower picosecond movement of the iron toward the planar heme configuration after NO binding. The time constant for this primary domed-to-planar heme transition varies among proteins (approximately 30 ps for myoglobin and its H64V mutant, approximately 15 ps for hemoglobin, approximately 7 ps for dehaloperoxidase, and approximately 6 ps for cytochrome c) and depends upon constraints exerted by the protein structure on the heme cofactor. This observed phenomenon constitutes the primary structural transition in heme proteins induced by NO binding.}, number={31}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Kruglik, Sergei G. and Yoo, Byung-Kuk and Franzen, Stefan and Vos, Marten H. and Martin, Jean-Louis and Negrerie, Michel}, year={2010}, month={Aug}, pages={13678–13683} }
 @article{d’antonio_d’antonio_thompson_bowden_franzen_smirnova_ghiladi_2010, title={Spectroscopic and Mechanistic Investigations of Dehaloperoxidase B fromAmphitrite ornata}, volume={49}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi100407v}, DOI={10.1021/bi100407v}, abstractNote={Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a bifunctional enzyme that possesses both hemoglobin and peroxidase activities. Of the two DHP isoenzymes identified to date, much of the recent focus has been on DHP A, whereas very little is known pertaining to the activity, substrate specificity, mechanism of function, or spectroscopic properties of DHP B. Herein, we report the recombinant expression and purification of DHP B, as well as the details of our investigations into its catalytic cycle using biochemical assays, stopped-flow UV-visible, resonance Raman, and rapid freeze-quench electron paramagnetic resonance spectroscopies, and spectroelectrochemistry. Our experimental design reveals mechanistic insights and kinetic descriptions of the dehaloperoxidase mechanism which have not been previously reported for isoenzyme A. Namely, we demonstrate a novel reaction pathway in which the products of the oxidative dehalogenation of trihalophenols (dihaloquinones) are themselves capable of inducing formation of oxyferrous DHP B, and an updated catalytic cycle for DHP is proposed. We further demonstrate that, unlike the traditional monofunctional peroxidases, the oxyferrous state in DHP is a peroxidase-competent starting species, which suggests that the ferric oxidation state may not be an obligatory starting point for the enzyme. The data presented herein provide a link between the peroxidase and oxygen transport activities which furthers our understanding of how this bifunctional enzyme is able to unite its two inherent functions in one system.}, number={31}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={D’Antonio, Jennifer and D’Antonio, Edward L. and Thompson, Matthew K. and Bowden, Edmond F. and Franzen, Stefan and Smirnova, Tatyana and Ghiladi, Reza A.}, year={2010}, month={Aug}, pages={6600–6616} }
 @article{serrano_d'antonio_franzen_ghiladi_2010, title={Structure of dehaloperoxidase B at 1.58 angstrom resolution and structural characterization of the AB dimer from Amphitrite ornata}, volume={66}, journal={Acta Crystallographica. Section D, Biological Crystallography}, author={Serrano, V. and D'Antonio, J. and Franzen, S. and Ghiladi, R. A.}, year={2010}, pages={529–538} }
 @article{serrano_davis_gaff_zhang_chen_d'antonio_bowden_rose_franzen_2010, title={X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: Evidence for photoreductive dissociation of the iron-cyanide bond}, volume={66}, journal={Acta Crystallographica. Section D, Biological Crystallography}, author={Serrano, V. S. and Davis, M. F. and Gaff, J. F. and Zhang, Q. and Chen, Z. and D'Antonio, E. L. and Bowden, E. F. and Rose, R. and Franzen, S.}, year={2010}, pages={770–782} }
 @article{gagnon_ju_goshe_maxwell_franzen_2009, title={A role for hydrophobicity in a DielsAlder reaction catalyzed by pyridyl-modified RNA}, volume={37}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkp177}, abstractNote={New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu2+, as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification's role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.}, number={9}, journal={NUCLEIC ACIDS RESEARCH}, author={Gagnon, Keith T. and Ju, Show-Yi and Goshe, Michael B. and Maxwell, E. Stuart and Franzen, Stefan}, year={2009}, month={May}, pages={3074–3082} }
 @article{feducia_dumarieh_gilvey_smirnova_franzen_ghiladi_2009, title={Characterization of Dehaloperoxidase Compound ES and Its Reactivity with Trihalophenols†}, volume={48}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi801916j}, DOI={10.1021/bi801916j}, abstractNote={Dehaloperoxidase (DHP), the oxygen transport hemoglobin from the terebellid polychaete Amphitrite ornata, is the first globin identified to possess a biologically relevant peroxidase activity. DHP has been shown to oxidize trihalophenols to dihaloquinones in a dehalogenation reaction that uses hydrogen peroxide as a substrate. Herein, we demonstrate that the first detectable intermediate following the addition of hydrogen peroxide to ferric DHP contains both a ferryl heme and a tyrosyl radical, analogous to Compound ES of cytochrome c peroxidase. Furthermore, we provide a detailed kinetic description for the reaction of preformed DHP Compound ES with the substrate 2,4,6-trichlorophenol and demonstrate the catalytic competency of this intermediate in generating the product 2,4-dichloroquinone. Using rapid-freeze-quench electron paramagnetic resonance spectroscopy, we detected a g ≈ 2.0058 signal confirming the presence of a protein radical in DHP Compound ES. In the absence of substrate, DHP Compound ES evolves to a new species, Compound RH, which is functionally unique to dehaloperoxidase. We propose that this intermediate plays a protective role against heme bleaching. While unreactive toward further oxidation, Compound RH can be reduced and subsequently bind dioxygen, generating oxyferrous DHP, which may represent the catalytic link between peroxidase and oxygen transport activities in this bifunctional protein.}, number={5}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Feducia, Jeremiah and Dumarieh, Rania and Gilvey, Lauren B. G. and Smirnova, Tatyana and Franzen, Stefan and Ghiladi, Reza A.}, year={2009}, month={Feb}, pages={995–1005} }
 @article{losego_efremenko_rhodes_cerruti_franzen_maria_2009, title={Conductive oxide thin films: Model systems for understanding and controlling surface plasmon resonance}, volume={106}, ISSN={0021-8979 1089-7550}, url={http://dx.doi.org/10.1063/1.3174440}, DOI={10.1063/1.3174440}, abstractNote={Degeneratively doped conductive oxides represent a unique host for exploring the inter-relationship between the properties of charge carriers and their collective plasmonic response. These materials often lack interband transitions that obfuscate interpretation of spectral response in elemental metals, and unlike metals, the electronic transport properties of conductive oxides are easily tunable. This work explores the process-structure-property relationships that regulate surface plasmon resonance (SPR) in sputter deposited indium tin oxide (ITO) thin films. Film deposition conditions are used to regulate film microstructure and tune the electronic mobility to between 7 and 40 cm2 V−1 s−1. Postdeposition annealing in low oxygen partial pressure atmospheres is used to engineer the ITO defect equilibrium and modulate carrier concentrations to between 1020 and 1021 cm−3. These electronic transport properties are modulated with near independence enabling straightforward interpretation of their influence on the SPR response observed in the infrared reflectivity spectrum. Higher electronic mobilities favor narrower surface plasmon absorption bands, while higher carrier concentrations favor higher absorption band frequencies. A simple free electron model, having only electronic carrier density and electronic mobility as variables, can be used to describe ITO’s dielectric response. Calculations that combine this dielectric function and the Fresnel equations provide simulated reflectivity spectra that match experimental data with remarkable accuracy. Because these spectra use no fitting parameters and are calculated with well-studied material properties, it opens the opportunity for future design of plasmonic response in advanced material systems including degeneratively doped semiconductors, silicides, and nitrides.}, number={2}, journal={Journal of Applied Physics}, publisher={AIP Publishing}, author={Losego, Mark D. and Efremenko, Alina Y. and Rhodes, Crissy L. and Cerruti, Marta G. and Franzen, Stefan and Maria, Jon-Paul}, year={2009}, month={Jul}, pages={024903} }
 @article{gerber_leonard_franzen_2009, title={Conductive thin film multilayers of gold on glass formed by self-assembly of multiple size gold nanoparticles}, volume={517}, ISSN={["0040-6090"]}, DOI={10.1016/j.tsf.2009.05.033}, abstractNote={Highly conductive thin films of gold have been fabricated on glass substrates by the deposition of gold nanoparticles of two different diameters. A deposition sequence, alternating between 2.6-nm and 12-nm diameter particles, was used whereby the 2.6-nm particles served to fill in the gaps created by the assembly of the larger 12-nm diameter particles. The resulting thin films, with thicknesses of less than 35 nm, displayed high conductivities, yet were fabricated in substantially fewer deposition cycles than required by previous methods. Analysis of surface morphology performed by atomic force microscopy and scanning electron microscopy showed that the high conductivity is the result of a less porous surface structure than can be achieved through the layering of a single size nanoparticle. Conductivity analysis was performed by 4-point probe with resistivities of 5.00 ± 0.4 × 10− 6 Ω m for 5 layers and 4.49 ± 0.2 × 10− 6 Ω m for the 6-layer films.}, number={24}, journal={THIN SOLID FILMS}, author={Gerber, Ralph W. and Leonard, Donovan N. and Franzen, Stefan}, year={2009}, month={Oct}, pages={6803–6808} }
 @article{davis_gracz_vendeix_serrano_somasundaram_decatur_franzen_2009, title={Different Modes of Binding of Mono-, Di-, and Trihalogenated Phenols to the Hemoglobin Dehaloperoxidase from Amphitrite ornata}, volume={48}, ISSN={["0006-2960"]}, DOI={10.1021/bi801568s}, abstractNote={The hemoglobin dehaloperoxidase (DHP), found in the coelom of the terebellid polychaete Amphitrite ornata, is a dual-function protein that has the characteristics of both hemoglobins and peroxidases. In addition to oxygen transport function, DHP readily oxidizes halogenated phenols in the presence of hydrogen peroxide. The peroxidase activity of DHP is high relative to that of wild-type myoglobin or hemoglobin, but the most definitive difference in DHP is a well-defined substrate-binding site in the distal pocket, which was reported for 4-iodophenol in the X-ray crystal structure of DHP. The binding of 2,4,6-trihalogenated phenols is relevant since 2,4,6-tribromophenol is considered to be the native substrate and 2,4,6-trichlorophenol also gives high turnover rates in enzymatic studies. The most soluble trihalogenated phenol, 2,4,6-trifluorophenol, acts as a highly soluble structural analogue to the native substrate 2,4,6-tribromophenol. To improve our understanding of substrate binding, we compared the most soluble substrate analogues, 4-bromophenol, 2,4-dichlorophenol, and 2,4,6-trifluorophenol, using (1)H and (19)F NMR to probe substrate binding interactions in the active site of the low-spin metcyano adduct of DHP. Both mono- and dihalogenated phenols induced changes in resonances of the heme prosthetic group and an internal heme edge side chain, while (1)H NMR, (19)F NMR, and relaxation data for a 2,4,6-trihalogenated substrate indicate a mode of binding on the exterior of DHP. The differences in binding are correlated with differences in enzymatic activity for the substrates studied.}, number={10}, journal={BIOCHEMISTRY}, author={Davis, Michael F. and Gracz, Hanna and Vendeix, Franck A. P. and Serrano, Vesna and Somasundaram, Aswin and Decatur, Sean M. and Franzen, Stefan}, year={2009}, month={Mar}, pages={2164–2172} }
 @article{chen_serrano_betts_franzen_2009, title={Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata}, volume={65}, ISSN={["2059-7983"]}, DOI={10.1107/S0907444908036548}, abstractNote={The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein which has a globin fold but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. As a hemoglobin, DHP cycles between the oxy and deoxy states as it reversibly binds oxygen for storage. Here, it is reported that the distal histidine, His55, exhibits conformational flexibility in the deoxy form and is consequently observed in two solvent-exposed conformations more than 9.5 A away from the heme. These conformations are analogous to the open conformation of sperm whale myoglobin. The heme iron in deoxy ferrous DHP is five-coordinate and has an out-of-plane displacement of 0.25 A from the heme plane. The observation of five-coordinate heme iron with His55 in a remote solvent-exposed conformation is consistent with the hypothesis that His55 interacts with heme iron ligands through hydrogen bonding in the closed conformation. Since His55 is also displaced by the binding of 4-iodophenol in an internal pocket, these results provide new insight into the correlation between heme iron ligation, molecular binding in the distal pocket and the conformation of the distal histidine in DHP.}, journal={ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY}, author={Chen, Zuxu and Serrano, Vesna and Betts, Laurie and Franzen, Stefan}, year={2009}, month={Jan}, pages={34–40} }
 @article{gaff_franzen_2009, title={Excited-State Geometry Method for Calculation of the Absolute Resonance Raman Cross Sections of the Aromatic Amino Acids}, volume={113}, ISSN={["1089-5639"]}, DOI={10.1021/jp809431k}, abstractNote={The time correlator formalism was used to calculate the absolute resonance Raman cross sections for the aromatic amino acids based on density functional theory calculations of the ground-state potential energy surfaces combined with projection along normal mode eigenvectors in the excited state. The geometric difference between the minima of the ground and excited states along each normal mode was calculated to provide inputs for the time correlator in the linear approximation. The calculated dimensionless nuclear displacements, Δi, provide the electron−phonon coupling constants, Si = Δi2/2, for the corresponding Raman active mode of frequency ωt. The method is generally applicable to molecules that are Franck−Condon active. As an example we have chosen to calculate the absolute resonance Raman cross sections of models of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. We discuss the role played by substituents on the aromatic ring that decrease vibronic activity to a level that permits application of the time correlator. While the method may have limitations for molecules of high symmetry, the current study of excited-state displacements and electronic structure indicates that the La,b states are Franck−Condon active in the aromatic molecules studied.}, number={18}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Gaff, John F. and Franzen, Stefan}, year={2009}, month={May}, pages={5414–5422} }
 @article{franzen_2009, title={Intrinsic Limitations on the vertical bar E vertical bar(4) Dependence of the Enhancement Factor for Surface-Enhanced Raman Scattering}, volume={113}, ISSN={["1932-7455"]}, DOI={10.1021/jp808107h}, abstractNote={Analysis of the bandwidth of the Clausius−Mosotti local field factor challenges the standard assumption that both incident and scattered fields are equally enhanced in surface-enhanced Raman scattering (SERS). The most common geometry for observation of SERS is on a nanoparticle or nanostructure where the localized surface plasmon resonance (LSPR) field enhancement arises from the electromagnetic environment produced by scattering off the conductor surface. Consequently, the electric field enhancement experienced by an adsorbate on the metal surface is a function of the magnitude of the transition dipole moment of the nanoparticle or nanostructure. Even in the treatment that considers the conducting nanostructure and molecule interactions as contributions to a collective scattering process, analytical expressions based on the Drude free-electron model reveal the importance of the bandwidth of the local field factor as a limitation on the SERS enhancement. These model calculations based on the Drude model are confirmed herein by explicit calculation using the dielectric functions for Au and Ag. The enhancement bandwidth depends on the ratio of the plasma frequency, ωp and the damping, Γ, such that the greater the enhancement ratio, ωp/Γ, the narrower the enhancement bandwidth. The relationship of the Raman shift to the enhancement bandwidth places severe constraints on the theoretical enhancement possible by the electromagnetic mechanism.}, number={15}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Franzen, Stefan}, year={2009}, month={Apr}, pages={5912–5919} }
 @article{leonard_franzen_2009, title={Is Pd-2(DBA)(3) a Feasible Precursor for the Synthesis of Pd Nanoparticles?}, volume={113}, ISSN={["1932-7447"]}, DOI={10.1021/jp903417r}, abstractNote={The organometallic reagent tris(dibenzylideneacetone) dipalladium(0) [Pd2(DBA)3] has been used as a reagent for synthesis of hexagonal microstructures ranging from 0.5−10 μm. We have shown elsewhere that Pd2(DBA)3 spontaneously forms hexagonal and cubic microstructures. The results obtained herein confirm that microstructures formed by spontaneous aggregation of Pd2(DBA)3 produce the same morphology and carbonaceous chemical composition as those produced with a process that has been called RNA-mediation by pyridyl-modified RNA (pmRNA). Synthesis products from both methods of preparation were analyzed using a combination of scanning transmission electron microscopy (STEM), electron energy loss spectroscopy, energy dispersive X-ray spectroscopy, and selected area electron diffraction. Indexing of electron diffraction patterns from hexagonal molecular crystals and metallic Pd nanoparticles combined with STEM Z-contrast imaging and X-ray dot maps were used to positively differentiate the two materials. On the basis of these results, we conclude that the observed microparticles with hexagonal morphology are composed of Pd2(DBA)3. Surfactants such as pmRNA sequence Pd017 or Triton X-100 stabilize suspensions of spontaneously formed crystalline aggregates of Pd2(DBA)3 in aqueous mixtures of tetrahydrofuran and H2O, but they are not required for their formation. Crystalline Pd metal nanoparticle composites that range from 50 to 200 nm in diameter, that are observed in both spontaneous and RNA-mediated preparations, are an impurity that arises during the synthesis of Pd2(DBA)3 by chemical reduction. There is no evidence for a competing decomposition process that forms crystalline Pd metal nanoparticles on the time scale of the experiments.}, number={29}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Leonard, D. N. and Franzen, S.}, year={2009}, month={Jul}, pages={12706–12714} }
 @article{franzen_rhodes_cerruti_gerber_losego_maria_aspnes_2009, title={Plasmonic phenomena in indium tin oxide and ITO-Au hybrid films}, volume={34}, ISSN={["1539-4794"]}, DOI={10.1364/OL.34.002867}, abstractNote={The observation of surface-plasmon resonances in indium tin oxide (ITO) thin films is complemented with the effects of hybrid ITO/Au conducting layers where charge densities can be tuned. Where carrier densities are similar (ITO and nanoparticle Au), the plasmonic behavior is that of a monolithic ITO thin film. Where the carrier density of one layer is much greater than that of the other (ITO and Au metal), boundary conditions lead to cancelation of the surface plasmon. In the latter case a capacitivelike plasmon resonance is observed for sufficiently thin films.}, number={18}, journal={OPTICS LETTERS}, author={Franzen, Stefan and Rhodes, Crissy and Cerruti, Marta and Gerber, Ralph W. and Losego, Mark and Maria, Jon-Paul and Aspnes, D. E.}, year={2009}, month={Sep}, pages={2867–2869} }
 @article{thompson_davis_franzen_2009, title={Resonance Raman Probes of the Internal Binding Pocket of Dehaloperoxidase from Amphitrite ornata}, volume={96}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2008.12.2239}, DOI={10.1016/j.bpj.2008.12.2239}, abstractNote={Using Resonance Raman spectroscopy and activity assays we have determined that there are potent inhibitors of DHP activity and these inhibitors play a major role in the biology of DHP. Resonance Raman spectroscopy can detect substrate or inhibitor binding by monitoring shifts in the core size marker modes, ν2 and ν3, and the vinyl substituent mode, νC=C, of the heme. Para-halogenated phenols bind internally, displacing the sixth position water molecule of the iron (in agreement with X-ray crystallography) resulting in a 5-coordinate high spin heme. Tri-halogenated phenols bind externally, forcing the distal histidine into the closed conformation (also in agreement with X-ray crystallography) resulting in a 6-coordinate high spin heme. The internal and external binding sites are supported by NMR data. X-ray crystallography shows when para-halogenated phenols bind internally, the halogen plugs into a hydrophobic cavity just above the back edge of the distal pocket that is analogous to the xenon 4 binding site in Sperm whale met-myoglobin often referred to as a “packing defect.” Analysis of the X-ray crystal structures of the 4-iodo-, 4-bromo-, and 4-chlorophenol/DHP complexes show a general trend in the position of the halogenated phenol with 4-iodophenol binding farthest into the cavity followed by 4-bromophenol, and 4-chlorophenol. Using RR spectroscopy, we demonstrate that the dissociation constants of the para-halogenated phenols mimic the trend observed in X-ray crystallography with 4-iodophenol being the most tightly bound in the distal pocket. DHP clearly demonstrates the importance of the hydrophobic cavity as an inherent selector for substrates entering the distal pocket by making use of the cavity-halogen hydrophobic interaction concomitantly preventing non-halogenated substrates from binding. Using activity assays, we demonstrate that internal binding of mono-halogenated phenols inhibits the function of DHP on the externally bound tri-halogenated substrates.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Thompson, Matthew K. and Davis, Michael F. and Franzen, Stefan}, year={2009}, month={Feb}, pages={437a} }
 @article{ghiladi_dumarieh_thompson_wang_smirnova_franzen_2009, title={Spectroscopic Probes of the Reactive Intermediates of Dehaloperoxidase from Amphitrite ornata}, volume={96}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2008.12.2240}, DOI={10.1016/j.bpj.2008.12.2240}, abstractNote={The enzyme intermediates of dehaloperoxidase (DHP) from the marine worm Amphitrite ornata are unique within both the globin and cytochrome c peroxidase superfamilies. DHP has been shown to oxidize trihalophenols to dihaloquinones in a dehalogenation reaction that uses hydrogen peroxide as a substrate. We show that the initially formed heme intermediate in this reaction is not Compound I as is often the case in peroxidases, but rather is a combination of Compound II and a tyrosyl radical that has similarity to the Compound ES intermediate of cytochrome c peroxidase. Using stopped-flow UV-visible spectroscopy, we provide a detailed kinetic description for the reaction of pre-formed DHP Compound II and tyrosyl radical with the substrate 2,4,6-trichlorophenol, and demonstrate the catalytic competency of this intermediate in generating the product 2,4-dichloroquinone. Furthermore, using rapid-freeze-quench electron paramagnetic resonance spectroscopy, we detected a signal at g ≈ 2.0058, confirming the presence of a protein radical in DHP Compound II, and assign it as a tyrosyl radical based upon mutagenesis studies and structural arguments. In the absence of a halophenol substrate, the DHP Compound II + tyrosyl radical intermediate decomposes to a new and significantly less active species, termed Compound RH, which is unique to dehaloperoxidase. We propose that this intermediate plays a protective role against heme bleaching. While unreactive toward further oxidation, Compound RH can be reduced and subsequently bind dioxygen, generating oxyferrous DHP, which may represent the catalytic link between the peroxidase and oxygen-transport activities in this bifunctional protein.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Ghiladi, Reza A. and Dumarieh, Rania and Thompson, Matthew and Wang, Zao and Smirnova, Tatyana and Franzen, Stefan}, year={2009}, month={Feb}, pages={437a} }
 @article{franzen_de serrano_davis_thompson_2009, title={Structural Probes Of Reactive Intermediates Of Dehaloperoxidase From Amphitrite ornata}, volume={96}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2008.12.3663}, DOI={10.1016/j.bpj.2008.12.3663}, abstractNote={The enzyme dehaloperoxidase (DHP) from the marine worm Amphitrite ornata is a unique hemoglobin that functions as a peroxidase, capable of converting 2,4,6-trihalo- phenols (TBP, TCP, and TFP) into the corresponding 2,6-dihalogenated quinones as well as other products. In this overview talk we discuss the structure and function of DHP using X-ray crystallography and nuclear magnetic resonance (NMR) to discuss the large differences between DHP function and hemoglobin function despite the strong structural similarities. The position of halogenated phenols inside the distal pocket is one anomalous feature of DHP that is not observed any other hemoglobin or myoglobin. The X-ray crystal structure of DHP reveals that the distal histidine is flexible and has two major conformations. The closed conformation (named by analogy with Sperm Whale myoglobin) is enforced by the binding of a sixth ligand to the heme iron. In the open conformation, observed in the deoxy DHP X-ray crystal structure, the distal histidine is in a solvent exposed conformation. The role of the histidine in coupling the binding of substrate and inhibitors will be discussed in the context of the mechanism for formation of compound I, compound II and a novel intermediate called compound RH that appears to be crucial to the cycling of DHP between hemoglobin and peroxidase function. The NMR data reveal that there are both interior and exterior binding sites for the substrate. This aspect will be discussed along with evidence from optical and EPR spectroscopy to understand the electron transfer kinetics of DHP.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Franzen, Stefan and de Serrano, Vesna and Davis, Michael F. and Thompson, Matt}, year={2009}, month={Feb}, pages={558a} }
 @article{smirnova_davis_weber_franzen_2009, title={Substrate binding triggers a switch in the iron coordination in dehaloperoxidase from Amphitrite Ornate}, volume={96}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2008.12.2241}, DOI={10.1016/j.bpj.2008.12.2241}, abstractNote={We have explored the effect of substrate binding on the heme iron conformation in the enzyme dehaloperoxidase (DHP). DHP is a dimeric hemoglobin that also has significant peroxidase activity under physiological conditions and has been shown to oxidize trihalophenols to dihaloquinones in a dehalogenation reaction that uses hydrogen peroxide as a cosubstrate. Hyperfine sublevel correlation spectroscopic (HYSCORE) analysis of the ferric form of DHP was carried out to characterize effects of the substrate 2,4,6-trifluorophenol (TFP) binding on the iron coordination in order to elucidate molecular mechanisms responsible for switching the protein function from a globin to a peroxidase. The CW EPR spectrum shows that at pH 6.0 DHP heme iron exists in a highly axial high spin (HS) state that could be interpreted as arising from two different populations of the HS iron centers. Substrate binding does not change the spin state at pH 6.0, however, affects the magnetic parameters of the signal. HYSCORE spectra recorded at magnetic field corresponding to g = 2 revealed the presence of exchangeable protons with hyperfine coupling of ca. 6 MHz, consistent with a water molecule being the sixth ligand in the iron coordination. These protons' spectral features disappeared upon substrate binding. At pH 9.6 the EPR spectrum from heme iron of DHP shows the presence of both high- and low-spin states with the low spin signal characteristic of hydroxyl form. Upon TFP binding the low spin signal disappears. HYSCORE spectra at pH 9.6 also show the presence of exchangeable protons that disappear upon substrate binding. This observation highlights the proposed role of molecules in the distal pocket to control the peroxidase function of DHP.Supported by the NSF Grant MCB-0451510 to T.I.S. and ARO grant 52278-LS to S.F.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Smirnova, Tatyana I. and Davis, Mike F. and Weber, Ralph T. and Franzen, Stefan}, year={2009}, month={Feb}, pages={437a} }
 @misc{franzen_lommel_2009, title={Targeting cancer with 'smart bombs': equipping plant virus nanoparticles for a 'seek and destroy' mission}, volume={4}, ISSN={["1743-5889"]}, DOI={10.2217/nnm.09.23}, abstractNote={This article discusses plant virus nanoparticles as a weapon in the war on cancer. The successes and failures of numerous nanoparticle strategies are discussed as a background to consideration of the plant virus nanoparticle approach. To have therapeutic benefit, the advantages of the targeted nanoparticle must outweigh the problems of colloidal stability, uptake by the reticuloendothelial system as well as the requirement for clearance from the body. Biodegradable nanoparticles are considered to have the most promise to address these complex phenomena. After justifying the choice of biodegradable particles, the article focuses on comparison of micelles, liposomes, polymers and modified plant viruses. The structural uniformity, cargo capacity, responsive behavior and ease of manufacturing of plant virus nanoparticles are unique properties that suggest they have a wider role to play in targeted therapy. The loading of chemotherapeutic cargo is discussed, with specific reference to the advantage of reversible transitions of the capsid of Red clover necrotic mosaic virus. These features will be contrasted and compared with other biodegradable ‘smart bombs’ that target cancer cells.}, number={5}, journal={NANOMEDICINE}, author={Franzen, Stefan and Lommel, Steven A.}, year={2009}, month={Jul}, pages={575–588} }
 @article{rhodes_lappi_fischer_sambasivan_genzer_franzen_2008, title={Characterization of monolayer formation on aluminum-doped zinc oxide thin films}, volume={24}, ISSN={["0743-7463"]}, DOI={10.1021/la701741m}, abstractNote={The optical and electronic properties of aluminum-doped zinc oxide (AZO) thin films on a glass substrate are investigated experimentally and theoretically. Optical studies with coupling in the Kretschmann configuration reveal an angle-dependent plasma frequency in the mid-IR for p-polarized radiation, suggestive of the detection of a Drude plasma frequency. These studies are complemented by oxygen depletion density functional theory studies for the calculation of the charge carrier concentration and plasma frequency for bulk AZO. In addition, we report on the optical and physical properties of thin film adlayers of n-hexadecanethiol (HDT) and n-octadecanethiol (ODT) self-assembled monolayers (SAMs) on AZO surfaces using reflectance FTIR spectroscopy, X-ray photoelectron spectroscopy (XPS), contact angle, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Our characterization of the SAM deposition onto the AZO thin film reveals a range of possible applications for this conducting metal oxide.}, number={2}, journal={LANGMUIR}, author={Rhodes, Crissy L. and Lappi, Simon and Fischer, Daniel and Sambasivan, Sharadha and Genzer, Jan and Franzen, Stefan}, year={2008}, month={Jan}, pages={433–440} }
 @article{miksovska_horsa_davis_franzen_2008, title={Conformational Dynamics Associated with Photodissociation of CO from Dehaloperoxidase Studied Using Photoacoustic Calorimetry}, volume={47}, ISSN={["0006-2960"]}, DOI={10.1021/bi8012033}, abstractNote={Herein, we present photoacoustic calorimetry and transient absorption studies of the dynamics and energetics associated with dissociation of a ligand from Fe(2+) dehaloperoxidase (DHP) from Amphitrite ornata. Our data show that CO photodissociation is associated with an endothermic (DeltaH = 8 +/- 3 kcal mol(-1)) volume expansion (DeltaV = 9.4 +/- 0.6 mL mol(-1)) that occurs within 50 ns upon photodissociation. No additional thermodynamics were detected on slower time scales (up to 10 micros), suggesting that the dissociated ligand rapidly escapes from the heme-binding pocket into the surrounding solvent. Similar volume and enthalpy changes were observed for CO photodissociation in the presence of the substrate, 2,4-dichlorophenol or 4-bromophenol, indicating that either the substrate does not bind in the protein distal cavity at ambient temperature or its presence does not impact the thermodynamic profile associated with ligand dissociation. We attribute a fast ligand exchange between the protein active site and the surrounding solvent to the high flexibility of the distal histidine residue, His55, that provides a direct pathway between the heme-binding pocket and the protein exterior. The dynamics and energetics of conformational changes observed for dissociation of a ligand from DHP differ significantly from those measured previously for photodissociation of CO from the structural homologue myoglobin, suggesting that structural dynamics in DHP are fine-tuned to enhance the peroxidase function of this protein.}, number={44}, journal={BIOCHEMISTRY}, author={Miksovska, Jaroslava and Horsa, Simona and Davis, Michael F. and Franzen, Stefan}, year={2008}, month={Nov}, pages={11510–11517} }
 @article{rhodes_cerruti_efremenko_losego_aspnes_maria_franzen_2008, title={Dependence of plasmon polaritons on the thickness of indium tin oxide thin films}, volume={103}, ISSN={0021-8979 1089-7550}, url={http://dx.doi.org/10.1063/1.2908862}, DOI={10.1063/1.2908862}, abstractNote={The evolution of polariton features with increasing thickness in p-polarized (TM) reflectance spectra of indium tin oxide (ITO) thin films deposited on BK7 glass reveals the nature of plasmons in conducting thin films without interference from band-to-band transitions or the tendency of very thin films to form islands, both of which are complicating factors with the noble metals Au and Ag. Although the dependence on energy, film thickness, and angle of incidence is complex, these features are accurately described by the three-phase (substrate/overlayer/ambient) Fresnel model using only the Drude free-electron representation for the dielectric function of the ITO film. For film thicknesses less than 80nm the relevant excitation is a one-dimensional screened-bulk plasmon (SBP) that corresponds to charge transfer across the entire film. The associated SBP polariton (SBPP) occurs at the energy of the SBP and is relatively independent of the angle of incidence. For film thicknesses greater than 120nm, the relevant excitation is the surface plasmons (SP). The associated surface plasmon polariton (SPP) exhibits the usual strong dependence of energy on the angle of incidence. For larger thicknesses this structure gradually weakens, in agreement with theory. No other collective excitations are observed. The optimum thicknesses for the SPP in ITO is 160nm, whereas the SBPP is observed only when the film thickness is less than 70nm. The SBPP exhibits many of the features that make the SPP attractive for both science and technology, but has not been observed previously. Our results show that ITO films, in particular, and conducting-metal-oxide films in general provide new opportunities for investigating plasmons in conductors and obtaining new insights into plasmons, plasmon polaritons, and related optical phenomena.}, number={9}, journal={Journal of Applied Physics}, publisher={AIP Publishing}, author={Rhodes, C. and Cerruti, M. and Efremenko, A. and Losego, M. and Aspnes, D. E. and Maria, J.-P. and Franzen, S.}, year={2008}, month={May}, pages={093108} }
 @article{nienhaus_nickel_davis_franzen_nienhaus_2008, title={Determinants of Substrate Internalization in the Distal Pocket of Dehaloperoxidase Hemoglobin of Amphitrite ornata}, volume={47}, ISSN={["0006-2960"]}, DOI={10.1021/bi801564r}, abstractNote={Dehaloperoxidase (DHP) is a small heme protein in the coelom of the terebellid polychaete Amphitrite ornata. It can act both as an oxygen storage protein (hemoglobin function) and as a dehaloperoxidase (peroxidase function). The X-ray structure of the ferric form shows that the phenolic substrate can bind inside the protein, which is not the case for a typical peroxidase. In the present study, we have used CO-ligated DHP to mimic the distal pocket of the peroxidase DHP and to probe under which conditions both a halophenol and a diatomic ligand can be accommodated in the distal pocket. To vary the structure of the distal pocket, we have compared wild-type DHP and mutants H55V and H55R at different pH values, using flash photolysis in the visible and FTIR spectroscopy in the CO stretching bands. The latter technique is extremely sensitive to even small structural changes in the CO environment and thus can report substrate binding in the distal pocket. Our results on wild-type DHP and its variants indicate that halophenols and a diatomic ligand can indeed simultaneously be present in the distal pocket if the distal histidine is in the low-pH conformation, in which its side chain is swung out of the distal pocket. The markedly different pH dependencies of enzyme activity and substrate binding are not consistent with the hypothesis that substrate dehalogenation occurs within the interior of DHP.}, number={49}, journal={BIOCHEMISTRY}, author={Nienhaus, Karin and Nickel, Elena and Davis, Michael F. and Franzen, Stefan and Nienhaus, G. Ulrich}, year={2008}, month={Dec}, pages={12985–12994} }
 @article{liu_franzen_2008, title={Factors determining the efficacy of nuclear delivery of antisense oligonucleotides by gold nanoparticles}, volume={19}, ISSN={["1520-4812"]}, DOI={10.1021/bc700421u}, abstractNote={The present study investigates the applicability of nanoparticle delivery vectors for two-stage targeting that involves both cell entry by endocytosis and nuclear targeting using viral peptide signals. A nanoparticle vector consists of four components: a carrier nanoparticle, a stabilizer, targeting peptides, and a therapeutic cargo. Extensive study of bovine serum albumin (BSA)-peptide stabilized nanoparticle conjugates demonstrated limitations of these systems due to colloidal instability when oligonucleotides and multiple peptides were attached to the BSA protein. We found that the widely used protein streptavidin (SA) was an appropriate alternative to BSA for cell-targeting experiments. Targeting peptides and gene splicing oligonucleotides were attached to SA-nanoparticles using biotin labels. The present study uses a gene-splicing assay as a test for oligonucleotide delivery to the cell nucleus. Successful modification of gene splicing by an antisense oligonucleotide indicates that the latter must have crossed the plasma membrane, entered the nucleus, found the target sequence in the newly transcribed pre-mRNA, and hybridized to it in the spliceosome strongly enough to displace the splicing factors designed to interact with the target sequence. Targeting nanoparticles that carry gene-splicing oligonucleotides were compared with a control experiment that used lipofectamine (LF). While enhanced activity was observed in the control experiment, in the presence of LF, no gene splicing was observed for the nanoparticle targeting vectors without LF. We conclude that sequestration of cargo from the harsh conditions of the endosome is a desirable strategy for cell-targeting nanoparticles.}, number={5}, journal={BIOCONJUGATE CHEMISTRY}, author={Liu, Yanli and Franzen, Stefan}, year={2008}, month={May}, pages={1009–1016} }
 @article{loo_guenther_lommel_franzen_2008, title={Infusion of dye molecules into Red clover necrotic mosaic virus}, ISSN={["1359-7345"]}, DOI={10.1039/b714748a}, abstractNote={The Red clover necrotic mosaic virus capsid is utilized to package and release molecules through reversible depletion and re-addition of divalent cations.}, number={1}, journal={CHEMICAL COMMUNICATIONS}, author={Loo, LiNa and Guenther, Richard H. and Lommel, Steven A. and Franzen, Stefan}, year={2008}, pages={88–90} }
 @article{leonard_cerruti_duscher_franzen_2008, title={Interfacial and solvent effects govern the formation of tris(dibenzylidenacetone)dipalladium(0) microstructures}, volume={24}, ISSN={["0743-7463"]}, DOI={10.1021/la801039j}, abstractNote={Organometallic palladium adducts have application as catalysts and as precursors for nanoparticle synthesis. Herein, we study the spontaneous formation of molecular crystals of the organometallic reagent tris(dibenzylidenacetone)dipalladium(0) (Pd2(DBA)3) in THF/H2O binary solvent systems. We report structural and chemical characterization of the resulting diverse structures with shapes including hexagonal platelets, rods, cubes, and stars. Optical microscopy, transmission electron microscopy, scanning electron microscopy, and energy-dispersive spectroscopy were used to determine representative structures and corresponding compositions when formed either in a binary solution or upon evaporation on a surface. The difference in Pd2(DBA)3 particle morphology was attributed to differences in the surface tension of growing crystalline faces. The formation of a majority of rods or hexagonal platelets in solution was shown to be determined by the ratio of THF to H2O in the solvent, whereas supersaturation effects and interfacial surface tension played a major role in creating the shape of particles formed upon evaporation of Pd2(DBA)3 droplets on a surface.}, number={15}, journal={LANGMUIR}, author={Leonard, Donovan N. and Cerruti, Marta and Duscher, Gerd and Franzen, Stefan}, year={2008}, month={Aug}, pages={7803–7809} }
 @article{rhodes_brewer_folmer_franzen_2008, title={Investigation of hexadecanethiol self-assembled monolayers on cadmium tin oxide thin films}, volume={516}, ISSN={["0040-6090"]}, DOI={10.1016/j.tsf.2007.08.098}, abstractNote={This study reports the use of variable angle reflectance Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy to investigate the formation of a 1-hexadecanethiol adlayer on cadmium tin oxide (CTO) thin film surfaces. These adlayers appear to be robust, ordered monolayers. The optical and electronic properties of CTO thin films chemically vapor deposited onto glass substrates were also investigated. The reflectance of the CTO films was dependent upon the incident angle of the impinging radiation and revealed a reflectance decrease indicative of a plasma frequency in the mid-IR using p-polarized radiation.}, number={8}, journal={THIN SOLID FILMS}, author={Rhodes, Cnissy L. and Brewer, Scott H. and Folmer, Jaap and Franzen, Stefan}, year={2008}, month={Feb}, pages={1838–1842} }
 @misc{franzen_feldheim_tkachenko_godek_ryan_anderson_2008, title={Nanoparticle delivery vehicle}, volume={7,332,586}, number={2008 Feb. 19}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Franzen, S. and Feldheim, D. L. and Tkachenko, A. G. and Godek, M. L. and Ryan, J. A. and Anderson, M. F.}, year={2008} }
 @article{smirnova_weber_davis_franzen_2008, title={Substrate binding triggers a switch in the iron coordination in dehaloperoxidase from Amphitrite ornata: HYSCORE experiments}, volume={130}, ISSN={["0002-7863"]}, DOI={10.1021/ja0772952}, abstractNote={Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is the first known hemoglobin to exhibit efficient peroxidase activity in the oxidation of phenolic substrates. Hyperfine sublevel correlation spectroscopic (HYSCORE) analysis of the ferric form of DHP was carried out to characterize effects of the substrate 2,4,6-trifluorophenol (TFP) binding on the iron coordination in order to elucidate the molecular mechanism of the change in protein function from a globin to a peroxidase. Continuous wave EPR spectra show that heme iron of DHP at pH 6.0 exists in the high spin state. HYSCORE spectra recorded at magnetic field corresponding to g = 2 revealed the presence of exchangeable protons with hyperfine coupling of ca. 6 MHz, consistent with a water molecule being the sixth ligand in the iron coordination. These protons' spectral features disappeared upon substrate binding. This observation highlights the proposed role of the substrate as a trigger for the switch from hemoglobin to peroxidase function.}, number={7}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Smirnova, Tatyana I. and Weber, Ralph T. and Davis, Mike F. and Franzen, Stefan}, year={2008}, month={Feb}, pages={2128-+} }
 @article{franzen_2008, title={Surface plasmon polaritons and screened plasma absorption in indium tin oxide compared to silver and gold}, volume={112}, ISSN={["1932-7455"]}, DOI={10.1021/jp7097813}, abstractNote={This study addresses the ability of a conducting metal oxide to act as a material capable of supporting surface plasmon polaritons (SPPs). By use of a two-phase Fresnel model that provides insight into the difference between polariton-induced and absorptive decreases in reflectivity, indium tin oxide (ITO) is compared to the noble metals gold and silver, which are widely used as materials for surface plasmon resonance (SPR) detection of analytes. The study builds on application of the Drude free electron model that provides an explanation for the observed optical extinctions as a function of ITO film thickness, including the dependence of wavenumber on angle, by use of only two adjustable parameters, the plasma frequency ωp and the damping Γ. Herein, models of the dispersion and absorption include both the real and imaginary parts of the dielectric function to obtain the plasma absorption spectra and dispersion curves for ITO, Ag, and Au. ITO is found to have surface plasmon dispersion curves and plasma absorption free from interband transitions as observed in Ag but not Au. Au has significant contribution from bound electrons that damps the plasma absorption and broadens the dispersion curve of the SPP. Ag is more like a free-electron conductor than Au but still has some absorption in the frequency range above the observed surface plasmon. ITO is a nearly ideal free-electron conductor.}, number={15}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Franzen, Stefan}, year={2008}, month={Apr}, pages={6027–6032} }
 @article{serrano_liu_franzen_2007, title={An infrared spectroscopic study of the conformational transition of elastin-like polypeptides}, volume={93}, ISSN={["0006-3495"]}, DOI={10.1529/biophysj.106.100594}, abstractNote={The infrared spectroscopy of elastin-like polypeptides and the relation to the inverse thermal transition are discussed. To correlate the spectroscopic observations with structure a density function theory model was created that captures the essential hydrogen bonding and packing of the beta-spiral structure proposed for elastin and elastin-like polypeptides. The infrared spectrum was calculated using periodic boundary conditions and a method for estimating the difference dipole moment permits both frequencies and intensities to be obtained for the modeling of spectra. The two observed amide I bands at 1615 cm(-1) and 1656 cm(-1) are shown to arise from the beta-spiral structure. The increase in intensity of these bands with increasing salt concentration and temperature is assigned to the closer association of strands of the beta-spiral. The sharp inverse temperature transition is observed within 1 degrees C and involves a change in secondary structure that involves formation of interstrand beta-sheets for approximately 25% of the amino acids. This conclusion is consistent with available data and simulations that have been reported to date.}, number={7}, journal={BIOPHYSICAL JOURNAL}, author={Serrano, Vesna and Liu, Wenge and Franzen, Stefan}, year={2007}, month={Oct}, pages={2429–2435} }
 @article{ryan_overton_speight_oldenburg_loo_robarge_franzen_feldheim_2007, title={Cellular uptake of gold nanoparticles passivated with BSA-SV40 large T antigen conjugates}, volume={79}, ISSN={["1520-6882"]}, DOI={10.1021/ac0715524}, abstractNote={Internalization and subcellular localization in HeLa cells of gold nanoparticles modified with the SV40 large T antigen were quantified using inductively coupled plasma optical emission spectroscopy (ICP-OES). Internalization was monitored as a function of incubation time, temperature, nanoparticle diameter, and large T surface coverage. Increasing the amount of large T peptides per gold nanoparticle complex, by either increasing the coverage at constant nanoparticle diameter or by increasing the nanoparticle diameter at constant large T coverage, resulted in more cellular internalization. In addition, nuclear fractionation was performed to quantify nuclear localization of these complexes as a function of large T coverage. In contrast to our prior qualitative investigations of nuclear localization by video-enhanced color differential interference contrast microscopy (VEC-DIC), ICP-OES was able to detect nanoparticles inside fractionated cell nuclei. Although increasing the large T coverage was found to afford higher cell internalization and nuclear targeting, quantitative evaluation of cytotoxicity revealed that higher large T coverages also resulted in greater cytotoxicity. The ICP-OES and nuclear fractionation techniques reported here are valuable tools that can add important quantitative information to optical and electron imaging methods such as VEC-DIC and transmission electron microscopy regarding the fate of nanoparticles in cells.}, number={23}, journal={ANALYTICAL CHEMISTRY}, author={Ryan, Joseph A. and Overton, K. Wesley and Speight, Molly E. and Oldenburg, Christine M. and Loo, Lina and Robarge, Wayne and Franzen, Stefan and Feldheim, Daniel L.}, year={2007}, month={Dec}, pages={9150–9159} }
 @article{moses_brewer_kraemer_fuierer_lowe_agbasi_sauthier_franzen_2007, title={Detection of DNA hybridization on indium tin oxide surfaces}, volume={125}, ISSN={["0925-4005"]}, DOI={10.1016/j.snb.2007.03.009}, abstractNote={Indium tin oxide (ITO) surfaces were modified with ssDNA by coupling oligonucleotides to a monolayer of 12-phosphonododecanoic acid (12-PDA) on ITO surfaces. This coupling involved the formation of an amide bond between the carboxylic acid moiety of 12-PDA to the amine group of a 5′-aminopropyl-labeled single strand of DNA. The self-assembled monolayer of 12-PDA and surface-attached oligonucleotides were characterized by X-ray photoelectron and reflectance FTIR spectroscopy. Detection of selective surface DNA hybridization was achieved by labeling the target ssDNA with gold nanoparticles. The presence of gold nanoparticles was probed using X-ray photoelectron spectroscopy, stripping voltammetry, atomic force microscopy, thermography, photoelectrochemistry (chronoamperometry) and cyclic voltammetry (CV). CV was used to successfully detect DNA hybridization for nanoparticle concentrations as low as 10 pM when using the gold nanoparticles bound to an ITO electrode as catalysts for the electrochemical oxidation of FeCl2. The studies described here provided the basis for surface attachment methodology for various electrochemical and thermographic sensing methods that use ITO thin films as a substrate.}, number={2}, journal={SENSORS AND ACTUATORS B-CHEMICAL}, author={Moses, Selina and Brewer, Scott H. and Kraemer, Stephan and Fuierer, Ryan R. and Lowe, Lisa B. and Agbasi, Chiamaka and Sauthier, Marc and Franzen, Stefan}, year={2007}, month={Aug}, pages={574–580} }
 @article{loo_guenther_lommel_franzen_2007, title={Encapsidation of nanoparticles by Red Clover Necrotic Mosaic Virus}, volume={129}, ISSN={["1520-5126"]}, DOI={10.1021/ja071896b}, abstractNote={Icosahedral virus capsids demonstrate a high degree of selectivity in packaging cognate nucleic acid genome components during virion assembly. The 36 nm icosahedral plant virus Red clover necrotic mosaic virus (RCNMV) packages its two genomic ssRNAs via a specific capsid protein (CP) genomic RNA interaction. A 20-nucleotide hairpin structure within the genomic RNA-2 hybridizes with RNA-1 to form a bimolecular complex, which is the origin of assembly (OAS) in RCNMV that selectively recruits and orients CP subunits initiating virion assembly. In this Article, an oligonucleotide mimic of the OAS sequence was attached to Au, CoFe2O4, and CdSe nanoparticles ranging from 3 to 15 nm, followed by addition of RNA-1 to form a synthetic OAS to direct the virion-like assembly by RCNMV CP. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) measurements were consistent with the formation of virus-like particles (VLPs) comparable in size to native RCNMV. Attempts to encapsidate nanoparticles with diameters larger than 17 nm did not result in well-formed viral capsids. These results are consistent with the presence of a 17 nm cavity in native RCNMV. Covalent linkage of the OAS to nanoparticles directs RNA-dependent encapsidation and demonstrates that foreign cargo can be packaged into RCNMV virions. The flexibility of the RCNMV CP to encapsidate different materials, as long as it is within encapsidation constraint, is a critical factor to be considered as a drug delivery and diagnostic vehicle in biomedical applications.}, number={36}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Loo, LiNa and Guenther, Richard H. and Lommel, Steven A. and Franzen, Stefan}, year={2007}, month={Sep}, pages={11111–11117} }
 @article{cerruti_rhodes_losego_efremenko_maria_fischer_franzen_genzer_2007, title={Influence of indium-tin oxide surface structure on the ordering and coverage of carboxylic acid and thiol monolayers}, volume={40}, ISSN={["1361-6463"]}, DOI={10.1088/0022-3727/40/14/016}, abstractNote={This paper analyses the variability of self-assembled monolayers (SAMs) formation on ITO depending on the substrate surface features. In particular, we report on the formation of carboxylic acid- and thiol-based SAMs on two lots of commercially prepared indium–tin oxide (ITO) thin films. Contact angle measurements, electrochemical experiments, and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy showed that the quality of monolayers formed differed substantially between the two ITO batches. Only one of the two ITO substrates was capable of forming well-organized thiol- and carboxylic acid-based SAMs. In order to rationalize these observations, atomic force microscopy and x-ray diffraction analyses were carried out, and SAMs were prepared on ITO substrates fabricated by sputtering in our laboratories. An attempt was made to influence the film microstructure and surface morphology by varying substrate temperatures during ITO deposition. Good-quality thiol and carboxylic acid SAMs were obtained on one of the ITO substrates prepared in-house. While our characterization could not single out conclusively one specific parameter in ITO surface structure that could be responsible for good SAMs formation, we could point out homogeneous surface morphology as a relevant factor for the quality of the SAMs. Evidence was also found for ITO crystallographic orientation to be a parameter influencing SAMs organization.}, number={14}, journal={JOURNAL OF PHYSICS D-APPLIED PHYSICS}, author={Cerruti, Marta and Rhodes, Crissy and Losego, Mark and Efremenko, Alina and Maria, Jon-Paul and Fischer, Daniel and Franzen, Stefan and Genzer, Jan}, year={2007}, month={Jul}, pages={4212–4221} }
 @article{kaufman_belyea_johnson_nicholson_ricks_shah_bayless_pettersson_feldoto_blomberg_et al._2007, title={Probing protein adsorption onto mercaptoundecanoic acid stabilized gold nanoparticles and surfaces by quartz crystal microbalance and zeta-potential measurements}, volume={23}, ISSN={["0743-7463"]}, DOI={10.1021/la063725a}, abstractNote={The adsorption characteristics of three proteins [bovine serum albumin (BSA), myoglobin (Mb), and cytochrome c (CytC)] onto self-assembled monolayers of mercaptoundecanoic acid (MUA) on both gold nanoparticles (AuNP) and gold surfaces (Au) are described. The combination of quartz crystal microbalance measurements with dissipation (QCM-D) and pH titrations of the zeta-potential provide information on layer structure, surface coverage, and potential. All three proteins formed adsorption layers consisting of an irreversibly adsorbed fraction and a reversibly adsorbed fraction. BSA showed the highest affinity for the MUA/Au, forming an irreversibly adsorbed rigid monolayer with a side-down orientation and packing close to that expected in the jamming limit. In addition, BSA showed a large change in the adsorbed mass due to reversibly bound protein. The data indicate that the irreversibly adsorbed fraction of CytC is a monolayer structure, whereas the irreversibly adsorbed Mb is present in form of a bilayer. The observation of stable BSA complexes on MUA/AuNPs at the isoelectric point by zeta-potential measurements demonstrates that BSA can sterically stabilize MUA/AuNP. On the other hand, MUA/AuNP coated with either Mb or CytC formed a reversible flocculated state at the isoelectric point. The colloidal stability differences may be correlated with weaker binding in the reversibly bound overlayer in the case of Mb and CytC as compared to BSA.}, number={11}, journal={LANGMUIR}, author={Kaufman, Eric D. and Belyea, Jennifer and Johnson, Marcus C. and Nicholson, Zach M. and Ricks, Jennifer L. and Shah, Pavak K. and Bayless, Michael and Pettersson, Torbjorn and Feldoto, Zsombor and Blomberg, Eva and et al.}, year={2007}, month={May}, pages={6053–6062} }
 @misc{franzen_lappi_2007, title={Single pass attenuated total reflection fourier transform infrared microscopy apparatus and method for identifying protein secondary structure, surface charge and binding affinity}, volume={7,255,835}, number={2007 Aug. 14}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Franzen, S. and Lappi, S. E.}, year={2007} }
 @article{liu_shipton_ryan_kaufman_franzen_feldheim_2007, title={Synthesis, stability, and cellular internalization of gold nanoparticles containing mixed peptide-poly(ethylene glycol) monolayers}, volume={79}, ISSN={["0003-2700"]}, DOI={10.1021/ac061578f}, abstractNote={Gold nanoparticles have shown great promise as therapeutics, therapeutic delivery vectors, and intracellular imaging agents. For many biomedical applications, selective cell and nuclear targeting are desirable, and these remain a significant practical challenge in the use of nanoparticles in vivo. This challenge is being addressed by the incorporation of cell-targeting peptides or antibodies onto the nanoparticle surface, modifications that frequently compromise nanoparticle stability in high ionic strength biological media. We describe herein the assembly of poly(ethylene glycol) (PEG) and mixed peptide/PEG monolayers on gold nanoparticle surfaces. The stability of the resulting bioconjugates in high ionic strength media was characterized as a function of nanoparticle size, PEG length, and monolayer composition. In total, three different thiol-modified PEGs (average molecular weight (MW), 900, 1500, and 5000 g mol-1), four particle diameters (10, 20, 30, and 60 nm), and two cell-targeting peptides were explored. We found that nanoparticle stability increased with increasing PEG length, decreasing nanoparticle diameter, and increasing PEG mole fraction. The order of assembly also played a role in nanoparticle stability. Mixed monolayers prepared via the sequential addition of PEG followed by peptide were more stable than particles prepared via simultaneous co-adsorption. Finally, the ability of nanoparticles modified with mixed PEG/RME (RME = receptor-mediated endocytosis) peptide monolayers to target the cytoplasm of HeLa cells was quantified using inductively coupled plasma optical emission spectrometry (ICP-OES). Although it was anticipated that the MW 5000 g mol-1 PEG would sterically block peptides from access to the cell membrane compared to the MW 900 PEG, nanoparticles modified with mixed peptide/PEG 5000 monolayers were internalized as efficiently as nanoparticles containing mixed peptide/PEG 900 monolayers. These studies can provide useful cues in the assembly of stable peptide/gold nanoparticle bioconjugates capable of being internalized into cells.}, number={6}, journal={ANALYTICAL CHEMISTRY}, author={Liu, Yanli and Shipton, Mathew K. and Ryan, Joseph and Kaufman, Eric D. and Franzen, Stefan and Feldheim, Daniel L.}, year={2007}, month={Mar}, pages={2221–2229} }
 @article{franzen_gilvey_belyea_2007, title={The pH dependence of the activity of dehaloperoxidase from Amphitrite ornata}, volume={1774}, ISSN={["1570-9639"]}, DOI={10.1016/j.bbapap.2006.09.019}, abstractNote={Dehaloperoxidase (DHP) from the terebellid polychaete, Amphitrite ornata, is the first hemoglobin that has peroxidase activity as part of its native function. The substrate 2,4,6-tribromophenol (TBP) is oxidatively debrominated by DHP to form 2,6-dibromoquinone (DBQ) in a two-electron process. There is a well-defined internal binding site for TBP above the heme, a feature not observed in other hemoglobins or peroxidases. A study of the pH dependence of the activity of DHP reveals a substantial difference in mechanism. From direct observation of the Soret band of the heme it is shown that the p K a for heme activation in protein DHP is 6.5. Below this pH the heme absorbance decreases in the presence of H 2 O 2 with or without addition of substrate. The low pH data are consistent with significant heme degradation. Above pH 6.5 addition of H 2 O 2 causes the heme to shift rapidly to a compound II spectrum and then slowly to an unidentified intermediate with an absorbance of 410 nm. However, the p K a of the substrate TBP is 6.8 and the greatest enzyme activity is observed above the p K a of TBP under conditions where the substrate is a phenolate anion (TPBO − ). Although the mechanisms may differ, the data show that both neutral TBP and anionic TPBO − are converted to the quinone product. The mechanistic implications of the pH dependence are discussed by comparison other known peroxidases, which oxidize substrates at the heme edge.}, number={1}, journal={BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS}, author={Franzen, Stefan and Gilvey, Lauren B. and Belyea, Jennifer L.}, year={2007}, month={Jan}, pages={121–130} }
 @article{franzen_cerruti_leonard_duscher_2007, title={The role of selection pressure in RNA-mediated evolutionary materials synthesis}, volume={129}, ISSN={["0002-7863"]}, DOI={10.1021/ja076054r}, abstractNote={Evolutionary materials synthesis is a provocative concept that has the potential for the discovery of novel compounds ranging from drugs to inorganic materials. RNA-mediated evolutionary materials synthesis requires aqueous solvent of moderate ionic strength, water-soluble precursors, and an appropriately designed selection pressure. Throughout the selection process, the RNA must be folded, stable, and accessible once it has bound to a target, catalyzed a chemical reaction, or templated formation of a structure. Subsequently, the RNA must be accessible to permit reverse transcriptase to create DNA copies for amplification. A well-designed selection will generate RNAs that can favor growth of a particular crystal habit or catalyze a specific reaction pathway. In this study we rigorously test the assumptions, procedures, and results of the only published example of an RNA-mediated evolutionary materials synthesis. The proof that a particular RNA sequence is responsible for a novel material synthesis must be established by control experiments as outlined in the present study. Furthermore, the product of nanoscale synthesis must be studied using state-of-the-art characterization methods to determine that selection pressure is exerted according to design. Herein, we demonstrate the use of advanced electron microscopy to determine chemical composition and structure as a critical step in analysis of the success of a selection. We conclude that RNA selections should not be carried out in binary solvent systems, such as tetrahydrofuran (THF) and water. A specific example, which is not consistent with rigorous selection of functional RNAs or RNA cognates, is provided by the precipitation of the water-insoluble precursor, tris(dibenzylideneacetone) dipalladium(0) Pd2(DBA)3.}, number={49}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Franzen, Stefan and Cerruti, Marta and Leonard, Donovan N. and Duscher, Gerd}, year={2007}, month={Dec}, pages={15340–15346} }
 @article{serrano_chen_davis_franzen_2007, title={X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata}, volume={63}, ISSN={["2059-7983"]}, DOI={10.1107/S0907444907043417}, abstractNote={The dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is an enzyme that converts para-halogen­ated phenols to the corresponding quinones in the presence of hydrogen peroxide. Its enzymatic activity is similar to that of heme peroxidases such as horseradish peroxidase, yet it has the structural characteristics of the globin family of proteins, the main functions of which are oxygen transport and storage. In order to investigate the dual function of this hemoglobin peroxidase, the enzyme was expressed in Escherichia coli as a recombinant protein in its wild-type form and as a mutant protein in which Cys73 was replaced by a serine residue (C73S). Both the wild-type and mutant proteins were crystallized and their structures were determined at 100 K to a resolution of 1.62 Å. The structure of the wild-type protein demonstrated that it was in the metaquo form, with the heme iron in the ferric oxidation state and the bound water lying 2.2 Å from the heme iron. The structure of the C73S mutant protein was shown to contain a ferrous heme iron with a bound oxygen molecule. The bent bonding geometry of the Fe–O(1)–O(2) adduct results in a hydrogen bond of length 2.8 Å between the second O atom, O(2), of molecular oxygen and N∊2 of the distal histidine residue (His55) in both subunits contained within the asymmetric unit. This hydrogen-bonding interaction between His55 and the bound diatomic oxygen molecule provides new insight into the catalytic activation of H2O2, which is essential for peroxidase activity.}, journal={ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY}, author={Serrano, Vesna and Chen, Zuxu and Davis, Michael F. and Franzen, Stefan}, year={2007}, month={Oct}, pages={1094–1101} }
 @article{loo_guenther_basnayake_lommel_franzen_2006, title={Controlled encapsidation of gold nanoparticles by a viral protein shell}, volume={128}, ISSN={["0002-7863"]}, DOI={10.1021/ja057332u}, abstractNote={Icosahedral virus capsids demonstrate a high degree of selectivity in packaging cognate nucleic acid components during assembly. This packaging specificity, when integrated as part of a nanotechnological protocol, has the potential to encapsidate a wide array of foreign materials for delivery of therapeutics or biosensors into target cells. Red clover necrotic mosaic virus (RCNMV) exclusively packages two genomic ssRNAs initiated by a specific protein:RNA interaction between the RCNMV coat protein (CP) and the viral RNA origin of assembly (OAS) element. In the present work, an oligonucleotide mimic of the RCNMV OAS sequences is attached to Au nanoparticles as a recognition signal to initiate the virion-like assembly by RCNMV CP. Covalent linkage of the OAS to Au functions as a trigger for specific encapsidation and demonstrates that foreign cargo can be packaged into RCNMV virions.}, number={14}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Loo, L and Guenther, RH and Basnayake, VR and Lommel, SA and Franzen, S}, year={2006}, month={Apr}, pages={4502–4503} }
 @article{cerruti_sauthier_leonard_liu_duscher_feldheim_franzen_2006, title={Gold and silica-coated gold nanoparticles as thermographic labels for DNA detection}, volume={78}, ISSN={["1520-6882"]}, DOI={10.1021/ac0600555}, abstractNote={The infrared emissivity of Au and silica-coated Au nanoparticles (Au NPs) deposited on indium tin oxide substrates was investigated. NPs were irradiated with laser light at a frequency close to the Au plasmon resonance band, and the blackbody radiation emitted as a result was monitored with an IR camera equipped with an InAs array detector. The differences in temperature before and after laser irradiation were recorded (T-jumps) and were found to be directly proportional to the number of particles present on the slide and to the laser power used in the experiment. Coating Au NPs with silica increased the measured T-jumps 2−5 times, depending on the thickness of the silica shell. This was in agreement with the observation that silica has a much higher IR emissivity than Au. Both Au and silica-coated Au NPs were then tested as labels for thermographic DNA detection. Target DNA concentrations as low as 100 pM were recorded when Au NPs were used as labels and as low as 10 pM when silica-coated Au NPs were used.}, number={10}, journal={ANALYTICAL CHEMISTRY}, author={Cerruti, Marta G. and Sauthier, Marc and Leonard, Donovan and Liu, Dage and Duscher, Gerard and Feldheim, Daniel L. and Franzen, Stefan}, year={2006}, month={May}, pages={3282–3288} }
 @article{franzen_jasaitis_belyea_brewer_casey_macfarlane_stanley_vos_martin_2006, title={Hydrophobic distal pocket affects NO-heme geminate recombination dynamics in dehaloperoxidase and H64V myoglobin}, volume={110}, ISSN={["1520-6106"]}, DOI={10.1021/jp056790m}, abstractNote={The recombination dynamics of NO with dehaloperoxidase (DHP) from Amphitrite ornata following photolysis were measured by femtosecond time-resolved absorption spectroscopy. Singular value decomposition (SVD) analysis reveals two important basis spectra. The first SVD basis spectrum reports on the population of photolyzed NO molecules and has the appearance of the equilibrium difference spectrum between the deoxy and NO forms of DHP. The first basis time course has two kinetic components with time constants of tau(11) approximately 9 ps and tau(12) approximately 50 ps that correspond to geminate recombination. The fast geminate process tau(11) arises from a contact pair with the heme iron in a bound state with S = 3/2 spin. The slow geminate process tau(12) corresponds to the recombination from a more remote docking site >3 A from the heme iron with the greater barrier corresponding to a S = 5/2 spin state. The second SVD basis spectrum represents a time-dependent Soret band shift indicative of heme photophysical processes and protein relaxation with time constants of tau(21) approximately 3 ps and tau(22) approximately 17 ps, respectively. A comparison between the more rapid rate constant of the slow geminate phase in DHP-NO and horse heart myoglobin (HHMbNO) or sperm whale myoglobin (SWMbNO) suggests that protein interactions with photolyzed NO are weaker in DHP than in the wild-type MbNOs, consistent with the hydrophobic distal pocket of DHP. The slower protein relaxation rate tau(22) in DHP-NO relative to HHMbNO implies less effective trapping in the docking site of the distal pocket and is consistent with a greater yield for the fast geminate process. The trends observed for DHP-NO also hold for the H64V mutant of SWMb (H64V MbNO), consistent with a more hydrophobic distal pocket for that protein as well. We examine the influence of solution viscosity on NO recombination by varying the glycerol content in the range from 0% to 90% (v/v). The dominant effect of increasing viscosity is the increase of the rate of the slow geminate process, tau(12), coupled with a population decrease of the slow geminate component. Both phenomena are similar to the effect of viscosity on wild-type Mb due to slowing of protein relaxation resulting from an increased solution viscosity and protein surface dehydration.}, number={29}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Franzen, Stefan and Jasaitis, Audrius and Belyea, Jennifer and Brewer, Scott H. and Casey, Robin and MacFarlane, Alexander W. and Stanley, Robert J. and Vos, Marten H. and Martin, Jean-Louis}, year={2006}, month={Jul}, pages={14483–14493} }
 @article{leonard_jarausch_cerruti_duscher_franzen_feldheim_2006, title={Nanoscale Structural and Chemical Characterization of Silica Coated Gold Nanoparticles Using STEM 3D Imaging and EELS}, volume={12}, ISSN={1431-9276 1435-8115}, url={http://dx.doi.org/10.1017/S1431927606062684}, DOI={10.1017/S1431927606062684}, abstractNote={Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006}, number={S02}, journal={Microscopy and Microanalysis}, publisher={Cambridge University Press (CUP)}, author={Leonard, DN and Jarausch, KF and Cerruti, MG and Duscher, G and Franzen, S and Feldheim, DL}, year={2006}, month={Jul}, pages={602–603} }
 @article{franzen_belyea_gilvey_davis_chaudhary_sit_lommel_2006, title={Proximal cavity, distal histidine, and substrate hydrogen-bonding mutations modulate the activity of Amphitrite ornata dehaloperoxidase}, volume={45}, ISSN={["0006-2960"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33746584767&partnerID=MN8TOARS}, DOI={10.1021/bi060020z}, abstractNote={Dehaloperoxidase (DHP) from Amphitrite ornata is the first globin that has peroxidase activity that approaches that of heme peroxidases. The substrates 2,4,6-tribromophenol (TBP) and 2,4,6-trichlorophenol are oxidatively dehalogenated by DHP to form 2,6-dibromo-1,4-benzoquinone and 2,6-dichloro-1,4-benzoquinone, respectively. There is a well-defined internal substrate-binding site above the heme, a feature not observed in other globins or peroxidases. Given that other known heme peroxidases act on the substrate at the heme edge there is great interest in understanding the possible modes of substrate binding in DHP. Stopped-flow studies (Belyea, J., Gilvey, L. B., Davis, M. F., Godek, M., Sit, T. L., Lommel, S. A., and Franzen, S. (2005) Biochemistry 44, 15637−15644) show that substrate binding must precede the addition of H2O2. This observation suggests that the mechanism of DHP relies on H2O2 activation steps unlike those of other known peroxidases. In this study, the roles of the distal histidine (H55) and proximal histidine (H89) were probed by the creation of site-specific mutations H55R, H55V, H55V/V59H, and H89G. Of these mutants, only H55R shows significant enzymatic activity. H55R is 1 order of magnitude less active than wild-type DHP and has comparable activity to sperm whale myoglobin. The role of tyrosine 38 (Y38), which hydrogen bonds to the hydroxyl group of the substrate, was probed by the mutation Y38F. Surprisingly, abolishing this hydrogen bond increases the activity of the enzyme for the substrate TBP. However, it may open a pathway for the escape of the one-electron product, the phenoxy radical leading to polymeric products.}, number={30}, journal={BIOCHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Franzen, Stefan and Belyea, Jennifer and Gilvey, Lauren B. and Davis, Michael F. and Chaudhary, Chelsea E. and Sit, Tim L. and Lommel, Steven A.}, year={2006}, month={Aug}, pages={9085–9094} }
 @article{belyea_belyea_lappi_franzen_2006, title={Resonance Raman study of ferric heme adducts of dehaloperoxidase from Amphitrite ornata}, volume={45}, ISSN={["0006-2960"]}, DOI={10.1021/bi0609218}, abstractNote={The study of axial ligation by anionic ligands to ferric heme iron by resonance Raman spectroscopy provides a basis for comparison of the intrinsic electron donor ability of the proximal histidine in horse heart myoglobin (HHMb), dehaloperoxidase (DHP), and horseradish peroxidase (HRP). DHP is a dimeric hemoglobin (Hb) originally isolated from the terebellid polychaete Amphitrite ornata. The monomers are structurally related to Mb and yet DHP has a peroxidase function. The core size marker modes, v2 and v3, were observed using Soret excitation, and DHP-X was compared to HHMb-X for the ligand series X = F, Cl, Br, SCN, OH, N3, and CN. Special attention was paid to the hydroxide adduct, which is also formed during the catalytic cycle of peroxidases. The Fe-OH stretching frequency was observed and confirmed by deuteration and is higher in DHP than in HHMb. The population of high-spin states of the heme iron in DHP was determined to be intermediate between HHMb and HRP. The data provide the first direct measurement of the effect of axial ligation on the heme iron in DHP. The Raman data support a modified charge relay in DHP, in which a strongly hydrogen-bonded backbone carbonyl (>C=O) polarizes the proximal histidine. The charge relay mechanism by backbone carbonyl >C=O-His-Fe is the analogue of the Asp-His-Fe of peroxidases and Glu-His-Fe of flavohemoglobins.}, number={48}, journal={BIOCHEMISTRY}, author={Belyea, Jennifer and Belyea, Curtis M. and Lappi, Simon and Franzen, Stefan}, year={2006}, month={Dec}, pages={14275–14284} }
 @article{negrerie_kruglik_lambry_vos_martin_franzen_2006, title={Role of heme iron coordination and protein structure in the dynamics and geminate rebinding of nitric oxide to the H93G myoglobin mutant - Implications for nitric oxide sensors}, volume={281}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M513375200}, abstractNote={The influence of the heme iron coordination on nitric oxide binding dynamics was investigated for the myoglobin mutant H93G (H93G-Mb) by picosecond absorption and resonance Raman timeresolved spectroscopies. In the H93G-Mb, the glycine replacing the proximal histidine does not interact with the heme iron so that exogenous substituents like imidazole may coordinate to the iron at the proximal position. Nitrosylation of H93G-Mb leads to either 6- or 5-coordinate species depending on the imidazole concentration. At high concentrations, (imidazole)-(NO)-6-coordinate heme is formed, and the photoinduced rebinding kinetics reveal two exponential picosecond phases (∼10 and ∼100 ps) similar to those of wild type myoglobin. At low concentrations, imidazole is displaced by the trans effect leading to a (NO)-5-coordinate heme, becoming 4-coordinate immediately after photolysis as revealed from the transient Raman spectrum. In this case, NO rebinding kinetics remain bi-exponential with no change in time constant of the fast component whose amplitude increases with respect to the 6-coordinate species. Bi-exponential NO geminate rebinding in 5-coordinate H93G-Mb is in contrast with the single-exponential process reported for nitrosylated soluble guanylate cyclase (Negrerie, M., Bouzhir, L., Martin, J. L., and Liebl, U. (2001) J. Biol. Chem. 276, 46815-46821). Thus, our data show that the iron coordination state or the heme iron out-of-plane motion are not at the origin of the bi-exponential kinetics, which depends upon the protein structure, and that the 4-coordinate state favors the fast phase of NO geminate rebinding. Consequently, the heme coordination state together with the energy barriers provided by the protein structure control the dynamics and affinity for NO-binding enzymes. The influence of the heme iron coordination on nitric oxide binding dynamics was investigated for the myoglobin mutant H93G (H93G-Mb) by picosecond absorption and resonance Raman timeresolved spectroscopies. In the H93G-Mb, the glycine replacing the proximal histidine does not interact with the heme iron so that exogenous substituents like imidazole may coordinate to the iron at the proximal position. Nitrosylation of H93G-Mb leads to either 6- or 5-coordinate species depending on the imidazole concentration. At high concentrations, (imidazole)-(NO)-6-coordinate heme is formed, and the photoinduced rebinding kinetics reveal two exponential picosecond phases (∼10 and ∼100 ps) similar to those of wild type myoglobin. At low concentrations, imidazole is displaced by the trans effect leading to a (NO)-5-coordinate heme, becoming 4-coordinate immediately after photolysis as revealed from the transient Raman spectrum. In this case, NO rebinding kinetics remain bi-exponential with no change in time constant of the fast component whose amplitude increases with respect to the 6-coordinate species. Bi-exponential NO geminate rebinding in 5-coordinate H93G-Mb is in contrast with the single-exponential process reported for nitrosylated soluble guanylate cyclase (Negrerie, M., Bouzhir, L., Martin, J. L., and Liebl, U. (2001) J. Biol. Chem. 276, 46815-46821). Thus, our data show that the iron coordination state or the heme iron out-of-plane motion are not at the origin of the bi-exponential kinetics, which depends upon the protein structure, and that the 4-coordinate state favors the fast phase of NO geminate rebinding. Consequently, the heme coordination state together with the energy barriers provided by the protein structure control the dynamics and affinity for NO-binding enzymes. Nitric oxide acts as a signal transmitter in several physiological pathways (1Denninger J.W. Marletta M.A. Biochim. Biophys. Acta. 1999; 1411: 334-350Crossref PubMed Scopus (864) Google Scholar, 2Cooper C.E. Biochim. Biophys. Acta. 1999; 1411: 290-309Crossref PubMed Scopus (452) Google Scholar, 3Rodgers K.R. Curr. Opin. Chem. Biol. 1999; 3: 158-167Crossref PubMed Scopus (200) Google Scholar) because it readily diffuses through cell membranes and reacts with the heme iron. It has been proposed that the ligation of NO 2The abbreviations used are: NO, nitric oxide; WT Mb, wild type myoglobin; Im, imidazole; sGC, soluble guanylate cyclase; SVD, singular value decomposition; MEM, maximum entropy method; DFT, density functional theory. FeP, iron-porphyrin; DNP, double-ζ plus polarization; DNPP, double-ζ plus extra polarization. 2The abbreviations used are: NO, nitric oxide; WT Mb, wild type myoglobin; Im, imidazole; sGC, soluble guanylate cyclase; SVD, singular value decomposition; MEM, maximum entropy method; DFT, density functional theory. FeP, iron-porphyrin; DNP, double-ζ plus polarization; DNPP, double-ζ plus extra polarization. to myoglobin has a physiological role for the in vivo regulation of the NO concentration in muscle cells (4Flögel U. Merx M.W. Gödecke A. Decking U.K. Schrader J. Proc. Natl. Acad. Sci. U. S. A. 2001; 98: 735-740Crossref PubMed Scopus (379) Google Scholar). Numerous hemoproteins are involved in diatomic ligand binding, such as CO, O2, and NO, and their regulation closely depends upon the dynamic behavior of these ligands. We have shown that the dynamics of nitric oxide, and hence the geminate rebinding to the heme, are closely related to the protein function and subtly controlled by the protein structure. This control is evident when comparing endothelial NO synthase (5Negrerie M. Berka V. Vos M.H. Liebl U. Lambry J.C. Tsai A.L. Martin J.L. J. Biol. Chem. 1999; 274: 24694-24702Abstract Full Text Full Text PDF PubMed Scopus (52) Google Scholar) and soluble guanylate cyclase (6Negrerie M. Bouzhir L. Martin J.L. Liebl U. J. Biol. Chem. 2001; 276: 46815-46821Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar), which are the source and the receptor of NO in cells, respectively, in which NO acts as a second messenger for signal transduction. These two proteins display a very contrasting behavior with respect to geminate rebinding of NO, which is multiphasic and relatively slow for endothelial nitric-oxide synthase, including important nanosecond phases correlated with the release of newly synthesized NO. On the other hand, NO recombination is mono-exponential and ultrafast for sGC, revealing a high trapping efficiency. The picosecond and nanosecond phases of the geminate recombination of a diatomic ligand to the heme (and its release from the heme) are modulated by several structural features linked to the intrinsic properties and function of hemoproteins. These features include the heme coordination state and protein structure whose respective contributions must be investigated for understanding the protein mechanism and regulation at the molecular level. Here we focus on the role of the iron proximal coordination in modulating the various phases of NO recombination.NO is a particularly versatile and intriguing ligand because it can give rise either to 5-coordinate or to 6-coordinate adducts, the latter having the proximal histidine involved in the second axial coordination, and both conformations presenting biological importance. Although the NO adducts of wild type myoglobin or hemoglobin are observed to be 6-coordinate, binding of NO to sGC leads to an NO-5-coordinate Fe2+ complex after breaking the bond between the proximal His and the heme iron by a trans effect, which corresponds to a weakening of the axial Fe-X bond following the trans-coordination of a sixth ligand with ferrous iron (7Ignarro L.J. Ballot B. Wood K.S. J. Biol. Chem. 1984; 259: 6201-6207Abstract Full Text PDF PubMed Google Scholar, 8Zhao Y. Brandish P.E. Ballou D.P. Marletta M.A. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 14753-14758Crossref PubMed Scopus (296) Google Scholar). The geminate recombination of NO to Mb or Hb always exhibits multiexponential kinetics on the picosecond time scale with two dominant phases (∼10 and ∼100 ps) for both proteins (9Petrich J.W. Poyart C. Martin J.L. Biochemistry. 1988; 27: 4049-4060Crossref PubMed Scopus (333) Google Scholar, 10Petrich J.W. Lambry J.C. Kuczera K. Karplus M. Poyart C. Martin J.L. Biochemistry. 1991; 30: 3975-3987Crossref PubMed Scopus (191) Google Scholar, 11Olson J.S. Phillips G.N. J. Biol. Chem. 1996; 271: 17593-17596Abstract Full Text Full Text PDF PubMed Scopus (290) Google Scholar, 12Ye X. Demidov A. Champion P.M. J. Am. Chem. Soc. 2002; 124: 5914-5924Crossref PubMed Scopus (128) Google Scholar, 13Kim S. Jin G. Lim M. J. Phys. Chem. B. 2004; 108: 20366-20375Crossref Scopus (83) Google Scholar). The origin of this multiphasic behavior has led to several hypotheses that are not mutually exclusive. The first one attributes the dynamics to relaxation of the protein structure initiated by the iron motion after NO dissociation (10Petrich J.W. Lambry J.C. Kuczera K. Karplus M. Poyart C. Martin J.L. Biochemistry. 1991; 30: 3975-3987Crossref PubMed Scopus (191) Google Scholar). The second hypothesis suggests that distal side chains present energy barriers to rebinding (14Gibson Q.H. Regan R. Elber R. Olson J.S. Carver T.E. J. Biol. Chem. 1992; 267: 22022-22034Abstract Full Text PDF PubMed Google Scholar, 15Petrich J.W. Lambry J.C. Balasubramanian S. Lambright D.G. Boxer S.G. Martin J.L. J. Mol. Biol. 1994; 238: 437-444Crossref PubMed Scopus (54) Google Scholar), with a possible contribution of the position of the heme metal atom (16Ikeda-Saito M. Dou Y. Yonetani T. Olson J.S. Li T. Regan R. Gibson Q.H. J. Biol. Chem. 1993; 268: 6855-6857Abstract Full Text PDF PubMed Google Scholar, 17Kholodenko Y. Gooding E.A. Dou Y. Ikeda-Saito M. Hochstrasser R.M. Biochemistry. 1999; 38: 5918-5924Crossref PubMed Scopus (54) Google Scholar). Contrary to Mb and Hb, a mono-exponential recombination of NO to the 4-coordinate Fe2+ after photodissociation is observed in sGC (6Negrerie M. Bouzhir L. Martin J.L. Liebl U. J. Biol. Chem. 2001; 276: 46815-46821Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar). On the other hand, the effects of distal mutations on the rebinding of NO to Mb (15Petrich J.W. Lambry J.C. Balasubramanian S. Lambright D.G. Boxer S.G. Martin J.L. J. Mol. Biol. 1994; 238: 437-444Crossref PubMed Scopus (54) Google Scholar, 17Kholodenko Y. Gooding E.A. Dou Y. Ikeda-Saito M. Hochstrasser R.M. Biochemistry. 1999; 38: 5918-5924Crossref PubMed Scopus (54) Google Scholar) or to leghemoglobin (18Chowdhury P.K. Kundu S. Halder M. Das K. Hargrove M.S. Petrich J.W. J. Phys. Chem. B. 2003; 107: 9122-9127Crossref Scopus (8) Google Scholar) suggest an important role for the amino acids in the distal pocket in governing the NO recombination rate. Thus, both the coordination state of the heme iron and the structure of the heme protein may influence the picosecond phases of NO geminate recombination and its bi-exponential character as suggested by the previous examples.The H93G-Mb mutant provides a unique opportunity to investigate these effects in more detail. The H93G mutant lacks the proximal histidine that normally coordinates to the iron, and glycine does not interact with the heme so that exogenous substituents such as imidazole, phenol, or thiophene may coordinate to the heme iron (19Barrick D. Biochemistry. 1994; 33: 6546-6554Crossref PubMed Scopus (167) Google Scholar). Imidazole mimics the proximal His coordination of WT Mb but is not covalently attached to the protein backbone. Moreover, the nitrosylation of H93G-Mb leads to either the 5- or the 6-coordinate form, depending on the concentration of exogenous imidazole. At imidazole concentrations less than 1 mm, the nitrosylated H93G-Mb is NO-5-coordinated, whereas above 1 mm it is 6-coordinated with spectroscopic properties similar to that of WT Mb (20Decatur S.M. De Pillis G.D. Boxer S.G. Biochemistry. 1996; 35: 3925-3932Crossref PubMed Scopus (44) Google Scholar, 21DePillis G.D. Decatur S.M. Barrick D. Boxer S.G. J. Am. Chem. Soc. 1994; 116: 6981-6982Crossref Scopus (92) Google Scholar, 22Decatur S.M. Franzen S. De Pillis G.D. Dyer R.B. Woodruff W.H. Boxer S.G. Biochemistry. 1996; 35: 4939-4944Crossref PubMed Scopus (74) Google Scholar). The H93G-Mb mutant is thus capable of mimicking both a 5-coordinate-NO complex like nitrosylated sGC and a 6-coordinate-NO form like Mb.In this study, we have measured the fast rebinding kinetics of NO to H93G-Mb on the picosecond time scale by time-resolved absorption spectroscopy, and we identified the transient species by time-resolved resonance Raman spectroscopy. The results are compared with WT Mb and to sGC and provide insight into the structural factors that affect the geminate rebinding process. The experiments were followed by electronic potential energy surface calculations using DFT methods (23Franzen S. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 16754-16759Crossref PubMed Scopus (97) Google Scholar). The potential surfaces of 5- and 6-coordinate heme were calculated as a function of the distance between the free diatomic ligand NO and the heme iron.EXPERIMENTAL PROCEDURESTo avoid confusion, the term “substituent” refers to the molecule bound at the proximal side of the heme in mutant Mb, replacing the coordinating histidine of WT Mb, although “ligand” refers to the diatomic molecule NO binding on the distal side.Preparation of the Samples—The H93G-Mb mutant of sperm whale was overexpressed and purified as described (19Barrick D. Biochemistry. 1994; 33: 6546-6554Crossref PubMed Scopus (167) Google Scholar). The expression was performed in the presence of imidazole. Removing of imidazole was achieved by ultrafiltration with successive concentration and dilution cycles in 5-kDa cut-off filters (Amicon). For exchange of the proximal substituents, the dilution was achieved with buffer (20 mm Tris, pH 7.4) containing the new substituent at final concentration that was 20 mm for imidazole, thiophene, and phenol, yielding the NO-6-coordinate heme, and it was 0.1 mm for the sample depleted in imidazole yielding an NO-5-coordinate heme. The samples were kept frozen (-80 °C) with a high concentration of imidazole, and the buffer exchange was performed immediately prior to the spectroscopic measurements.The solution of ferric Mb mutant (100 μl at a concentration of 50 μm) was put in a 1-mm optical path length quartz cell (Hellma 110-QX) sealed with a rubber stopper and degassed by means of four successive cycles of vacuum and purging with pure argon. The heme iron was reduced by the addition of 10 μl of degassed sodium dithionite solution (5 mm final concentration). For preparing the NO-liganded species, gas phase NO diluted to 1% in N2 (Alphagaz) was directly introduced into the spectroscopic cell by a syringe connected to the gas manifold, and a second silicone rubber stopper was stacked over the first one. The resulting NO concentration was 20 μm in the aqueous phase. Equilibrium spectra were recorded at each step for monitoring the evolution of ligation. Wild type myoglobin was similarly prepared from lyophilized powder (Sigma) dissolved in 50 mm Tris, pH 7.5. The absorbance of the sample was in the range 0.7-1 at the Soret maximum of liganded protein for 1 mm.Soluble guanylate cyclase was purified from beef lung as described previously (6Negrerie M. Bouzhir L. Martin J.L. Liebl U. J. Biol. Chem. 2001; 276: 46815-46821Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar). Because it is directly purified in its ferrous state, no reducing agent was added. The final buffer was 25 mm triethanolamine, 50 mm NaCl, pH 7.5, and it was equilibrated with 1% NO gas phase in the same manner as Mb.Picosecond Transient Absorption Spectroscopy—Transient spectra were recorded simultaneously to kinetics as a time-wavelength matrix data, using the pump-probe laser system described previously (24Martin J.L. Vos M.H. Annu. Rev. Biophys. Biomol. Struct. 1992; 21: 199-222Crossref PubMed Scopus (99) Google Scholar) and allowing the use of a white light continuum for generating the broad band probe pulse. The photodissociation of NO was achieved with an excitation wavelength in the a band at 560 nm with a pulse duration of about 40 fs and a repetition rate of 30 Hz. The transient absorption spectrum after a variable delay between pump and probe pulses was recorded by a CCD detector. The same 1-mm sample cell was used for recording the equilibrium spectra and the kinetics. The sample was continuously moved perpendicularly to the laser beam during the recording, and the temperature was 18 °C. The 100-ps time window was scanned with a dwell time of 1 sat each time point, and up to 40 scans were averaged. The two first spectra containing the cross-phase modulation artifact were removed. Analyses of the data were performed by a singular value decomposition of the time-wavelength matrix (25Press W.H. Teukolsky S.A. Vetterling W.T. Flannery B.P. Numerical Recipes. Cambridge University Press, New York1988: 59-70Google Scholar), and the kinetics associated with the SVD components having the highest singular value were fit to a minimum number of exponential components. The maximum entropy method analysis was performed on the kinetics obtained from SVD analysis.Time-resolved Raman Spectroscopy—For sub-picosecond Raman spectroscopy, we used a femtosecond Ti:Sapphire oscillator pumped by a solid-state laser and producing 50-fs pulses (λ = 810 nm) subsequently amplified with a repetition rate of 1 kHz (26Cianetti S. Negrerie M. Vos M.H. Martin J.L. Kruglik S.G. J. Am. Chem. Soc. 2004; 126: 13932-13933Crossref PubMed Scopus (33) Google Scholar, 27Negrerie M. Cianetti S. Vos M.H. Martin J.L. Kruglik S.G. J. Phys. Chem. B. 2006; (in press)PubMed Google Scholar). The output beam was frequency doubled at 405 nm and used to provide tunable pump and probe beams by means of an optical parametric generator and two optical parametric amplifiers based on BBO crystals. The photodissociating pulse energy was about 2 μJ in a sample cell with a 100-fs duration and had a wavelength centered at 560 nm. Narrow band interference filters allowed us to obtain probe pulses at a wavelength of either 420 nm (for 5C species) or 435 nm (for 6C species) and to achieve the best compromise between spectral (30 cm-1) and temporal (0.6 ps) resolutions in time-resolved Raman measurements. The probe pulse energy was 20-30 nJ in the sample cell. The pump and probe beams were colinearly superimposed and focused on the sample, and the optical delay time between both pulses was controlled by a translation stage. Raman scattering light was collected through a spectrograph (Jobin-Yvon) by a CCD (Roper Scientific). The sample (100 μl) was placed in a cylindrical spinning cell whose gas phase contained the NO diluted in nitrogen. The integrity of the sample was verified after the experiment by recording its absorption spectrum in anaerobic conditions. Measurements were performed at 18 °C.The spectrum before photodissociation at -5 ps (in the presence of the pump pulse) is that of the pure liganded species and was subtracted from that after NO dissociation (at +3 ps). It was multiplied by a coefficient (0.6 for these measurements) to suppress the contribution from still liganded species and to obtain a difference spectrum corresponding to the pure transient H93G Mb photoproduct.Potential Energy Surfaces DFT Calculation—We have modeled potential energy surfaces by means of density functional calculations using the generalized gradient approximation (28Perdew J.P. Chevary J.A. Vosko S.H. Jackson K.A. Pederson M.R. Singh D.J. Fiolhais C. Phys. Rev. B. 1992; 46: 6671-6687Crossref PubMed Scopus (18903) Google Scholar) and the Becke-Lee-Yang-Parr functions (29Becke A.D. J. Chem. Phys. 1997; 107: 8554-8560Crossref Scopus (1522) Google Scholar) in the program DMol3 (30Delley B. J. Chem. Phys. 1990; 92: 508-517Crossref Scopus (8699) Google Scholar, 31Delley B. J. Chem. Phys. 2000; 113: 7756-7764Crossref Scopus (8213) Google Scholar). To calculate the potential energy surface accurately, an extended basis set was used corresponding to a double-ζ plus two polarization functions (DNPP) as described elsewhere (23Franzen S. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 16754-16759Crossref PubMed Scopus (97) Google Scholar). All calculations were performed at the High Performance Computing resource at the North Carolina State University. The potential energy surfaces were generated for low spin S = 1/2, intermediate spin S = 3/2, and high spin S = 5/2 forms for Im-FeP-NO and FeP-NO (used in the geometry optimization). The potential energy surface of the total higher spin states of the system is assumed to be relevant for the dissociated form at the transition state, although the low spin forms correspond to the ground bound state (23Franzen S. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 16754-16759Crossref PubMed Scopus (97) Google Scholar, 32Franzen S. J. Phys. Chem. 2002; 106: 4533-4542Crossref Scopus (27) Google Scholar). The transition state is assumed to be in the geometry where the iron is in the heme plane of the (Im)-FeP-NO structures. The structures from the Protein Data Bank were compared by using the software Raster3D (33Merritt E.A. Bacon D.J. Methods Enzymol. 1997; 277: 505-524Crossref PubMed Scopus (3869) Google Scholar) and Molscript (34Kraulis P.J. J. Appl. Crystalllogr. 1991; 24: 946-950Crossref Google Scholar).RESULTSSteady-state Equilibrium and Imidazole Content—The mutation H93G induces neither a change of the protein fold (Fig. 1A) nor a change of the heme position (Fig. 1B) so that the overall structure is not perturbed. The superposition of WT (35Kachalova G.S. Popov A.N. Bartunik H.D. Science. 1999; 284: 473-476Crossref PubMed Scopus (303) Google Scholar) and mutant Mb (19Barrick D. Biochemistry. 1994; 33: 6546-6554Crossref PubMed Scopus (167) Google Scholar) structures reveals only a slight rotation of the distal His-64. The absence of the proximal coupling between the heme and the backbone induces a relaxation of the helix end, leading to a slight change of the position of the peptide bonds 92-93 and 93-94. Compared with His-93, the exogenous imidazole, free from the constraint exerted by the helix F, appears rotated. The absorption spectra of unliganded WT and H93G-Mb(imidazole) are identical in both ferric and ferrous states. Fig. 2 depicts the five species depending upon the imidazole concentration, which are involved in the photodissociation experiments, and the steady-state spectra of the corresponding NO-liganded species are compared in Fig. 3A. When imidazole is the proximal substituent, the position of the maximum of the Soret band of NO-liganded mutant Mb depends upon concentration. In the presence of 20 mm imidazole (i.e. a concentration high enough for saturating the H93G-Mb at 50 μm), the absorption maximum is located at 418 nm when NO is bound (Fig. 3A). This wavelength is characteristic for an NO-6-coordinate species and is similar to that of WT Mb. Conversely, in the presence of 100 μm imidazole the binding of NO gives rise to a Soret maximum located at 399 nm, indicating that the equilibrium is displaced toward almost 100% NO-5-coordinate population. Indeed, this wavelength was observed for the endogenous NO receptor guanylate cyclase (6Negrerie M. Bouzhir L. Martin J.L. Liebl U. J. Biol. Chem. 2001; 276: 46815-46821Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar), which is a 5-coordinate nitrosylated species. The spectrum of the sample containing 100 μm imidazole exhibits an isosbestic point at 408 nm and a shoulder around 420 nm because of a very minor remaining population of 6-coordinate nitrosylated species. These observations are in agreement with the value of KD = 0.7 mm for imidazole binding to the heme of the H93G-Mb at 295 K (22Decatur S.M. Franzen S. De Pillis G.D. Dyer R.B. Woodruff W.H. Boxer S.G. Biochemistry. 1996; 35: 4939-4944Crossref PubMed Scopus (74) Google Scholar).FIGURE 2a, the five species of ferrous H93G Mb involved in this study are represented. The mutant H93G is purified in the presence of imidazole that remains bound at the proximal side of the heme both at 20 mm and 100 μm (a). However, because of the so-called “trans effect,” the affinity for imidazole changes after NO binding to Fe2+.At2 mm imidazole, it remains bound as the proximal substituent and the heme iron is 6-coordinate (b) giving a transient 5-coordinate species (d) after NO release. When the imidazole concentration is lower, the ligation of NO results in a 5-coordinate iron (c) that leads to a transient 4-coordinate species after photodissociation of NO (e). Fe* denotes an excited heme iron immediately after photodissociation (t < 1 ps), and GR stands for the geminate rebinding process.View Large Image Figure ViewerDownload Hi-res image Download (PPT)FIGURE 3Comparison of the absorption spectra of H93G mutant myoglobin reconstituted with three different proximal substituents and liganded with 1 mm CO and 2 μm NO. A, different imidazole concentrations were used, 100 μm and 20 mm for the NO-liganded species and 20 mm for the CO-liganded mutant. B, spectra of mutants in buffer containing 20 mm thiophene and 20 mmphenol and incubated either with [NO] = 20 μm or [CO] = 1mm.View Large Image Figure ViewerDownload Hi-res image Download (PPT)To investigate the influence of the nature of the proximal substituent itself, we replaced imidazole by phenol and thiophene in H93G-Mb. The absorption spectra of the corresponding NO-liganded H93G-Mb are compared in Fig. 3B. Included are the spectra of the CO-liganded mutant to compare the influence on both NO- and CO-6-coordinate species. Dialyzing the H93G-Mb with either thiophene or phenol even at concentrations as high as 20 mm always leads to a 5-coordinate species in the presence of NO (Soret band at 398 nm) because of a weaker bond strength between these proximal substituents and the heme iron; this indicates a much larger KD value for these two substituents. The binding of CO to the imidazole-containing mutant only gives rise to the 6-coordinate species with a Soret band located at 421 nm. Similarly, CO does not displace thiophene or phenol but induces a slight shift to the Soret maximum at 418 nm, like for the 6C-NO species, indicating that whatever the substituent the proximally uncoupled 6-coordinate heme is slightly electronically perturbed, which is likely due to the relaxation of constraints within the heme pocket.Geminate Rebinding of Nitric Oxide—Fig. 4 presents the transient absorption spectra associated with the geminate rebinding of NO after photodissociation from global analysis of the 100-ps data matrix. These SVD spectral components in Fig. 4 correspond to the highest singular value (27Negrerie M. Cianetti S. Vos M.H. Martin J.L. Kruglik S.G. J. Phys. Chem. B. 2006; (in press)PubMed Google Scholar) and contain only a minor contribution from the excited electronic states relaxation that occurs in the 2-3-ps time-range (9Petrich J.W. Poyart C. Martin J.L. Biochemistry. 1988; 27: 4049-4060Crossref PubMed Scopus (333) Google Scholar, 36Franzen S. Kiger L. Poyart C. Martin J.L. Biophys. J. 2001; 80: 2372-2385Abstract Full Text Full Text PDF PubMed Scopus (114) Google Scholar). This relaxation (not investigated here) presents a red-shift induced absorption (27Negrerie M. Cianetti S. Vos M.H. Martin J.L. Kruglik S.G. J. Phys. Chem. B. 2006; (in press)PubMed Google Scholar) and has been separated as another SVD spectral component.FIGURE 4A, differential absorption transient spectra associated with the SVD kinetics component of NO rebinding process (i. e. without excited states contribution) to the five species. The H93G mutant is supplemented with 20 and 0.1 mm imidazole yielding a 6- and a 5-coordinate heme, respectively, and is compared with wild type myoglobin and with H93G mutant in the presence of 20 mm thiophene or 20 mm phenol. Only the differential spectra in the presence of 20 mm imidazole matches the equilibrium difference absorption spectra of unliganded Mb minus NO-liganded Mb. B, comparison of transient spectra from SVD analysis associated with the geminate rebinding for three proteins: WT myoglobin (solid line), H93G mutant myoglobin with 100 μm imidazole (dashed line), and soluble guanylate cyclase (dotted line).View Large Image Figure ViewerDownload Hi-res image Download (PPT)The four substituted H93G-Mb mutants are compared with the WT Mb. More importantly, in the presence of 20 mm imidazole, the transient spectrum is very similar to that of WT Mb (Fig. 4A), with a bleaching maximum located at 418-420 nm and an induced absorption centered at 438 nm. This transient spectrum corresponds to the steady-state difference spectrum NO-liganded minus unliganded species and is thus characteristic of the photodissociation of an NO-6-coordinate ground state species with subsequent NO rebinding to a 5-coordinate photoproduct.In contrast, for the lower imidazole concentration (100 μm), the difference spectrum possesses a minimum of bleaching at 400 nm shifted with respect to H93G-Mb at high imidazole concentration and a maximum of absorption at 434 nm. The bleaching at 400 nm corresponds to an NO-5-coordinate heme before photodissociation, and the NO rebinding should therefore occur to a 4-coordinate heme. Its transient spectrum is compared with that of guanylate cyclase (Fig. 4B) for which the photodissociation of NO induces a bleaching at 394 nm and creates a 4-coordinate transient species whose induced ab}, number={15}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Negrerie, M and Kruglik, SG and Lambry, JC and Vos, MH and Martin, JL and Franzen, S}, year={2006}, month={Apr}, pages={10389–10398} }
 @article{nienhaus_deng_belyea_franzen_nienhaus_2006, title={Spectroscopic study of substrate binding to the carbonmonoxy form of dehaloperoxidase from Amphitrite ornata}, volume={110}, ISSN={["1520-6106"]}, DOI={10.1021/jp060278z}, abstractNote={Dehaloperoxidase (DHP) is a globular heme enzyme found in the marine worm Amphitrite ornata that can catalyze the dehalogenation of halophenols to the corresponding quinones by using hydrogen peroxide as a cosubstrate. Its three-dimensional fold is surprisingly similar to that of the oxygen storage protein myoglobin (Mb). A key structural feature common to both DHP and Mb is the existence of multiple conformations of the distal histidine. In DHP, the conformational flexibility may be involved in promotion of substrate and cosubstrate entry and exit. Here we have explored the dynamics of substrate binding in DHP using Fourier transform infrared spectroscopy and flash photolysis. A number of discrete conformations at the active site were identified from the appearance of multiple CO absorbance bands in the infrared region of the spectrum. Upon photolysis at cryogenic temperatures, the CO molecules are trapped at docking sites within the protein matrix, as inferred from the appearance of several photoproduct bands characteristic of each site. Substrate binding stabilizes the protein by approximately 20 kJ/mol. The low yield of substrate-bound DHP at ambient temperature points toward a steric inhibition of substrate binding by carbon monoxide.}, number={26}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Nienhaus, Karin and Deng, Pengchi and Belyea, Jennifer and Franzen, Stefan and Nienhaus, G. Ulrich}, year={2006}, month={Jul}, pages={13264–13276} }
 @article{rhodes_franzen_maria_losego_leonard_laughlin_duscher_weibel_2006, title={Surface plasmon resonance in conducting metal oxides}, volume={100}, ISSN={["1089-7550"]}, DOI={10.1063/1.2222070}, abstractNote={We report the initial observation of surface plasmon resonance (SPR) in a conducting metal oxide thin film. The SPR phenomenon has been observed by attenuated total reflection of near-infrared radiation and is in agreement with electron energy loss spectroscopy measurements. To date, only metals are known to exhibit surface plasmon resonance and only noble metals have practical application. According to theory SPR should be observable in any conductor. This theoretical prediction is verified in the present study. The compositions of many conducting metal oxides are systematically variable, suggesting a significant advance in thin film characterization and innovative possibilities for versatile and sensitive chemical sensing applications.}, number={5}, journal={JOURNAL OF APPLIED PHYSICS}, author={Rhodes, Crissy and Franzen, Stefan and Maria, Jon-Paul and Losego, Mark and Leonard, Donovan N. and Laughlin, Brian and Duscher, Gerd and Weibel, Stephen}, year={2006}, month={Sep} }
 @misc{franzen_brewer_2006, title={Surface plasmon resonance systems and methods having a variable charge density layer}, volume={7,015,471}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Franzen, S. and Brewer, S.}, year={2006} }
 @article{bin-salamon_brewer_depperman_franzen_kampf_kirk_kumar_lappi_peariso_preuss_et al._2006, title={Testing Bridge-Mediated Differences in Dinuclear Valence Tautomeric Behavior}, volume={45}, ISSN={0020-1669 1520-510X}, url={http://dx.doi.org/10.1021/ic060170y}, DOI={10.1021/ic060170y}, abstractNote={Two structurally characterized dinuclear valence tautomers are described. Cobalt ions are bridged by p- and m-phenylene units connected to 2,2‘-bipyridines. X-ray crystal structures show that the molecules are in the [(CoIII)(CoIII)] forms at ca. 125 K, while spectroscopic studies show that both molecules can achieve the [(CoII)(CoII)] form above 400 K and confirm the [(CoIII)(CoIII)] form below 10 K. Magnetic susceptibility studies are also included. Our results highlight the necessity of studying both crystalline and amorphous samples to distinguish the effects of intrinsic electronic structure and intermolecular forces on valence tautomeric behavior.}, number={11}, journal={Inorganic Chemistry}, publisher={American Chemical Society (ACS)}, author={Bin-Salamon, Sofi and Brewer, Scott H. and Depperman, Ezra C. and Franzen, Stefan and Kampf, Jeff W. and Kirk, Martin L. and Kumar, R. Krishna and Lappi, Simon and Peariso, Katrina and Preuss, Kathryn E. and et al.}, year={2006}, month={May}, pages={4461–4467} }
 @article{agbasi-porter_ryman-rasmussen_franzen_feldheim_2006, title={Transcription inhibition using oligonucleotide-modified gold nanoparticles}, volume={17}, ISSN={["1043-1802"]}, DOI={10.1021/bc060100f}, abstractNote={The capture of T7 RNA polymerase using double-stranded promoter DNA on the surface of gold nanoparticles has been demonstrated. The competitive binding and inhibition of T7 RNA polymerase due to specific interactions on the nanoparticle surface represents a transcription factor decoy approach in a model system. The efficiency of inhibition was determined for various nanoparticle sizes, surface coverage, and linker length for double-stranded promoter DNA on gold nanoparticles. The experiments provide a basis for determining the accessibility of binding sites on nanoparticle surfaces for applications involving cell targeting or the use of nanoparticles as binding agents in solution.}, number={5}, journal={BIOCONJUGATE CHEMISTRY}, author={Agbasi-Porter, Chiamaka and Ryman-Rasmussen, Jessica and Franzen, Stefan and Feldheim, Daniel}, year={2006}, month={Sep}, pages={1178–1183} }
 @article{glomm_moses_brennaman_papanikolas_franzen_2005, title={Detection of adsorption of Ru(II) and Os(II) polypyridyl complexes on gold and silver nanoparticles by single-photon counting emission measurements}, volume={109}, ISSN={["1520-6106"]}, DOI={10.1021/jp049184k}, abstractNote={The present study describes a new application of ruthenium(II) tris(bipyridine) (Ru(bpy)3(2+)) and osmium(II) tris(bipyridine) (Os(bpy)3(2+)) as phosphorescent labels for the quantification of surface binding of molecules to gold and silver nanoparticles. The fraction of Ru(bpy)3(2+) and Os(bpy)3(2+) that is in solution can be distinguished from the surface-bound fraction by the relative lifetimes and integrated emission yields as determined by time-correlated single-photon counting (TCSPC) spectroscopy. Complementary steady-state measurements were carried out to confirm surface attachment of the phosphorescent label molecules. Although the emission of solutions of Ru(bpy)3(2+) and Os(bpy)3(2+) is quenched proportional to the concentration of 10 nm Au or 20 nm Ag nanoparticles, the quenching is static and not diffusional quenching observed in Stern-Volmer plots. The results demonstrate that time-resolved spectroscopy provides a rapid method for the measurement of surface binding of labeled molecules on metallic nanoparticles. While steady-state measurements require the preparation of a series of samples with varying quencher concentrations and a reference, the method described herein requires a single sample plus reference. The mechanism for phosphorescence quenching on Au and Ag nanoparticles is discussed in terms of energy and electron transfer theories.}, number={2}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Glomm, WR and Moses, SJ and Brennaman, MK and Papanikolas, JM and Franzen, S}, year={2005}, month={Jan}, pages={804–810} }
 @article{brewer_vu_tang_li_franzen_raleigh_dyer_2005, title={Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain}, volume={102}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0505432102}, abstractNote={Equilibrium Fourier transform infrared (FTIR) and temperature-jump (T-jump) IR spectroscopic techniques were used to study the thermodynamics and kinetics of the unfolding and folding of the villin headpiece helical subdomain (HP36), a small three-helix protein. A double phenylalanine mutant (HP36 F47L, F51L) that destabilizes the hydrophobic core of this protein also was studied. The double mutant is less stable than wild type (WT) and has been shown to contain less residual secondary structure and tertiary contacts in its unfolded state. The relaxation kinetics after a T-jump perturbation were studied for both HP36 and HP36 F47L, F51L. Both proteins exhibited biphasic relaxation kinetics in response to a T-jump. The folding times for the WT (3.23 μs at 60.2°C) and double phenylalanine mutant (3.01 μs at 49.9°C) at the approximate midpoints of their thermal unfolding transitions were found to be similar. The folding time for the WT was determined to be 3.34 μs at 49.9°C, similar to the folding time of the double phenylalanine mutant at that temperature. The double phenylalanine mutant, however, unfolds faster with an unfolding time of 3.01 μs compared with 6.97 μs for the WT at 49.9°C.}, number={46}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Brewer, SH and Vu, DM and Tang, YF and Li, Y and Franzen, S and Raleigh, DP and Dyer, RB}, year={2005}, month={Nov}, pages={16662–16667} }
 @article{belyea_gilvey_davis_godek_sit_lommel_franzen_2005, title={Enzyme function of the globin dehaloperoxidase from Amphitrite ornata is activated by substrate binding}, volume={44}, ISSN={["0006-2960"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-28544440508&partnerID=MN8TOARS}, DOI={10.1021/bi051731k}, abstractNote={Amphitrite ornata dehaloperoxidase (DHP) is a heme enzyme with a globin structure, which is capable of oxidizing para-halogenated phenols to the corresponding quinones. Cloning, high-level expression, and purification of recombinant DHP are described. Recombinant DHP was assayed by stopped-flow experiments for its ability to oxidatively debrominate 2,4,6-tribromophenol (TBP). The enzymatic activity of the ferric form of recombinant DHP is intermediate between that of a typical peroxidase (horseradish peroxidase) and a typical globin (horse heart myoglobin). The present study shows that, unlike other known peroxidases, DHP activity requires the addition of substrate, TBP, prior to the cosubstrate, peroxide. The presence of a substrate-binding site in DHP is consistent with a two-electron oxidation mechanism and an obligatory order for activation of the enzyme by addition of the substrate prior to the cosubstrate.}, number={48}, journal={BIOCHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Belyea, J and Gilvey, LB and Davis, MF and Godek, M and Sit, TL and Lommel, SA and Franzen, S}, year={2005}, month={Dec}, pages={15637–15644} }
 @article{dyer_maness_franzen_fesinmeyer_olsen_andersen_2005, title={Hairpin folding dynamics: The cold-denatured state is predisposed for rapid refolding}, volume={44}, ISSN={["0006-2960"]}, DOI={10.1021/bi050698z}, abstractNote={Cold denaturation is a general phenomenon in globular proteins, and the associated cold-denatured states of proteins have important fundamental and practical significance. Here, we have characterized the cold-denatured state of a beta-hairpin forming peptide, MrH3a, in 8% hexafluoro-2-propanol (HFIP) and the dynamics of its refolding following a laser-induced T-jump. Beta-hairpins constitute an important class of protein structural elements, yet their folding mechanisms are not fully understood. Characterization of MrH3a using NMR, CD, and IR spectroscopies reveals residual structure in the cold-denatured state, in contrast with the highly disordered heat-denatured state. The residual structure in the cold-denatured state comprises relatively compact and solvent protected conformations. Furthermore, we find a substantial acceleration in the rate of folding from the cold-denatured state compared to that of the heat-denatured state. In addition, the cold-denatured state is not populated in 20% HFIP; folding occurs only from the fully unfolded state and is significantly slower. We interpret the acceleration of the folding rate of MrH3a in 8% HFIP as a direct consequence of the collapsed conformations of the cold-denatured state. Finally, there may be some reduction of the loop search cost when starting from the cold-denatured state, since this state may have some of the stabilizing cross-strand interactions already formed.}, number={30}, journal={BIOCHEMISTRY}, author={Dyer, RB and Maness, SJ and Franzen, S and Fesinmeyer, RM and Olsen, KA and Andersen, NH}, year={2005}, month={Aug}, pages={10406–10415} }
 @article{brewer_wicaksana_maria_kingon_franzen_2005, title={Investigation of the electrical and optical properties of iridium oxide by reflectance FTIR spectroscopy and density functional theory calculations}, volume={313}, ISSN={0301-0104}, url={http://dx.doi.org/10.1016/j.chemphys.2004.11.014}, DOI={10.1016/j.chemphys.2004.11.014}, abstractNote={Variable angle reflectance FTIR spectroscopy was used to investigate the optical properties of iridium oxide thin films deposited on glass substrates in the near-IR spectral region. The reflectance was studied as a function of incident angle and wavenumber for p-polarized radiation. The Drude free-electron model along with the Fresnel equations of reflection were utilized to fit the experimental reflectance FTIR data to determine the plasma frequency and electronic scattering time of this conducting metal oxide thin film. These experimental studies were complemented by density functional theory (DFT) calculations of the electronic and optical properties of iridium oxide. The calculations used the crystal structure of iridium oxide with periodic boundary conditions. These theoretical studies yielded the optical band gap, Fermi energy, charge carrier concentration, effective electron mass, plasma frequency and the conduction band orbital character of iridium oxide. The computed dependence of the optical band gap, Fermi energy, charge carrier concentration and the plasma frequency on compression or expansion of the iridium oxide unit cell was investigated.}, number={1-3}, journal={Chemical Physics}, publisher={Elsevier BV}, author={Brewer, Scott H. and Wicaksana, Dwi and Maria, Jon-Paul and Kingon, Angus I. and Franzen, Stefan}, year={2005}, month={Jun}, pages={25–31} }
 @article{brewer_glomm_johnson_knag_franzen_2005, title={Probing BSA binding to citrate-coated gold nanoparticles and surfaces}, volume={21}, ISSN={["0743-7463"]}, DOI={10.1021/la050588t}, abstractNote={The interaction of bovine serum albumin (BSA) with gold colloids and surfaces was studied using ζ-potential and quartz crystal microbalance (QCM) measurements, respectively, to determine the surface charge and coverage. The combination of these two measurements suggests that BSA binding to gold nanoparticles and gold surfaces occurs by an electrostatic mechanism when citrate is present. The binding of BSA to bare gold is nearly two times greater than the binding of BSA to a citrate-coated gold surface, suggesting that protein spreading (denaturation) on the surface may occur followed by secondary protein binding. On the other hand, binding to citrate-coated gold surfaces can be fit to a Langmuir isotherm model to obtain a maximum surface coverage of (3.7 ± 0.2) × 1012 molecules/cm2 and a binding constant of 1.0 ± 0.3 μM-1. The ζ-potential measurements show that the stabilization of colloids by BSA has a significant contribution from a steric mechanism because the colloids are stable, even at their isoelectric point (pI ≈ 4.6). To be consistent with the observed phenomena, the electrostatic interactions between BSA and citrate must consist of salt-bridges, for example, of the carboxylate−ammonium type, between the citrate and the lysine on the protein surface. The data support the role of strong electrostatic binding but do not exclude contributions from steric or hydrophobic interactions with the surface adlayer.}, number={20}, journal={LANGMUIR}, author={Brewer, SH and Glomm, WR and Johnson, MC and Knag, MK and Franzen, S}, year={2005}, month={Sep}, pages={9303–9307} }
 @article{masternak_wenska_milecki_skalski_franzen_2005, title={Solvatochromism of a novel betaine dye derived from purine}, volume={109}, ISSN={["1089-5639"]}, DOI={10.1021/jp047098e}, abstractNote={A novel solvatochromic betaine dye has been synthesized from xanthosine and characterized spectroscopically by UV-vis in a broad range of solvents. The dye 9-(2',3',5'-tri-O-acetyl-beta-d-ribofuranosyl)-2-(pyridinium-1-yl)-9H-purin-6-olate, 1a, exhibits solvent-induced spectral band shifts that are (2)/(3) as large as that of the betaine known as Reichardt's dye, which forms the basis of the E(T)(30) solvent polarity scale. Moreover, the dye 1a is a ribonucleoside and hence has the potential application as a polarity probe for application in RNA oligonucleotides. The isomeric dye 6-(pyridinium-1)-yl-9H-purin-2-olate, 2a, has also been synthesized and exhibits slightly smaller solvatochromic band shifts. The new betaine dyes have also been studied by comparing the experimental and calculated solvatochromic shifts based on the calculation of the UV/vis absorption spectra, using a combination of methods with density functional theory (DFT). The COSMO continuum dielectric method, an applied electric field term in the Hamiltonian, and time-dependent density functional theory (TD-DFT) methods were used to obtain absorption energies, ground-state dipole moments, and the difference dipole moment between the ground and excited states. The calculations predict a lower energy absorption band of charge-transfer character that is highly solvatochromic, and a higher energy absorption band that has pi-pi character which is not solvatochromic, in agreement with the experimental data. For Reichardt's dye the difference dipole moment between the ground and excited state (Deltamu = mu(e) - mu(g)) was also calculated and compared to experiment: Deltamu(calcd) = -6 D and Deltamu(exptl) = -9 +/- 1 D.(1) The ground-state dipole moment was found to be mu(g)(calcd) = 18 D and mu(g)(exptl) = 14.8 +/- 1.2 D.(1).}, number={5}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Masternak, A and Wenska, G and Milecki, J and Skalski, B and Franzen, S}, year={2005}, month={Feb}, pages={759–766} }
 @article{bin-salamon_brewer_franzen_feldheim_lappi_shultz_2005, title={Supramolecular control of valence-tautomeric equilibrium on nanometer-scale gold clusters}, volume={127}, ISSN={["0002-7863"]}, DOI={10.1021/ja042520q}, abstractNote={This communication describes the preparation and characterization of a valence tautomer complex covalently attached to gold nanoparticles. Variable-temperature IR spectroscopy is used to determine the equilibrium thermodynamic parameters for the valence tautomerization. These results are compared with a nonsurface combined valence tautomer complex. The results show that surface confinement attenuates both DeltaH degrees and DeltaS degrees . We attribute these changes to a reduced accessible molecular surface area.}, number={15}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Bin-Salamon, S and Brewer, S and Franzen, S and Feldheim, DL and Lappi, S and Shultz, DA}, year={2005}, month={Apr}, pages={5328–5329} }
 @article{nienhaus_olson_franzen_nienhaus_2005, title={The origin of stark splitting in the initial photoproduct state of MbCO}, volume={127}, ISSN={["1520-5126"]}, DOI={10.1021/ja0466917}, abstractNote={Ligand migration and binding in heme proteins have been measured by X-ray diffraction and time-resolved spectroscopy of photoproduct intermediates. In myoglobin (Mb), internal cavities serve as docking sites for carbon monoxide (CO) ligands. In these sites, the CO ligands display characteristic infrared (IR) stretching bands due to interactions with the local electrical field. In the primary docking site, a CO can reside in two opposite orientations, characterized by a doublet of infrared bands, B1 at approximately 2130 and B2 at approximately 2120 cm-1. To assign these bands to the specific orientations, we have reexamined the effects of mutating His64 and Val68 on the infrared stretching bands associated with the B1 and B2 photoproduct states. Wild-type, H64L, V68F, and H64L-V68F MbCO were selected for experimental and theoretical analyses. Fourier transform infrared (FTIR) spectroscopy and density functional theory (DFT) calculations were used to interpret the effects of the electrostatic environment on the B state bands. The imidazole side chain of His64 appears to be the primary cause of the observed Stark splitting. The high-frequency B1 band is assigned to the CO orientation in which the carbon (white atom) is directed toward the heme iron and the Nepsilon-H proton of His64. At low temperatures, CO molecules in the opposite orientational conformer, B2 with the O atom (red) toward His64, first rotate by 180 degrees into the more stable B1 state and then rebind.}, number={1}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Nienhaus, K and Olson, JS and Franzen, S and Nienhaus, GU}, year={2005}, month={Jan}, pages={40–41} }
 @article{polack_ogilvie_franzen_vos_joffre_martin_alexandrou_2004, title={CO vibration as a probe of ligand dissociation and transfer in myoglobin}, volume={93}, ISSN={["0031-9007"]}, DOI={10.1103/physrevlett.93.018102}, abstractNote={We report femtosecond visible pump, midinfrared probe, spectrally integrated experiments resolving the dynamics of CO in myoglobin upon photodissociation. Our results show a progressive change in absorption strength of the CO vibrational transition during its transfer from the heme to the docking site, whereas the vibrational frequency change is faster than our time resolution. A phenomenological model gives good qualitative agreement with our data for a time constant of 400 fs for the change in oscillator strength. Density-functional calculations demonstrate that indeed vibrational frequency and absorption strength are not linearly coupled and that the absorption strength varies in a slower manner due to charge transfer from the heme iron to CO.}, number={1}, journal={PHYSICAL REVIEW LETTERS}, author={Polack, T and Ogilvie, JP and Franzen, S and Vos, MH and Joffre, M and Martin, JL and Alexandrou, A}, year={2004}, month={Jul} }
 @article{brewer_franzen_2004, title={Calculation of the electronic and optical properties of indium tin oxide by density functional theory}, volume={300}, ISSN={["1873-4421"]}, DOI={10.1016/j.chemphys.2003.11.039}, abstractNote={Density functional theory (DFT) was used to calculate the bulk electronic and optical properties of indium tin oxide (ITO). The ITO model was constructed replacing indium atoms with tin atoms in the cubic unit cell of indium oxide. To allow more possibilities for tin atom substitution than afforded by the forty-atom primitive cell of indium oxide all eighty atoms of the unit cell were included in the stoichiometry (In32−xSnxO48) using periodic boundary conditions. A number of properties of ITO were calculated including the optical band gap, charge carrier density and plasma frequency. The dependence of the electronic and optical properties of ITO on a variety of parameters such as the tin content, cubic lattice parameter and the distance between adjacent tin atoms was investigated. The electronic and optical properties agreed well with experimental data and allowed insight into the origin of the electronic and optical properties of ITO.}, number={1-3}, journal={CHEMICAL PHYSICS}, author={Brewer, SH and Franzen, S}, year={2004}, month={May}, pages={285–293} }
 @article{tkachenko_xie_liu_coleman_ryan_glomm_shipton_franzen_feldheim_2004, title={Cellular trajectories of peptide-modified gold particle complexes: Comparison of nuclear localization signals and peptide transduction domains}, volume={15}, ISSN={["1520-4812"]}, DOI={10.1021/bc034189q}, abstractNote={Gold nanoparticles modified with nuclear localization peptides were synthesized and evaluated for their subcellular distribution in HeLa human cervical epithelium cells, 3T3/NIH murine fibroblastoma cells, and HepG2 human hepatocarcinoma cells. Video-enhanced color differential interference contrast microscopy and transmission electron microscopy indicated that transport of nanoparticles into the cytoplasm and nucleus depends on peptide sequence and cell line. Recently, the ability of certain peptides, called protein transduction domains (PTDs), to transclocate cell and nuclear membranes in a receptor- and temperature-independent manner has been questioned (see for example, Lundberg, M.; Wikstrom, S.; Johansson, M. (2003) Mol. Ther. 8, 143−150). We have evaluated the cellular trajectory of gold nanoparticles carrying the PTD from HIV Tat protein. Our observations were that (1) the conjugates did not enter the nucleus of 3T3/NIH or HepG2 cells, and (2) cellular uptake of Tat PTD peptide−gold nanoparticle conjugates was temperature dependent, suggesting an endosomal pathway of uptake. Gold nanoparticles modified with the adenovirus nuclear localization signal and the integrin binding domain also entered cells via an energy-dependent mechanism, but in contrast to the Tat PTD, these signals triggered nuclear uptake of nanoparticles in HeLa and HepG2 cell lines.}, number={3}, journal={BIOCONJUGATE CHEMISTRY}, author={Tkachenko, AG and Xie, H and Liu, YL and Coleman, D and Ryan, J and Glomm, WR and Shipton, MK and Franzen, S and Feldheim, DL}, year={2004}, pages={482–490} }
 @article{moses_brewer_lowe_lappi_gilvey_sauthier_tenent_feldheim_franzen_2004, title={Characterization of single- and double-stranded DNA on gold surfaces}, volume={20}, ISSN={["0743-7463"]}, DOI={10.1021/la0492815}, abstractNote={Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5‘-C6H12SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation−infrared reflection absorption spectroscopy (PM−IRRAS). The formation of dsDNA on the surface was identified by PM−IRRAS by a dsDNA IR signature at ∼1678 cm-1 that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 °C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au−S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.}, number={25}, journal={LANGMUIR}, author={Moses, S and Brewer, SH and Lowe, LB and Lappi, SE and Gilvey, LBG and Sauthier, M and Tenent, RC and Feldheim, DL and Franzen, S}, year={2004}, month={Dec}, pages={11134–11140} }
 @article{smith_lappi_brewer_dembowy_belyea_franzen_2004, title={Covalent attachment of a nickel nitrilotriacetic acid group to a germanium attenuated total reflectance element}, volume={20}, ISSN={["0743-7463"]}, DOI={10.1021/la034194i}, abstractNote={The surface of a germanium internal reflectance element (IRE) was modified to bind 6X-histidine (his)-tagged biomolecules. The step-by-step surface modification was monitored via single-pass attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR). Initially an adlayer of 7-octenyltrimethoxysilane (7-OTMS) was formed on the Ge crystal through the surface hydroxyl groups, which were produced via ozonolysis of the Ge surface. The vinyl moiety of 7-OTMS was oxidized to a carboxylic acid, which was activated by 1,1‘-carbonydiimidazole (CDI) to produce a labile imidazole. The labile imidazole that resulted from the CDI coupling was then displaced by the primary amine of nitrilotriacetic acid (NTA). Nickel sulfate was added to the system, and it coordinated with the three carbonyl groups and the nitrogen on NTA, thus leaving the ability of Ni to coordinate with two adjacent histidine residues. Binding of his-tagged biotin to nickel nitrilotriacetic acid (Ni-NTA) was observed by ATR-FT-IR spectroscopy. The surface modification method presented in this paper had minimal nonspecific binding, the Ni-NTA surface was reusable if stored properly, and complete removal of the organic surface was achievable.}, number={4}, journal={LANGMUIR}, author={Smith, BM and Lappi, SE and Brewer, SH and Dembowy, S and Belyea, J and Franzen, S}, year={2004}, month={Feb}, pages={1184–1188} }
 @article{shapkina_lappi_franzen_wollenzien_2004, title={Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome}, volume={32}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkh320}, abstractNote={Escherichia coli ribosomes were irradiated with a KrF excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10-40 mJ for a 1 cm2 area, corresponding to fluences of 4.5 to 18 x 10(9) W m(-2), to determine strand breakage yields and the frequency and pattern of RNA-RNA cross- linking in the 16S rRNA. Samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. The yield of strand breaks per photon was intensity dependent, with values of 0.7 to 1.3 x 10(-3) over the incident intensity range studied. The yield for RNA-RNA cross-linking was 3 x 10(-4) cross-links/photon at the intensity of 4.5 x 10(9) W m(-2), an approximately 4-fold higher yield per photon than obtained with a transilluminator. The cross-link yield/photon decreased at higher light intensities, probably due to intensity-dependent photoreversal. The pattern of cross-linking was similar to that observed with low intensity irradiation but with four additional long-range cross-links not previously seen in E.coli ribosomes. Cross- linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than are frequencies obtained with transilluminator irradiation.}, number={4}, journal={NUCLEIC ACIDS RESEARCH}, author={Shapkina, T and Lappi, S and Franzen, S and Wollenzien, P}, year={2004}, month={Feb}, pages={1518–1526} }
 @article{lappi_franzen_2004, title={Eigenvector mapping: a method for discerning solvent effects on vibrational spectra}, volume={60}, DOI={10.1016/S1386-1425(03)00248-8}, abstractNote={This paper reports a density functional theory (DFT) analysis of the adenine spectra in a hydrogen-bonding environment. We compare the theoretical vibrational spectra of 26 model systems in which water has been hydrogen bonded to adenine with the experimental frequencies of the solid state infrared spectra (150-1700 cm(-1)) of polycrystalline adenine and the experimental frequencies observed in matrix isolation spectra of adenine [J. Phys. Chem. 100 (1996) 3527]. The vibrational eigenvectors of adenine are compared by taking the dot product to determine how the normal modes of the 15-adenine atoms are affected by different hydrogen bonding geometries. Using the isolated adenine molecule as a reference permits a comparison of different calculated spectra in terms of the projections of various normal modes and the determination of the potential energy redistribution among normal modes. This method creates a map of the normal modes using the isolated adenine molecule as a reference. Improvement in agreement between the polycrystalline data and a model of adenine with four waters is most striking. The improvement in the fit between matrix isolation data and a model of adenine with a single water was not as dramatic as the fit seen for the polycrystalline data, but the fact that a single hydrogen-bonded water shifted the spectra of the model to a closer fit than that of isolated adenine is important. We call this method eigenvector mapping. The eigenvector mapping method can be used to extract the normal modes of a parent molecule from a solvent model system. The application of this method is important because it aids in the interpretation of complex molecular interactions in terms of the spectrum of an isolated molecule. The eigenvector mapping procedure will be shown to greatly improve the correspondence between the model and the experimental data.}, number={02-Jan}, journal={Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy.}, author={Lappi, S. E. and Franzen, Stefan}, year={2004}, pages={357–370} }
 @article{brewer_allen_lappi_chasse_briggman_gorman_franzen_2004, title={Infrared detection of a phenylboronic acid terminated alkane thiol monolayer on gold surfaces}, volume={20}, ISSN={["0743-7463"]}, DOI={10.1021/la035037m}, abstractNote={Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid moiety to form a phenylboronate ester. Vibrationally resonant sum frequency generation (VR-SFG) spectroscopy confirmed the ordering of the substituted phenyl groups of the PBA adlayer on the gold surface. Solution FTIR spectra and density functional theory were used to confirm the identity of the observed vibrational modes on the gold surface of PBA with and without bound sugar. The detection of the binding of glucose on the gold surface was confirmed in part by the presence of a C−O stretching mode of glucose and the observed O−H stretching mode of glucose that is shifted in position relative to the O−H stretching mode of boronic acid. An IR marker mode was also observed at 1734 cm-1 upon the binding of glucose. Additionally, changes in the peak profile of the B−O stretching band were observed upon binding, confirming formation of a phenylboronate ester on the gold surface. The binding of mannose and lactose were also detected primarily through the IR marker mode at ∼1736 to 1742 cm-1 depending on the identity of the bound sugar.}, number={13}, journal={LANGMUIR}, author={Brewer, SH and Allen, AM and Lappi, SE and Chasse, TL and Briggman, KA and Gorman, CB and Franzen, S}, year={2004}, month={Jun}, pages={5512–5520} }
 @article{lappi_smith_franzen_2004, title={Infrared spectra of (H2O)-O-16, (H2O)-O-18 and D2O in the liquid phase by single-pass attenuated total internal reflection spectroscopy}, volume={60}, ISSN={["1386-1425"]}, DOI={10.1016/j.saa.2003.12.042}, abstractNote={Mid-infrared attenuated total internal reflection (ATR) spectra of H216O, H218O and D216O in the liquid state were obtained and normal coordinate analysis was performed based on the potential energy surface obtained from density functional theory (DFT) calculations. Fits of the spectra to multiple Gaussians showed a consistent fit of three bands for the bending region and five bands for the stretching region for three isotopomers, H216O, H218O and D216O. The results are consistent with previous work and build on earlier studies by the inclusion of three isotopomers and mixtures using the advantage of single-pass ATR to obtain high quality spectra of the water stretching bands. DFT calculation of the vibrational spectrum of liquid water was conducted on seven model systems, two systems with periodic boundary conditions (PBC) consisting of four and nine H216O molecules, and five water clusters consisting of 4, 9, 19, 27 and 32 H216O molecules. The PBC and cluster models were used to obtain a representation of bulk water for comparison with experiment. The nine-water PBC model was found to give a good fit to the experimental line shapes. A difference is observed in the broadening of the water bending and stretching vibrations indicative of a difference in the rate of pure dephasing. The nine-water PBC calculation was also used to calculate the wavenumber shifts observed in the water isotopomers.}, number={11}, journal={SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY}, author={Lappi, SE and Smith, B and Franzen, S}, year={2004}, month={Sep}, pages={2611–2619} }
 @article{ni_kaur_springsteen_wang_franzen_2004, title={Regulating the fluorescence intensity of an anthracene boronic acid system: a B-N bond or a hydrolysis mechanism?}, volume={32}, ISSN={["1090-2120"]}, DOI={10.1016/j.bioorg.2004.06.004}, abstractNote={An anthracene-based fluorescent boronic acid system developed by the Shinkai group has been widely used for the preparation of fluorescent sensors for carbohydrates. Such application is based on the significant fluorescence intensity increase of this system upon binding with a carbohydrate. The mechanism through which this fluorescence intensity change happens was originally proposed to go through a B-N bond formation mechanism, which masks the nitrogen lone pair electrons. However, our own fluorescence studies suggest a possible alternative mechanism for the fluorescence change upon the formation of a boronic acid (1a) complex with diols. In this new proposed mechanism, complex formation induces solvolysis, which results in the protonation of the amine nitrogen if the reactions are carried out in a protic solvent such as water. This protonation prevents the photoinduced electron transfer, resulting in reduced quenching of the anthracene fluorescence. Such a solvolysis mechanism is supported by evidence from various types of experiments and theoretical calculations.}, number={6}, journal={BIOORGANIC CHEMISTRY}, author={Ni, WJ and Kaur, G and Springsteen, G and Wang, BH and Franzen, S}, year={2004}, month={Dec}, pages={571–581} }
 @article{dyer_maness_peterson_franzen_fesinmeyer_andersen_2004, title={The mechanism of beta-hairpin formation}, volume={43}, ISSN={["0006-2960"]}, DOI={10.1021/bi049177m}, abstractNote={β-Hairpins constitute an important class of connecting protein secondary structures. Several groups have postulated that such structures form early in the folding process and serve to nucleate the formation of extended β-sheet structures. Despite the importance of β-hairpins in protein folding, little is known about the mechanism of formation of these structures. While it is well established that there is a complex interplay between the stability of a β-hairpin and loop conformational propensity, loop length, and the formation of stabilizing cross-strand interactions (H-bonds and hydrophobic interactions), the influence of these factors on the folding rate is poorly understood. Peptide models provide a simple framework for exploring the molecular details of the formation of β-hairpin structures. We have explored the fundamental processes of folding in two linear peptides that form β-hairpin structures, having a stabilizing hydrophobic cluster connected by loops of differing lengths. This approach allows us to evaluate existing models of the mechanism of β-hairpin formation. We find a substantial acceleration of the folding rate when the connecting loop is made shorter (i.e., the hydrophobic cluster is moved closer to the turn). Analysis of the folding kinetics of these two peptides reveals that this acceleration is a direct consequence of the reduced entropic cost of the smaller loop search.}, number={36}, journal={BIOCHEMISTRY}, author={Dyer, RB and Maness, SJ and Peterson, ES and Franzen, S and Fesinmeyer, RM and Andersen, NH}, year={2004}, month={Sep}, pages={11560–11566} }
 @article{brewer_franzen_2003, title={A quantitative theory and computational approach for the vibrational Stark effect}, volume={119}, ISSN={["0021-9606"]}, DOI={10.1063/1.1578471}, abstractNote={Density functional theory (DFT) has been used to calculate the vibrational Stark tuning rates of a variety of nitriles and carbonyls in quantitative agreement with experimental values with a correction factor of f=1.1 for the local electric field. These calculations show that the vibrational Stark tuning rate has an anharmonic contribution and a contribution due to geometric distortions caused in the molecules due to the applied electric field. The anharmonic and geometric distortion components of the vibrational Stark tuning rate were calculated by the frequency dependence of the CN or CO stretching mode with varying applied electric fields by using the optimized structure in zero applied field or allowing the structure to optimize in the applied electric field, respectively. The changes in the calculated frequency of the CN or CO stretching mode, bond length, and dipole moment of this bond with varying applied electric fields are shown. The transition polarizability and the difference polarizability were also calculated by DFT for comparison to the experimental data on nitriles and carbonyls. The DFT calculations suggest that the sign of the transition polarizability is negative and this result in turn has an effect on the experimental data analysis since the sign of the transition polarizability is not determined by experiment.}, number={2}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Brewer, SH and Franzen, S}, year={2003}, month={Jul}, pages={851–858} }
 @article{franzen_2003, title={Density functional calculation of a potential energy surface for alkane thiols on Au(111) as function of alkane chain length}, volume={381}, ISSN={["1873-4448"]}, DOI={10.1016/j.cplett.2003.08.126}, abstractNote={Density functional theory calculations of alkane thiols on Au(1 1 1) have been carried out as a function of the alkane chain length from 1 to 12 carbons using a slab geometry with periodic boundary conditions. Geometry optimized structures were obtained and the potential energy was calculated as a function of the binding site and distance from the surface. While the binding site of minimum energy is only subtly different for different chain lengths there is a pronounced difference in the Au–S bonding and side chain interactions of the methyl group of methane thiol compared to ethane thiol or any longer alkane thiol self-assembled monolayer. For example, the barrier to lateral motion along the surface is lowest for motion through fcc sites for methane thiol while the twofold bridge sites present the lowest barrier to ethane thiol and all longer alkane thiols. The hexagonal close-packed (hcp) and face-centered cubic (fcc) threefold sites were found to differ in energy by less than 1 kJ/mol and therefore only fcc sites were considered in the study. According to the calculated potential energy surfaces the top sites have weaker binding than either the bridge or threefold sites in all cases. The calculations show that ethane thiol is a reasonable model for longer alkane chains.}, number={3-4}, journal={CHEMICAL PHYSICS LETTERS}, author={Franzen, S}, year={2003}, month={Nov}, pages={315–321} }
 @article{lowe_brewer_kramer_fuierer_qian_agbasi-porter_moses_franzen_feldheim_2003, title={Laser-induced temperature jump electrochemistry on gold nanoparticle-coated electrodes}, volume={125}, ISSN={["0002-7863"]}, DOI={10.1021/ja036672h}, abstractNote={Laser-induced temperature jumps (LITJs) at gold nanoparticle-coated indium tin oxide (ITO) electrodes in contact with electrolyte solutions have been measured using temperature-sensitive redox probes and an infrared charge-coupled device. Upon irradiation with 532 nm light, interfacial temperature changes of ca. 20 degrees C were recorded for particle coverages of ca. 1 x 1010 cm-2. In the presence of a redox molecule, LITJ yields open-circuit photovoltages and photocurrents that are proportional to the number of particles on the surface. When ssDNA was used to chemisorb nanoparticles to the ITO surface, solution concentrations as low as 100 fM of target ssDNA-modified nanoparticles could be detected at the electrode surface.}, number={47}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Lowe, LB and Brewer, SH and Kramer, S and Fuierer, RR and Qian, GG and Agbasi-Porter, CO and Moses, S and Franzen, S and Feldheim, DL}, year={2003}, month={Nov}, pages={14258–14259} }
 @article{tkachenko_xie_coleman_glomm_ryan_anderson_franzen_feldheim_2003, title={Multifunctional gold nanoparticle-peptide complexes for nuclear targeting}, volume={125}, ISSN={["0002-7863"]}, DOI={10.1021/ja0296935}, abstractNote={The ability of peptide-modified gold nanoparticles to target the nucleus of HepG2 cells was explored. Five peptide/nanoparticle complexes were investigated, particles modified with (1) the nuclear localization signal (NLS) from the SV 40 virus; (2) the adenovirus NLS; (3) the adenovirus receptor-mediated endocytosis (RME) peptide; (4) one long peptide containing the adenovirus RME and NLS; and (5) the adenovirus RME and NLS peptides attached to the nanoparticle as separate pieces. Gold nanoparticles were used because they are easy to identify using video-enhanced color differential interference contrast microscopy, and they are excellent scaffolds from which to build multifunctional nuclear targeting vectors. For example, particles modified solely with NLS peptides were not able to target the nucleus of HepG2 cells from outside the plasma membrane, because they either could not enter the cell or were trapped in endosomes. The combination of NLS/RME particles (4) and (5) did reach the nucleus; however, nuclear targeting was more efficient when the two signals were attached to nanoparticles as separate short pieces versus one long peptide. These studies highlight the challenges associated with nuclear targeting and the potential advantages of designing multifunctional nanostructured materials as tools for intracellular diagnostics and therapeutic delivery.}, number={16}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Tkachenko, AG and Xie, H and Coleman, D and Glomm, W and Ryan, J and Anderson, MF and Franzen, S and Feldheim, DL}, year={2003}, month={Apr}, pages={4700–4701} }
 @article{maness_franzen_gibbs_causgrove_dyer_2003, title={Nanosecond temperature jump relaxation dynamics of cyclic beta-hairpin peptides}, volume={84}, ISSN={["0006-3495"]}, DOI={10.1016/S0006-3495(03)75115-7}, abstractNote={The thermal unfolding of a series of 6-, 10-, and 14-mer cyclic beta-hairpin peptides was studied to gain insight into the mechanism of formation of this important secondary structure. The thermodynamics of the transition were characterized using temperature dependent Fourier transform infrared spectroscopy. Thermodynamic data were analyzed using a two-state model which indicates increasing cooperativity along the series. The relaxation kinetics of the peptides in response to a laser induced temperature jump were probed using time-resolved infrared spectroscopy. Single exponential relaxation kinetics were observed and fit with a two-state model. The folding rate determined for these cyclic peptides is accelerated by some two orders of magnitude over the rate of a linear peptide that forms a beta-hairpin. This observation supports the argument that the rate limiting step in the linear system is either stabilization of compact collapsed structures or rearrangement of collapsed structures over a barrier to achieve the native interstrand registry. Small activation energies for folding of these peptides obtained from an Arrhenius analysis of the rates imply a primarily entropic barrier, hence an organized transition state having specific stabilizing interactions.}, number={6}, journal={BIOPHYSICAL JOURNAL}, author={Maness, SJ and Franzen, S and Gibbs, AC and Causgrove, TP and Dyer, RB}, year={2003}, month={Jun}, pages={3874–3882} }
 @article{franzen_shultz_2003, title={New paradigm for design of high-spin organic molecules: The mechanism of spin-dependent delocalization in exchange-coupled, mixed-valent organic species}, volume={107}, ISSN={["1520-5215"]}, DOI={10.1021/jp0276000}, abstractNote={A theory is developed to describe the electronic structure of mixed-valent, exchange-coupled organic biradicals. The phenomena described are analogous to those of spin-dependent delocalization observed in binuclear inorganic complexes in the sense that coupling of delocalized hole states favors a triplet state over a singlet state. However, the mathematical description of the delocalization is quite similar to Kramers' treatment of antiferromagnetic and ferromagnetic terms in metal oxides (Physica 1934, 1, 182). There is a similarity in that a delocalized orbital in the mixed-valent biradical anion can play the role of oxide in conventional superexchange. As in Kramers' theory, there are two terms that result from the analysis, a second-order term and a third-order term. However, the significance of the terms is different for delocalized magnetic orbitals than for the metal-bridge-metal system considered by Kramers. The computational chemistry shows that the third-order ferromagnetic term dominates for large dihedral angles, in agreement with previous experimental results. The mechanism presented suggests a new paradigm for the design of high-spin organic molecules.}, number={21}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Franzen, S and Shultz, DA}, year={2003}, month={May}, pages={4292–4299} }
 @article{folmer_franzen_2003, title={Study of polymer glasses by modulated differential scanning calorimetry in the undergraduate physical chemistry laboratory}, volume={80}, ISSN={["0021-9584"]}, DOI={10.1021/ed080p813}, abstractNote={Recent technological advances in thermal analysis present educational opportunities. In particular, modulated differential scanning calorimetry (MDSC) can be used to contrast reversing and nonreversing processes in practical laboratory experiments. The introduction of these concepts elucidates the relationship between experimental timescales and reversibility. The latter is a key concept of undergraduate thermodynamics theory that deserves reinforcement. In this paper, the theory and application of MDSC to problems of current interest is outlined with special emphasis on the contrast between crystallization and vitrification. Glass formation deserves greater emphasis in the undergraduate curriculum. Glass transitions are increasingly recognized as an important aspect of materials properties and dynamics in fields ranging from polymer science to protein folding. The example chosen for study is a comparison of polyethylene glycol and atactic polypropylene glycol. The experiment is easily performed in a typi...}, number={7}, journal={JOURNAL OF CHEMICAL EDUCATION}, author={Folmer, JCW and Franzen, S}, year={2003}, month={Jul}, pages={813–818} }
 @article{franzen_ni_wang_2003, title={Study of the mechanism of electron-transfer quenching by boron-nitrogen adducts in fluorescent sensors}, volume={107}, ISSN={["1520-5207"]}, DOI={10.1021/jp027457a}, abstractNote={The mechanism of the change in fluorescence quenching by the amine in boronic acid-based carbohydrate sensor molecules has been explored using density functional theory (DFT). The geometric constra...}, number={47}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Franzen, S and Ni, WJ and Wang, BH}, year={2003}, month={Nov}, pages={12942–12948} }
 @article{franzen_stanley_2002, title={A theoretical explanation for quantum yield failure in bacterial photosynthetic reaction centers}, volume={276}, ISSN={["0301-0104"]}, DOI={10.1016/S0301-0104(01)00582-1}, abstractNote={A new theoretical model addresses the reduction in the quantum yield for primary charge separation in bacterial photosynthetic reaction centers (RCs) in an applied electric field. The electric field dependence of the internal conversion rate constant for the primary donor is proposed to act as a drain that competes with primary charge separation. The field dependence of the internal conversion process is based on experimental data that have shown that the excited state of the primary donor has a large polarizability suggesting that the excitonic basis of the primary donor is mixed with charge transfer (CT) basis states. The model provides analytic expressions for the electric field dependence of the primary charge separation rate constant, prompt and delayed fluorescence, and predicts an effect on the intersystem crossing rate constant. The model provides a mechanism for a reduction of the quantum yield and an explanation for the lack of a concomitant increase in either prompt or delayed fluorescence.}, number={2}, journal={CHEMICAL PHYSICS}, author={Franzen, S and Stanley, RJ}, year={2002}, month={Feb}, pages={115–127} }
 @article{franzen_2002, title={An electrostatic model for the frequency shifts in the carbonmonoxy stretching band of myoglobin: Correlation of hydrogen bonding and the Stark tuning rate}, volume={124}, DOI={10.1021/ja01778d}, number={44}, journal={Journal of the American Chemical Society}, author={Franzen, Stefan}, year={2002}, pages={13271–13281} }
 @article{franzen_2002, title={Carbonmonoxy rebinding kinetics in H93G myoglobin: Separation of proximal and distal side effects}, volume={106}, ISSN={["1520-5207"]}, DOI={10.1021/jp015567w}, abstractNote={The kinetics of carbon monoxide (CO) recombination in H93G myoglobin has been studied as a function of temperature in aqueous buffer solution and in 75% glycerol/buffer solutions. H93G adducts with imidazole (Im), 4-methyl imidazole (4-Me Im), 1-methyl imidazole (1-Me Im), and 4-bromoimidazole (4-Br Im) were analyzed by means of three-state and four-state sequential models. Rate constants for the inner process of CO forming a bond with iron and for CO ligand escape into the solvent were extracted from the analysis. At 310 K, where the largest differences are observed in buffer solution data, the rate constant for CO recombination to the heme iron differs by a factor of ≈15 for the various H93G proximal adducts, while the rate constant for CO escape differs by a factor of only ≈1.4. Thermodynamic analysis based on microscopic reversibility shows that the effect of proximal adducts on equilibrium constant for the intrinsic CO binding to heme iron, KCO, is 15 times larger than the effect on the equilibrium constant for ligand escape, Kescape. Arrhenius plots of the CO recombination rate constant yielded an average activation enthalpy of ≈17 kJ/mol for the rebinding rate constant for the CO recombination process in three of the adducts: Im, 1-Me Im, and 4-Br Im. A Landau−Zener model of the rate constant for the CO recombination process is introduced to account for differences observed in the prefactor of the rate constants. Combination of this analysis with potential energy surfaces calculated using the BLYP functional in a density functional theory approach with a large basis set indicates that the barrier to rebinding should be the same for the adducts studied in the absence of interaction with the protein. The origin of differences in activation enthalpy or entropy for substituted imidazole adducts of H93G therefore should arise from steric interactions of the proximal ligand with the protein.}, number={17}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Franzen, S}, year={2002}, month={May}, pages={4533–4542} }
 @article{marinkovic_huang_bromberg_sullivan_toomey_miller_sperber_moshe_jones_chouparova_et al._2002, title={Center for Synchrotron Biosciences' U2B beamline: an international resource for biological infrared spectroscopy}, volume={9}, ISSN={["1600-5775"]}, DOI={10.1107/S0909049502008543}, abstractNote={A synchrotron infrared (IR) beamline, U2B, dedicated to the biomedical and biological sciences has been constructed and is in operation at the National Synchrotron Light Source (NSLS) of Brookhaven National Laboratory. The facility is operated by the Center for Synchrotron Biosciences of the Albert Einstein College of Medicine in cooperation with the NSLS. Owing to the broadband nature of the synchrotron beam with brightness 1000 times that of conventional sources, Fourier transform IR spectroscopy experiments are feasible on diffraction-limited sample areas at high signal-to-noise ratios and with relatively short data-acquisition times. A number of synchrotron IR microscopy experiments that have been performed in the mid-IR spectral range (500-5000 cm(-1)) are summarized, including time-resolved protein-folding studies in the microsecond time regime, IR imaging of neurons, bone and other biological tissues, as well as imaging of samples of interest in the chemical and environmental sciences. Owing to the high flux output of this beamline in the far-IR region (50-500 cm(-1)), investigations of hydrogen bonding and dynamic molecular motions of biomolecules have been carried out from 10 to 300 K using a custom-made cryostat and an evacuated box. This facility is intended as an international resource for biological IR spectroscopy fully available to outside users based on competitive proposal.}, number={2002 Jul}, journal={JOURNAL OF SYNCHROTRON RADIATION}, author={Marinkovic, NS and Huang, R and Bromberg, P and Sullivan, M and Toomey, J and Miller, LM and Sperber, E and Moshe, S and Jones, KW and Chouparova, E and et al.}, year={2002}, month={Jul}, pages={189–197} }
 @article{lappi_collier_franzen_2002, title={Density functional analysis of anharmonic contributions to adenine matrix isolation spectra}, volume={106}, ISSN={["1089-5639"]}, DOI={10.1021/jp026017g}, abstractNote={This paper reports the analysis of adenine spectra using both harmonic and anharmonic approximations to the vibrational frequencies reported in matrix isolation studies. The harmonic approximation procedure consists of the application of a scaled ab initio calculated harmonic force field to predict the frequencies, and infrared intensities, of adenine. Theoretical calculations were made using Hartree−Fock density functional theory (DFT) B3-LYP/6-31G* and GGA/DNP computational methods. The equilibrium calculated force constants were scaled according to the method of Pulay (Pulay, P.; Fogarasi, G.; Pang, F.; Boggs, J. E. J. Am. Chem. Soc. 1979, 101, 2550−2560) and compared with the experimentally determined frequencies, and intensities, to assess the accuracy and fit of the theoretical calculation. Good agreement is found except for the in-plane X−H bending or stretching and the out-of-plane X−H bending or wagging modes (X = C and N) which exhibit cubic and quartic anharmonicity, respectively. The NH2 pucke...}, number={47}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Lappi, SE and Collier, W and Franzen, S}, year={2002}, month={Nov}, pages={11446–11455} }
 @article{brewer_anthireya_lappi_drapcho_franzen_2002, title={Detection of DNA hybridization on gold surfaces by polarization modulation infrared reflection absorption spectroscopy}, volume={18}, ISSN={["0743-7463"]}, DOI={10.1021/la025613z}, abstractNote={Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) was used to detect DNA hybridization on gold surfaces. Mixed monolayers of 6-mercapto-1-hexanol (MCH) and single-stranded DNA (ssDNA) with a C6−SH 5‘ modifier were first formed on the gold surface by co-deposition. Then hybridization with the complementary ssDNA strand was performed to obtain double-stranded DNA (dsDNA). The PM-IRRAS spectra obtained contained absorptive features indicative of DNA arising from the phosphodiester backbone and the purine and pyrimidine rings. An infrared signature of dsDNA was observed at 1655 cm-1 that was absent in the ssDNA spectra. This band permitted the distinction between ssDNA and dsDNA to be made thus allowing for the detection of DNA hybridization on gold surfaces by PM-IRRAS.}, number={11}, journal={LANGMUIR}, author={Brewer, SH and Anthireya, SJ and Lappi, SE and Drapcho, DL and Franzen, S}, year={2002}, month={May}, pages={4460–4464} }
 @article{franzen_fritsch_brewer_2002, title={Experimental observation of anharmonic coupling of the heme-doming and iron-ligand out-of-plane vibrational modes confirmed by density functional theory}, volume={106}, ISSN={["1520-6106"]}, DOI={10.1021/jp0261197}, abstractNote={In the deoxy ferrous state of histidine-ligated heme proteins, the iron−histidine band (νFe-His) has been assigned as a stretching mode that involves a two-body motion involving the iron and histidine combined with a minor amount of heme doming. An analogous Raman band, νFe-L has been observed in the proximal cavity mutant of H93G myoglobin where the Raman band of a series of nonnative axial ligands, L, can be compared. The H93G mutant of myoglobin consists of substitution of the proximal histidine, H93, by glycine. This replacement abolishes the sole covalent connection between the globin and the heme iron and creates a cavity that can be occupied by exogenous ligands, L, by dialysis. In the present study, the iron−axial-ligand out-of-plane vibration, νFe-L, for a series deoxy ferrous heme-iron adducts H93G(L) has been measured as a function of temperature, where L = imidazole (Im), 4-methyl imidazole (4-Me Im), 2-methyl imidazole (2-Me Im), 1-methyl imidazole (1-Me Im), 4-bromo imidazole (4-Br Im), and 2,4-dimethyl imidazaole (2,4-diMe Im). Density functional theory calculations show that anharmonic coupling between low wavenumber heme-doming and iron−ligand out-of-plane modes can account for the calculated νFe-L frequency shifts. These calculations parallel the experimental observed trends for temperature-dependent Raman spectra for all of the adducts except H93G(1-Me Im).}, number={44}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Franzen, S and Fritsch, K and Brewer, SH}, year={2002}, month={Nov}, pages={11641–11646} }
 @article{brewer_brown_franzen_2002, title={Formation of thiolate and phosphonate adlayers on indium-tin oxide: Optical and electronic characterization}, volume={18}, DOI={10.1021/la01572d}, number={18}, journal={Langmuir}, author={Brewer, S. H. and Brown, D. A. and Franzen, Stefan}, year={2002}, pages={6857–6865} }
 @article{franzen_wallace-williams_shreve_2002, title={Heme charge-transfer band III is vibronically coupled to the soret band}, volume={124}, ISSN={["0002-7863"]}, DOI={10.1021/ja0172722}, abstractNote={A complete resonance Raman excitation profile of the heme charge-transfer band known as band III is presented. The data obtained throughout the near-infrared region show preresonance with the Q-band, but the data also clearly show the enhancement of a number of modes in the spectral region of band III. Only nontotally symmetric modes are observed to have resonance enhancement in the band III region. The observed resonance enhancements in modes of B(1g) symmetry are compared with the enhancements of those same modes in the excitation profiles of the Q-band of deoxy myoglobin, also presented here for this first time. The Q-band data agree well with the theory of vibronic coupling in metalloporphyrins (Shelnutt, J. A. J. Chem. Phys. 1981, 74, 6644-6657). The strong vibronic coupling of the Q-band of the deoxy form of hemes is discussed in terms of the enhancement of modes with both B(1g) and A(2g) symmetry. The comparison between the Q-band and band III reveals that, consistent with the theory, only modes of B(1g) symmetry are enhanced in the vicinity of band III. These results show that band III is vibronically coupled to the Soret band. The coupling of band III to modes with strong rhombic distortion of the heme macrocycle calls into question the hypothesis that the axial iron out-of-plane displacement is primarily responsible for the structure-dynamics correlations observed in myoglobin.}, number={24}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Franzen, S and Wallace-Williams, SE and Shreve, AP}, year={2002}, month={Jun}, pages={7146–7155} }
 @article{brewer_franzen_2002, title={Indium tin oxide plasma frequency dependence on sheet resistance and surface adlayers determined by reflectance FTIR spectroscopy}, volume={106}, ISSN={["1520-6106"]}, DOI={10.1021/jp026600x}, abstractNote={Variable angle reflectance FTIR spectroscopy was used to investigate the optical properties of indium tin oxide (ITO) and fluorine-doped tin oxide (SFO) thin films in the near-IR spectral region. T...}, number={50}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Brewer, SH and Franzen, S}, year={2002}, month={Dec}, pages={12986–12992} }
 @article{sauthier_carroll_gorman_franzen_2002, title={Nanoparticle Layers Assembled through DNA Hybridization:  Characterization and Optimization}, volume={18}, ISSN={["0743-7463"]}, DOI={10.1021/la0112763}, abstractNote={The hybridization of nanoparticle-labeled DNA targets to surface-attached DNA probes has been investigated. Scanning tunneling microscopy (STM) and Raman and Fourier transform infrared (FTIR) spectroscopy were used to elucidate surface morphology, coverage, and the presence of aggregates. The factors that affect surface coverage, such as probe density, labeled target concentration, and particle size, were systematically investigated by STM in order to determine the best set of experimental conditions allowing the formation of dense monolayers with a minimal number of surface defects for both 5(′1) nm and 10(′2) nm gold nanoparticle labels on the target strand. Grazing-angle FTIR spectroscopy demonstrates that DNA is largely oriented once the labeled targets hybridized to the probes. Raman microscopy was used to probe the surface for the presence of large aggregates that would give rise to large scattering signals. Both STM and optical experiments provide evidence that dense surface layers can be formed without extensive aggregation. Nonselective binding was shown to be a function of the target concentration and nanoparticle size. Propensity for both aggregation and nonspecific binding is greater for 10(′2) nm than for 5(′1) nm gold nanoparticles.}, number={5}, journal={Langmuir}, author={Sauthier, M.L. and Carroll, R.L. and Gorman, C.B. and Franzen, S.}, year={2002}, pages={1825–1830} }
 @article{franzen_folmer_glomm_r o'neal_2002, title={Optical properties of dye molecules adsorbed on single gold and silver nanoparticles}, volume={106}, ISSN={["1520-5215"]}, DOI={10.1021/jp025536g}, abstractNote={Despite the well-known relationship between the resonance Raman excitation profile and the absorption line shape, there is scant experimental evidence for effects in absorption or fluorescence spectroscopy related to the observations of surface-enhanced Raman scattering (SERS). On the other hand, numerous Raman studies have been done on the SERS phenomenon, where large enhancement factors have been determined. In this work, the absorption properties of molecules adsorbed on single gold and silver nanoparticles (monomers) have been investigated, with particular emphasis on an examination of the effect on the spectrum of the adsorbate. A number of the adsorbates studied are similar to those reported in SERS studies. The adsorbates can be divided into two classes according to the nature of the interaction with the adsorbent. Class I shows little change in the absorption spectrum. Class II shows a large reduction in absorption. The only examples of an increase in absorption arise from solvatochromic effects. The implication of these observations for the mechanism of SERS is discussed.}, number={28}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Franzen, S and Folmer, JCW and Glomm, WR and R O'Neal}, year={2002}, month={Jul}, pages={6533–6540} }
 @article{brewer_franzen_2002, title={Optical properties of indium tin oxide and fluorine-doped tin oxide surfaces: correlation of reflectivity, skin depth, and plasmon frequency with conductivity}, volume={338}, ISSN={["0925-8388"]}, DOI={10.1016/S0925-8388(02)00217-7}, abstractNote={Variable angle reflectance FTIR was used to investigate the reflectance of thin films of either indium tin oxide (ITO) or fluorine-doped tin oxide (SFO) on glass substrates in the mid-IR. The reflectance was observed to depend on the incident angle, wavenumber, and the polarization used. The Drude model and the Fresnel equations for reflection at a single dielectric boundary were used to interpret these results in terms of the conductivity, reflectivity, skin depth, and plasmon frequency of the metal oxides. The skin depth of thin film ITO electrodes was found to depend on the sheet resistance linearly, while the reflectance varied according to the square root of the sheet resistance. The method shows that an optical probe can be used to determine the electrical properties of metal oxide films in a noninvasive approach.}, number={1-2}, journal={JOURNAL OF ALLOYS AND COMPOUNDS}, author={Brewer, SH and Franzen, S}, year={2002}, month={May}, pages={73–79} }
 @article{franzen_2002, title={Perimeter model for the magnetic circular dichroism spectrum of deoxy ferrous heme in myoglobin}, volume={106}, ISSN={["1520-6106"]}, DOI={10.1021/jp025616k}, abstractNote={The magnetic circular dichroism (MCD) spectra of deoxy heme in Sperm whale myoglobin are explained by using a theory based on the perimeter model (PM) of metalloporphyrin spectra. The perimeter model is shown to be valid by comparison with the heme of carbonmonoxy myoglobin and previous reports including both Zn protoporphyrin and ferric heme MCD spectra. The PM approach, applied to closed shell metalloporphyrins, models the highest occupied molecular orbital as Lz = ±4 and the lowest unoccupied molecular orbital as Lz = ±5. According to the PM, the allowed intense Soret band transition has Lz = ±1, while the vibronically allowed weak Q-band has Lz = ±9.1 Analysis of the experimental spectra based on the scaled first derivative of the absorption spectrum is demonstrated to give good agreement with calculated spectra, although the experimentally measured values of Lz are somewhat smaller than those predicted by the PM theory. Application of the PM to open shell metals, and in particular deoxy heme, is shown using a vibronic approach that accounts for mixing of charge-transfer states. A Soret excited-state split due to vibronic coupling (VC) is modeled by a porphyrin π excited state (Lz = ±5) that strongly vibronically couples with a dπ state (Lz = ±1). The vibronic coupling model has relevance not only for deoxy heme but also for species such as the heme oxo species known as compound I.2 The model developed for MCD spectra is consistent with recent resonant Raman spectroscopic studies of deoxy heme.}, number={40}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Franzen, S}, year={2002}, month={Oct}, pages={10482–10491} }
 @article{franzen_peterson_brown_friedman_thomas_boxer_2002, title={Proximal ligand motions in H93G myoglobin}, volume={269}, ISSN={["0014-2956"]}, DOI={10.1046/j.1432-1033.2002.03193.x}, abstractNote={Resonance Raman spectroscopy has been used to observe changes in the iron-ligand stretching frequency in photoproduct spectra of the proximal cavity mutant of myoglobin H93G. The measurements compare the deoxy ferrous state of the heme iron in H93G(L), where L is an exogenous imidazole ligand bound in the proximal cavity, to the photolyzed intermediate of H93G(L)*CO at 8 ns. There are significant differences in the frequencies of the iron-ligand axial out-of-plane mode nu(Fe-L) in the photoproduct spectra depending on the nature of L for a series of methyl-substituted imidazoles. Further comparison was made with the proximal cavity mutant of myoglobin in the absence of exogenous ligand (H93G) and the photoproduct of the carbonmonoxy adduct of H93G (H93G-*CO). For this case, it has been shown that H2O is the axial (fifth) ligand to the heme iron in the deoxy form of H93G. The photoproduct of H93G-*CO is consistent with a transiently bound ligand proposed to be a histidine. The data presented here further substantiate the conclusion that a conformationally driven ligand switch exists in photolyzed H93G-*CO. The results suggest that ligand conformational changes in response to dynamic motions of the globin on the nanosecond and longer time scales are a general feature of the H93G proximal cavity mutant.}, number={19}, journal={EUROPEAN JOURNAL OF BIOCHEMISTRY}, author={Franzen, S and Peterson, ES and Brown, D and Friedman, JM and Thomas, MR and Boxer, SG}, year={2002}, month={Oct}, pages={4879–4886} }
 @article{smith_franzen_2002, title={Single-pass attenuated total reflection Fourier transform infrared spectroscopy for the analysis of proteins in H2O solution}, volume={74}, ISSN={["0003-2700"]}, DOI={10.1021/ac020103v}, abstractNote={The application of single-pass attenuated total reflection Fourier transform infrared (ATR-FT-IR) microscopy was investigated for secondary structure analysis of 15 representative proteins in H2O solution. This is the first reported application of single-pass ATR-FT-IR for protein analysis; thus, the method was validated using transmission FT-IR and multipass ATR-FT-IR as referee methods. The single-pass ATR-FT-IR technique was advantageous since the single-pass geometry permits rapid secondary structure analysis on small volumes of protein in H2O solution without the use of demountable thin path length sample cells. Moreover, the fact that H2O backgrounds were small allowed the simultaneous observation of the amide I-III, A, and B regions without having to perform H2O subtraction. A comparison of replicate protein spectra indicated that the single-pass ATR-FT-IR method yields more reproducible data than those acquired by transmission FT-IR. The observed trends for the amide I-III and A bands obtained by single-pass ATR-FT-IR agreed with those in the literature for conventional transmission FT-IR.}, number={16}, journal={ANALYTICAL CHEMISTRY}, author={Smith, BM and Franzen, S}, year={2002}, month={Aug}, pages={4076–4080} }
 @article{smith_oswald_franzen_2002, title={Single-pass attenuated total reflection Fourier transform infrared spectroscopy for the prediction of protein secondary structure}, volume={74}, ISSN={["0003-2700"]}, DOI={10.1021/ac020104n}, abstractNote={Principal component regression (PCR) was applied to a spectral library of proteins in H2O solution acquired by single-pass attenuated total reflectance (ATR) Fourier transform infrared (FT-IR) spectroscopy. PCR was used to predict the secondary structure content, principally alpha-helical and the beta-sheet content, of proteins within a spectral library. Quantitation of protein secondary structure content was performed as a proof of principle that use of single-pass ATR-FT-IR is an appropriate method for protein secondary structure analysis. The ATR-FT-IR method permits acquisition of the entire spectral range from 700 to 3900 cm(-1) without significant interference from water bands. An "inside model space" bootstrap and a genetic algorithm (GA) were used to improve prediction results. Specifically, the bootstrap was utilized to increase the number of replicates for adequate training and validation of the PCR model. The GA was used to optimize PCR parameters, particularly wavenumber selection. The use of the bootstrap allowed for adequate representation of variability in the amide A, amide B, and C-H stretching regions due to differing levels of sample hydration. Implementation of the bootstrap improved the robustness of the PCR models significantly; however, the use of a GA only slightly improved prediction results. Two spectral libraries are presented where one was better suited for beta-sheet content prediction and the other for alpha-helix content prediction. The GA-optimized PCR method for alpha-helix content prediction utilized 120 wavenumbers within the amide I, II, A, B, and IV and the C-H stretching regions and 18 factors. For beta-sheet content predictions, 580 wavenumbers within the amide I, II, A, and B and the C-H stretching regions and 18 factors were used. The validation results using these two methods yielded an average absolute error of 1.7% for alpha-helix content prediction and an average absolute error of 2.3% for beta-sheet content prediction. After the PCR models were developed and validated, they were used to predict the alpha-helix and beta-sheet content of two unknowns, casein and immunoglobulin G.}, number={14}, journal={ANALYTICAL CHEMISTRY}, author={Smith, BM and Oswald, L and Franzen, S}, year={2002}, month={Jul}, pages={3386–3391} }
 @article{franzen_2002, title={Spin-dependent mechanism for diatomic ligand binding to heme}, volume={99}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.252590999}, abstractNote={The nature of diatomic ligand recombination in heme proteins is elucidated by using a Landau-Zener model for the electronic coupling in the recombination rate constant. The model is developed by means of explicit potential energy surfaces calculated by using density functional theory (DFT). The interaction of all possible spin states of the three common diatomic ligands, CO, NO, and O2, and high-spin heme iron is compared. The electronic coupling, rebinding barrier, and Landau-Zener force terms can be obtained and used to demonstrate significant differences among the ligands. In particular the intermediate spin states of NO (S = 32) and O2 (S = 1) are shown to be bound states. Rapid recombination occurs from these bound states in agreement with experimental data. The slower phases of O2 recombination can be explained by the presence of two higher spin states, S = 2 and S = 3, which have a small and relatively large barrier to ligand recombination, respectively. By contrast, the intermediate spin state for CO is not a bound state, and the only recombination pathway for CO involves direct recombination from the S = 2 state. This process is significantly slower according to the Landau-Zener model. Quantitative estimates of the parameters used in the rate constants provide a complete description that explains rebinding rates that range from femtoseconds to milliseconds at ambient temperature.}, number={26}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Franzen, S}, year={2002}, month={Dec}, pages={16754–16759} }
 @article{franzen_bailey_dyer_woodruff_hu_thomas_boxer_2001, title={A photolysis-triggered heme ligand switch in H93G myoglobin}, volume={40}, ISSN={["0006-2960"]}, DOI={10.1021/bi0023403}, abstractNote={Resonance Raman spectroscopy and step-scan Fourier transform infrared (FTIR) spectroscopy have been used to identify the ligation state of ferrous heme iron for the H93G proximal cavity mutant of myoglobin in the absence of exogenous ligand on the proximal side. Preparation of the H93G mutant of myoglobin has been previously reported for a variety of axial ligands to the heme iron (e.g., substituted pyridines and imidazoles) [DePillis, G., Decatur, S. M., Barrick, D., and Boxer, S. G. (1994) J. Am. Chem. Soc. 116, 6981−6982]. The present study examines the ligation states of heme in preparations of the H93G myoglobin with no exogenous ligand. In the deoxy form of H93G, resonance Raman spectroscopic evidence shows water to be the axial (fifth) ligand to the deoxy heme iron. Analysis of the infrared C−O and Raman Fe−C stretching frequencies for the CO adduct indicates that it is six-coordinate with a histidine trans ligand. Following photolysis of CO, a time-dependent change in ligation is evident in both step-scan FTIR and saturation resonance Raman spectra, leading to the conclusion that a conformationally driven ligand switch exists in the H93G protein. In the absence of exogenous nitrogenous ligands, the CO trans effect stabilizes endogenous histidine ligation, while conformational strain favors the dissociation of histidine following photolysis of CO. The replacement of histidine by water in the five-coordinate complex is estimated to occur in <5 μs. The results demonstrate that the H93G myoglobin cavity mutant has potential utility as a model system for studying the conformational energetics of ligand switching in heme proteins such as those observed in nitrite reductase, guanylyl cyclase, and possibly cytochrome c oxidase.}, number={17}, journal={BIOCHEMISTRY}, author={Franzen, S and Bailey, J and Dyer, RB and Woodruff, WH and Hu, RB and Thomas, MR and Boxer, SG}, year={2001}, month={May}, pages={5299–5305} }
 @article{franzen_2001, title={Effect of a charge relay on the vibrational frequencies of carbonmonoxy iron porphine adducts: The coupling of changes in axial ligand bond strength and porphine core size}, volume={123}, ISSN={["1520-5126"]}, DOI={10.1021/ja0108988}, abstractNote={The effect of a charge relay involving Asp-His-Fe in peroxidase enzymes is explored using density functional theory (DFT) calculations of vibrational spectra and potential energy surfaces of carbonmonoxy model systems. The series of models consists of a carbonmonoxy iron porphine molecule with a trans imidazole ligand hydrogen-bonded to six different partners at the Ndelta position. Calculations on the oxy system and on models of the Asp-His-Ser catalytic triad of serine proteases were also performed to obtain an understanding of how the redistribution of charge in these systems may contribute to enzymatic function. The goal of the study is to relate the experimental frequencies in resonance Raman and Fourier transform infrared studies to bonding that is important for the function of heme enzymes. Calculations of both axial and in-plane modes exhibit trends that agree with experimental data. Comparisons of the charge distribution on the different models show that polarization of iron carbonomonoxy bonds consistent with the mechanism for peroxidase function leads to a frequency reduction in the C-O stretching mode nuCO. The combination of axial trans sigma-bonding and pi-bonding effects that include expansion of the porphine core result in little change in the Fe-C stretching frequency nuFe-CO in the series of molecules studied with different Ndelta-H hydrogen bonding. A particular role for the core size is discussed that demonstrates the applicability of trends observed in vibrational spectroscopy of hemes to the charge relay mechanism and other axial ligation effects. The bonding interactions described account for the increase in electron density on bound diatomic ligands, which is required for peroxidase function.}, number={50}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Franzen, S}, year={2001}, month={Dec}, pages={12578–12589} }
 @article{franzen_miskowski_shreve_wallace-williams_woodruff_ondrias_barr_moore_boxer_2001, title={Electrostatic and conformational effects on the electronic structures of distortional isomers of a mixed-valence binuclear Cu complex}, volume={40}, ISSN={["0020-1669"]}, DOI={10.1021/ic010494g}, abstractNote={The electronic structure of the binuclear copper complex [Cu(2)(L)](3+) [L = N(CH(2)CH(2)N(H)CH(2)CH(2)N(H)CH(2)CH(2))(3)N] has been investigated by resonance Raman and electroabsorption spectroscopy. Crystallographic Cu(2) distances of 2.364(1) and 2.415(1) A determined for the nitrate and acetate salts, respectively, are consistent with a substantial metal-metal interaction. The Cu-Cu bonding interaction in the binuclear complex is modulated both in the solid state and in solution by the ligand environment through coupling to ligand torsional modes that are, in turn, stabilized by hydrogen bonding. Electroabsorption data on the three major visible and near-infrared electronic transitions of Cu(2)L, lambda(max) (epsilon(max)) = 1000 nm ( approximately 1200 M(-1) cm(-1)), 748 nm (5600 M(-1) cm(-1)), and 622 nm (3350 M(-1) cm(-1)), reveal a difference dipole moment between the ground and excited states (Deltamu(A)) because of symmetry breaking. The difference polarizability for all three of the transitions is negative, indicating that the ground state is more polarizable than the excited state. A general model to explain this behavior in terms of the proximity of accessible transitions involving copper d electrons is proposed to explain the larger polarizability of the ground state. Raman excitation profiles (REPs) provide evidence for multiple conformational states of [Cu(2)(L)](3+). Separate REPs were obtained for each of the components of the two major Raman bands for nu(1) (a Cu-Cu stretching mode) and nu(2) (a Cu-Cu-N(eq) bending mode). The Raman data along with quantum chemical ZINDO/S CI calculations provide evidence for isomeric forms of Cu(2)L with strong coupling between the conformation of L and the Cu-Cu bond length.}, number={25}, journal={INORGANIC CHEMISTRY}, author={Franzen, S and Miskowski, VM and Shreve, AP and Wallace-Williams, SE and Woodruff, WH and Ondrias, MR and Barr, ME and Moore, L and Boxer, SG}, year={2001}, month={Dec}, pages={6375–6382} }
 @article{thomas_brown_franzen_boxer_2001, title={FTIR and resonance Raman studies of nitric oxide binding to H93G cavity mutants of myoglobin}, volume={40}, ISSN={["0006-2960"]}, DOI={10.1021/bi011440l}, abstractNote={Nitric oxide (NO) binds to the myoglobin (Mb) cavity mutant, H93G, forming either a five- or six-coordinate Fe−NO complex. The H93G mutation eliminates the covalent attachment between the protein and the proximal ligand, allowing NO to bind H93G possibly from the proximal side of the heme rather than the typical diatomic binding pocket on the distal side. The question of whether NO binds on the distal or proximal side was addressed by FTIR spectroscopy of the N−O vibrational frequency ν̄N-O for a set of Mb mutants that perturb the electrostatic environment of the heme pocket. Vibrational spectra of five- and six-coordinate MbNO complexes indicate that ν̄N-O shifts (by as much as 26 cm-1) to higher energies for the distal mutants H64V and H64V/H93G relative to the energies of wild-type and H93G MbNO, while ν̄N-O is not affected by the proximal side mutation S92A/H93G. This result suggests that NO binds on the distal side of heme in the five- and six-coordinate MbNO complexes of H93G. Additionally, values of the Fe−NO vibrational frequency ν̄Fe-NO as measured by resonance Raman spectroscopy are reported for the distal and proximal double mutants of H93G. These results suggest that ν̄Fe-NO is not very sensitive to mutations that perturb the electrostatic environment of the heme pocket, leading to the observation that ν̄N-O and ν̄Fe-NO are not quantitatively correlated for the MbNO complexes presented here. Furthermore, ν̄N-O and ν̄Fe-NO do not correlate well with equilibrium constants for imidazole binding to the five-coordinate MbNO complexes of the H93G double mutants. The data presented here do not appear to support the presence of π-back-bonding or an inverse trans effect of NO binding in Mb mutants that alter the electrostatic environment of the heme pocket.}, number={49}, journal={BIOCHEMISTRY}, author={Thomas, MR and Brown, D and Franzen, S and Boxer, SG}, year={2001}, month={Dec}, pages={15047–15056} }
 @article{franzen_kiger_poyart_martin_2001, title={Heme photolysis occurs by ultrafast excited state metal-to-ring charge transfer}, volume={80}, ISSN={["0006-3495"]}, DOI={10.1016/S0006-3495(01)76207-8}, abstractNote={Ultrafast time-resolved resonance Raman spectra of carbonmonoxy hemoglobin (Hb), nitroxy Hb, and deoxy Hb are compared to determine excited state decay mechanisms for both ligated and unligated hemes. Transient absorption and Raman data provide evidence for a sequential photophysical relaxation pathway common to both ligated and unligated forms of Hb* (photolyzed heme), in which the excited state 1Q decays sequentially: 1Q-->Hb*I-->Hb*II-->Hb ground state. Consistent with the observed kinetics, the lifetimes of these states are <50 fs, approximately 300 fs, and approximately 3 ps for 1Q, Hb*I, and Hb*II, respectively. The transient absorption data support the hypothesis that the Hb*I state results from an ultrafast iron-to-porphyrin ring charge transfer process. The Hb*II state arises from porphyrin ring-to-iron back charge transfer to produce a porphyrin ground state configuration a nonequilibrium iron d-orbital population. Equatorial d-pi* back-bonding of the heme iron to the porphyrin during the lifetime of the Hb*II state accounts for the time-resolved resonance Raman shifts on the approximately 3 ps time scale. The proposed photophysical pathway suggests that iron-to-ring charge transfer is the key event in the mechanism of photolysis of diatomic ligands following a porphyrin ring pi-pi* transition.}, number={5}, journal={BIOPHYSICAL JOURNAL}, author={Franzen, S and Kiger, L and Poyart, C and Martin, JL}, year={2001}, month={May}, pages={2372–2385} }
 @article{novak_nickerson_franzen_feldheim_2001, title={Purification of molecularly bridged metal nanoparticle arrays by centrifugation and size exclusion chromatography}, volume={73}, ISSN={["0003-2700"]}, DOI={10.1021/ac010812t}, abstractNote={Size exclusion chromatography and centrifugation separation protocols were developed and compared for isolating enriched fractions of phenylethynyl-bridged metal nanoparticle dimers and trimers from the monomeric particle starting material. Both methods enabled the isolation of enriched fractions of a desired array without causing significant sample aggregation or replacement of the phenylethynyl bridge. Solutions containing ca. 70% bridged gold dimers were obtained using either method. The further development of methods for separating discrete arrays of covalently bridged nanoparticle homo and hetero structures is expected to help advance our understanding of collective metal particle electronic structure−function relationships.}, number={23}, journal={ANALYTICAL CHEMISTRY}, author={Novak, JP and Nickerson, C and Franzen, S and Feldheim, DL}, year={2001}, month={Dec}, pages={5758–5761} }
 @article{pop_chen_smith_bose_bobay_tripathy_franzen_clark_2001, title={Removal of the pro-domain does not affect the conformation of the procaspase-3 dimer}, volume={40}, ISSN={["0006-2960"]}, DOI={10.1021/bi011037e}, abstractNote={We have investigated the oligomeric properties of procaspase-3 and a mutant that lacks the pro-domain (called pro-less variant). In addition, we have examined the interactions of the 28 amino acid pro-peptide when added in trans to the pro-less variant. By sedimentation equilibrium studies, we have found that procapase-3 is a stable dimer in solution at 25 °C and pH 7.2, and we estimate an upper limit for the equilibrium dissociation constant of ∼50 nM. Considering the expression levels of caspase-3 in Jurkat cells, we predict that procaspase-3 exists as a dimer in vivo. The pro-less variant is also a dimer, with little apparent change in the equilibrium dissociation constant. Thus, in contrast with the long pro-domain caspases, the pro-peptide of caspase-3 does not appear to be involved in dimerization. Results from circular dichroism, fluorescence anisotropy, and FTIR studies demonstrate that the pro-domain interacts weakly with the pro-less variant. The data suggest that the pro-peptide adopts a β-structure when in contact with the protein, but it is a random coil when free in solution. In addition, when added in trans, the pro-peptide does not inhibit the activity of the mature caspase-3 heterotetramer. On the other hand, the active caspase-3 does not efficiently hydrolyze the pro-domain at the NSVD9 sequence as occurs when the pro-peptide is in cis to the protease domain. Based on these results, we propose a model for maturation of the procaspase-3 dimer.}, number={47}, journal={BIOCHEMISTRY}, author={Pop, C and Chen, YR and Smith, B and Bose, K and Bobay, B and Tripathy, A and Franzen, S and Clark, AC}, year={2001}, month={Nov}, pages={14224–14235} }