@article{popescu_dinh_chen_miller_washburn_mcguire_dumarieh_d'antonio_ghiladi_2022, title={Mossbauer studies of the ferryl, ferrous and ferric states of dehaloperoxidase from A. ornata}, volume={234}, ISSN={["1873-3344"]}, DOI={10.1016/j.jinorgbio.2022.111867}, abstractNote={Dehaloperoxidase (DHP) is a multi-functional catalytic globin from the marine worm A. ornata, whose physiological functions include oxygen transport and oxidation of toxic substrates present in its habitat. In the Fe(III) state, DHPA has an isomer shift of 0.42 mm/s, characteristic for high-spin heme proteins. Changes in pH have subtle effects on the electronic structure of DHP in the Fe(III) state detectable in the high-field spectra, which show a pH-dependent mixture of species with different zero-field splittings between 5 and 18 cm-1. The short-lived intermediate obtained by direct reaction of the Fe(III) enzyme with H2O2 has an isomer shift of 0.10 mm/s, indicative of an Fe(IV)-oxo state and of an S = 1 electronic ground state confirmed by variable field studies. The O2-bound state of DHP has an isomer shift of 0.28 mm/s and a high-field spectrum characteristic for diamagnetic heme complexes, similarly to other haemoglobins. Overall, the isomer shift and quadrupole splitting of DHP in the four states studied are expectedly similar to both peroxidases and to myoglobin. The differences in electronic structure between DHP and other heme proteins and enzyme are observed in the high-field Mössbauer spectra of the ferric state, which show pH-dependent zero-field splittings suggesting a heme site in which the ligand field strength at the iron ion is tuned by pH. This tunability is correlated with variable electron-donating properties of the iron, which can perform multiple functions.}, journal={JOURNAL OF INORGANIC BIOCHEMISTRY}, author={Popescu, C. V. and Dinh, Thanhminh and Chen, Hongli and Miller, Danielle and Washburn, Anastasia and McGuire, Ashlyn and Dumarieh, Rania and D'Antonio, Jennifer and Ghiladi, Reza A.}, year={2022}, month={Sep} }
 @article{mccombs_d’antonio_barrios_carey_ghiladi_2016, title={Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin fromAmphitrite ornata}, volume={55}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/acs.biochem.6b00143}, DOI={10.1021/acs.biochem.6b00143}, abstractNote={The marine hemoglobin dehaloperoxidase (DHP) from Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of nitrophenols, an unprecedented nonmicrobial degradation pathway for nitrophenols by a hemoglobin. Using 4-nitrophenol (4-NP) as a representative substrate, the major monooxygenated product was 4-nitrocatechol (4-NC). Isotope labeling studies confirmed that the O atom incorporated was derived exclusively from H2O2, indicative of a peroxygenase mechanism for 4-NP oxidation. Accordingly, X-ray crystal structures of 4-NP (1.87 Å) and 4-NC (1.98 Å) bound to DHP revealed a binding site in close proximity to the heme cofactor. Peroxygenase activity could be initiated from either the ferric or oxyferrous states with equivalent substrate conversion and product distribution. The 4-NC product was itself a peroxidase substrate for DHP, leading to the secondary products 5-nitrobenzene-triol and hydroxy-5-nitro-1,2-benzoquinone. DHP was able to react with 2,4-dinitrophenol (2,4-DNP) but was unreactive against 2,4,6-trinitrophenol (2,4,6-TNP). pH dependence studies demonstrated increased reactivity at lower pH for both 4-NP and 2,4-DNP, suggestive of a pH effect that precludes the reaction with 2,4,6-TNP at or near physiological conditions. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the mechanism of 4-NP oxidation. The results demonstrate that there may be a much larger number of nonmicrobial enzymes that are underrepresented when it comes to understanding the degradation of persistent organic pollutants such as nitrophenols in the environment.}, number={17}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={McCombs, Nikolette L. and D’Antonio, Jennifer and Barrios, David A. and Carey, Leiah M. and Ghiladi, Reza A.}, year={2016}, month={Apr}, pages={2465–2478} }
 @article{stockdale_murphy_d'antonio_manning_al-azzam_2015, title={Comparability of Higher Order Structure in Proteins: Chemometric Analysis of Second-Derivative Amide I Fourier Transform Infrared Spectra}, volume={104}, ISSN={["1520-6017"]}, DOI={10.1002/jps.24218}, abstractNote={Comparing higher order structure (HOS) in therapeutic proteins is a significant challenge. Previously, we showed that changes in solution conditions produced detectable changes in the second-derivative amide I Fourier transform infrared (FTIR) spectra for a variety of model proteins. Those comparisons utilized vector-based approaches, such as spectral overlap and spectral correlation coefficients to quantify differences between spectra. In this study, chemometric analyses of the same data were performed, to classify samples into different groups based on the solution conditions received. The solution conditions were composed of various combinations of temperature, pH, and salt types. At first, principal component analysis (PCA) was used to visually demonstrate that FTIR spectra respond to changes in solution conditions, which, presumably indicates variations in HOS. This observed when samples from the same solution condition form clusters within a PCA score plot. The second approach, called soft independent modeling of class analogy (SIMCA), was conducted to account for the within-class experimental error for the lysozyme spectra. The DModX values, indicative of the distance of each spectra to their respective class models, was found to be a more sensitive quantitative indicator of changes in HOS, when compared with the modified area of overlap algorithm. The SIMCA approach provides a metric to determine whether new observations do, or do not belong to a particular class or group. Thus, SIMCA is the recommended approach when multiple samples from each condition are available. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:25–33, 2015 Comparing higher order structure (HOS) in therapeutic proteins is a significant challenge. Previously, we showed that changes in solution conditions produced detectable changes in the second-derivative amide I Fourier transform infrared (FTIR) spectra for a variety of model proteins. Those comparisons utilized vector-based approaches, such as spectral overlap and spectral correlation coefficients to quantify differences between spectra. In this study, chemometric analyses of the same data were performed, to classify samples into different groups based on the solution conditions received. The solution conditions were composed of various combinations of temperature, pH, and salt types. At first, principal component analysis (PCA) was used to visually demonstrate that FTIR spectra respond to changes in solution conditions, which, presumably indicates variations in HOS. This observed when samples from the same solution condition form clusters within a PCA score plot. The second approach, called soft independent modeling of class analogy (SIMCA), was conducted to account for the within-class experimental error for the lysozyme spectra. The DModX values, indicative of the distance of each spectra to their respective class models, was found to be a more sensitive quantitative indicator of changes in HOS, when compared with the modified area of overlap algorithm. The SIMCA approach provides a metric to determine whether new observations do, or do not belong to a particular class or group. Thus, SIMCA is the recommended approach when multiple samples from each condition are available. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:25–33, 2015}, number={1}, journal={JOURNAL OF PHARMACEUTICAL SCIENCES}, author={Stockdale, Gregory and Murphy, Brian M. and D'Antonio, Jennifer and Manning, Mark Cornell and Al-Azzam, Wasfi}, year={2015}, month={Jan}, pages={25–33} }
 @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{murphy_d'antonio_manning_al-azzam_2014, title={Use of the Amide II Infrared Band of Proteins for Secondary Structure Determination and Comparability of Higher Order Structure}, volume={15}, ISSN={["1873-4316"]}, DOI={10.2174/1389201015666141012181609}, abstractNote={Demonstrating comparability of secondary structure composition as part of higher order structure (HOS) in therapeutic proteins is a significant challenge. Previously, we showed that the variability of second derivative amide I Fourier transform infrared (FTIR) spectra were small enough that significant differences in secondary structures could be seen for a variety of model proteins. Those comparisons used spectral overlap and spectral correlation coefficients to quantify spectral differences. However, many of the excipients used in downstream purification process, drug substance, and drug product formulation, such as free amino acids and sugars, can interfere with the absorbance in the amide I region. In this study, analysis of amide II FTIR spectra is shown as an alternative to using spectral data from the amide I region to analyze protein secondary structure to assess their HOS. This research provided spectral overlap and spectral correlation coefficient mathematical approaches for analysis of amide II FTIR spectra to demonstrate comparability of protein secondary structure. Spectral overlap and spectral correlation coefficients results show strong correlations between changes in the second derivative of amide II and amide I FTIR spectra for various model proteins under different conditions, which demonstrate the applicability of using amide II FTIR spectra for the comparability of protein secondary structure. These results indicate that the analysis of the second derivative of amide II FTIR spectra may be used to monitor and demonstrate comparability of protein secondary structure during downstream process and formulation development of protein therapeutics. Keywords: Amide I, Amide II, chemometrics, formulation development, FTIR, higher order structure, therapeutic proteins, secondary structure.}, number={9}, journal={CURRENT PHARMACEUTICAL BIOTECHNOLOGY}, author={Murphy, Brian M. and D'Antonio, Jennifer and Manning, Mark C. and Al-Azzam, Wasfi}, year={2014}, pages={880–889} }
 @article{d'antonio_murphy_manning_al-azzam_2012, title={Comparability of protein therapeutics: Quantitative comparison of second-derivative amide I infrared spectra}, volume={101}, ISSN={["0022-3549"]}, DOI={10.1002/jps.23133}, abstractNote={Comparability determination for protein therapeutics requires an assessment of their higher order structure, usually by using spectroscopic methods. One of the most common techniques used to determine secondary structure composition of proteins is analysis of the second derivative of the amide I region of Fourier transform infrared (FTIR) spectra. A number of algorithms have been described for quantitative comparison of second-derivative amide I FTIR spectra, but no systematic evaluation has been conducted to assess these approaches. In this study, the two most common methods, spectral correlation coefficient and area of overlap (AO), are compared for their ability to determine spectral comparability of a protein as a function of changes in pH or temperature. Two other algorithms were considered as well. Recently, a QC compare similarity function found in OMNIC software has been reported as being useful in comparing amide I FTIR spectra. In addition, a new algorithm, termed modified AO, is described herein. These four methods were evaluated for their ability to determine comparability for second-derivative amide I FTIR spectra of four model proteins. The result is a framework for quantitative determination of whether any two spectra differ significantly.}, number={6}, journal={JOURNAL OF PHARMACEUTICAL SCIENCES}, author={D'Antonio, Jennifer and Murphy, Brian M. and Manning, Mark Cornell and Al-Azzam, Wasfi A.}, year={2012}, month={Jun}, pages={2025–2033} }
 @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 H(2)O(2) 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 H(2)O(2) 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 H(2)O(2) 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 (13)C- and (15)N-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 N(δ) 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{d’antonio_ghiladi_2011, title={Reactivity of Deoxy- and Oxyferrous Dehaloperoxidase B fromAmphitrite ornata:Identification of Compound II and Its Ferrous–Hydroperoxide Precursor}, volume={50}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi200311u}, DOI={10.1021/bi200311u}, abstractNote={Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a bifunctional enzyme that possesses both hemoglobin and peroxidase activities. The bifunctional nature of DHP as a globin peroxidase appears to be at odds with the traditional starting oxidation state for each individual activity. Namely, reversible oxygen binding is only mediated via a ferrous heme in globins, and peroxidase activity is initiated from ferric centers and to the exclusion of the oxyferrous oxidation state from the peroxidase cycle. Thus, to address what appears to be a paradox, herein we report the details of our investigations into the DHP catalytic cycle when initiated from the deoxy- and oxyferrous states using biochemical assays, stopped-flow UV–visible, and rapid-freeze-quench electron paramagnetic resonance spectroscopies, and anaerobic methods. We demonstrate the formation of Compound II directly from deoxyferrous DHP B upon its reaction with hydrogen peroxide and show that this occurs both in the presence and in the absence of trihalophenol. Prior to the formation of Compound II, we have identified a new species that we have preliminarily attributed to a ferrous–hydroperoxide precursor that undergoes heterolysis to generate the aforementioned ferryl intermediate. Taken together, the results demonstrate that the oxyferrous state in DHP is a peroxidase competent starting species, and an updated catalytic cycle for DHP is proposed in which the ferric oxidation state is not an obligatory starting point for the peroxidase catalytic cycle of dehaloperoxidase. 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={27}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={D’Antonio, Jennifer and Ghiladi, Reza A.}, year={2011}, month={Jul}, pages={5999–6011} }
 @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} }