@article{schwabe_holzapfel_mattos_2020, title={Exploring the Rap1A Active Site Through Accelerated Molecular Dynamic Simulations}, volume={34}, ISSN={["1530-6860"]}, DOI={10.1096/fasebj.2020.34.s1.02775}, abstractNote={GTPases are hydrolytic proteins that convert GTP to GDP and serve as bivalent switches, where the GTP‐bound state is active, and the GDP‐bound state is inactive. Although Ras is the archetypal GTPase, Rap1A is closely related with 50% sequence homology and similar tertiary structure; a key difference occurs at position 61. In Ras Q61 participates in the hydrolysis mechanism and mutation leads to oncogenesis, while T61 in Rap1A is not thought to be involved in catalysis. The goal of this project is to explore the Rap1A active site and method of intrinsic hydrolysis. Two crystal structures were obtained with differing conformations of T61 in the Rap1A active site. Accelerated molecular dynamic simulations were run for 200 ns to sample the variety of motion present in Rap1A. Results indicate coordinated movements between the switch I, switch II, and helix 3 regions. Further, switch II appears less mobile than simulations with Ras isoforms.Support or Funding InformationMCB‐1517295, MCB‐0818678}, journal={FASEB JOURNAL}, author={Schwabe, Michael and Holzapfel, Genevieve and Mattos, Carla}, year={2020}, month={Apr} }
 @article{kearney_schwabe_marcus_roberts_dechene_swartz_mattos_2020, title={DRoP: Automated detection of conserved solvent-binding sites on proteins}, volume={88}, ISSN={["1097-0134"]}, DOI={10.1002/prot.25781}, abstractNote={AbstractWater and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X‐ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein‐protein or protein‐ligand interactions, as well as conserved water‐binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.}, number={1}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Kearney, Bradley M. and Schwabe, Michael and Marcus, Kendra C. and Roberts, Daniel M. and Dechene, Michelle and Swartz, Paul and Mattos, Carla}, year={2020}, month={Jan}, pages={152–165} }
 @article{knihtila_volmar_meilleur_mattos_2019, title={Titration of ionizable groups in proteins using multiple neutron data sets from a single crystal: application to the small GTPase Ras}, volume={75}, ISSN={["2053-230X"]}, url={https://doi.org/10.1107/S2053230X18018125}, DOI={10.1107/S2053230X18018125}, abstractNote={Neutron protein crystallography (NPC) reveals the three-dimensional structures of proteins, including the positions of H atoms. The technique is particularly suited to elucidate ambiguous catalytic steps in complex biochemical reactions. While NPC uniquely complements biochemical assays and X-ray structural analyses by revealing the protonation states of ionizable groups at and around the active site of enzymes, the technique suffers from a major drawback: large single crystals must be grown to compensate for the relatively low flux of neutron beams. However, in addition to revealing the positions of hydrogens involved in enzyme catalysis, NPC has the advantage over X-ray crystallography that the crystals do not suffer radiation damage. The lack of radiation damage can be exploited to conduct in crystallo parametric studies. Here, the use of a single crystal of the small GTPase Ras to collect three neutron data sets at pD 8.4, 9.0 and 9.4 is reported, enabling an in crystallo titration study using NPC. In addition to revealing the behavior of titratable groups in the active site, the data sets will allow the analysis of allosteric water-mediated communication networks across the molecule, particularly regarding Cys118 and three tyrosine residues central to these networks, Tyr32, Tyr96 and Tyr137, with pK
                  a values expected to be in the range sampled in our experiments.}, number={2}, journal={ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS}, publisher={International Union of Crystallography (IUCr)}, author={Knihtila, Ryan and Volmar, Alicia Y. and Meilleur, Flora and Mattos, Carla}, year={2019}, month={Feb}, pages={111–115} }
 @article{ashkar_bilheux_bordallo_briber_callaway_cheng_chu_curtis_dadmun_fenimore_et al._2018, title={Neutron scattering in the biological sciences: progress and prospects}, volume={74}, ISSN={["2059-7983"]}, DOI={10.1107/S2059798318017503}, abstractNote={The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.}, journal={ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY}, author={Ashkar, Rana and Bilheux, Hassina Z. and Bordallo, Heliosa and Briber, Robert and Callaway, David J. E. and Cheng, Xiaolin and Chu, Xiang-Qiang and Curtis, Joseph E. and Dadmun, Mark and Fenimore, Paul and et al.}, year={2018}, month={Dec}, pages={1129–1168} }
 @article{fetics_guterres_kearney_buhrman_ma_nussinov_mattos_2015, title={Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD}, volume={23}, ISSN={["1878-4186"]}, DOI={10.1016/j.str.2014.12.017}, abstractNote={The Ras/Raf/MEK/ERK signal transduction pathway is a major regulator of cell proliferation activated by Ras-guanosine triphosphate (GTP). The oncogenic mutant RasQ61L is not able to hydrolyze GTP in the presence of Raf and thus is a constitutive activator of this mitogenic pathway. The Ras/Raf interaction is essential for the activation of the Raf kinase domain through a currently unknown mechanism. We present the crystal structures of the Ras-GppNHp/Raf-RBD and RasQ61L-GppNHp/Raf-RBD complexes, which, in combination with MD simulations, reveal differences in allosteric interactions leading from the Ras/Raf interface to the Ras calcium-binding site and to the remote Raf-RBD loop L4. In the presence of Raf, the RasQ61L mutant has a rigid switch II relative to the wild-type and increased flexibility at the interface with switch I, which propagates across Raf-RBD. We show that in addition to local perturbations on Ras, RasQ61L has substantial long-range effects on the Ras allosteric lobe and on Raf-RBD.}, number={3}, journal={STRUCTURE}, author={Fetics, Susan K. and Guterres, Hugo and Kearney, Bradley M. and Buhrman, Greg and Ma, Buyong and Nussinov, Ruth and Mattos, Carla}, year={2015}, month={Mar}, pages={505–516} }
 @article{knihtila_holzapfel_weiss_meilleur_mattos_2015, title={Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP gamma-Phosphate}, volume={290}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m115.679860}, abstractNote={Background: The GTP nucleotide is thought to be fully deprotonated when bound to RAS. Results: The neutron crystal structure of RAS bound to the GTP analogue GppNHp shows a protonated γ-phosphate. Conclusion: The active site of RAS significantly increases the pKa of the nucleotide. Significance: This work provides insight to the GTP hydrolysis mechanism, with implications to the superfamily of small GTPases. RAS GTPase is a prototype for nucleotide-binding proteins that function by cycling between GTP and GDP, with hydrogen atoms playing an important role in the GTP hydrolysis mechanism. It is one of the most well studied proteins in the superfamily of small GTPases, which has representatives in a wide range of cellular functions. These proteins share a GTP-binding pocket with highly conserved motifs that promote hydrolysis to GDP. The neutron crystal structure of RAS presented here strongly supports a protonated γ-phosphate at physiological pH. This counters the notion that the phosphate groups of GTP are fully deprotonated at the start of the hydrolysis reaction, which has colored the interpretation of experimental and computational data in studies of the hydrolysis mechanism. The neutron crystal structure presented here puts in question our understanding of the pre-catalytic state associated with the hydrolysis reaction central to the function of RAS and other GTPases.}, number={52}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Knihtila, Ryan and Holzapfel, Genevieve and Weiss, Kevin and Meilleur, Flora and Mattos, Carla}, year={2015}, month={Dec}, pages={31025–31036} }
 @article{kearney_johnson_roberts_swartz_mattos_2014, title={DRoP: A Water Analysis Program Identifies Ras-GTP-Specific Pathway of Communication between Membrane-Interacting Regions and the Active Site}, volume={426}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2013.10.036}, abstractNote={Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras.}, number={3}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Kearney, Bradley Ni. and Johnson, Christian W. and Roberts, Daniel M. and Swartz, Paul and Mattos, Carla}, year={2014}, month={Feb}, pages={611–629} }
 @article{walters_schipper_swartz_mattos_clark_2012, title={Allosteric modulation of caspase 3 through mutagenesis}, volume={32}, ISSN={["0144-8463"]}, DOI={10.1042/bsr20120037}, abstractNote={A mutation in the allosteric site of the caspase 3 dimer interface of Val266 to histidine abolishes activity of the enzyme, and models predict that the mutation mimics the action of small molecule allosteric inhibitors by preventing formation of the active site. Mutations were coupled to His266 at two sites in the interface, E124A and Y197C. We present results from X-ray crystallography, enzymatic activity and molecular dynamics simulations for seven proteins, consisting of single, double and triple mutants. The results demonstrate that considering allosteric inhibition of caspase 3 as a shift between discrete ‘off-state’ or ‘on-state’ conformations is insufficient. Although His266 is accommodated in the interface, the structural defects are propagated to the active site through a helix on the protein surface. A more comprehensive view of allosteric regulation of caspase 3 requires the representation of an ensemble of inactive states and shows that subtle structural changes lead to the population of the inactive ensemble.}, number={4}, journal={BIOSCIENCE REPORTS}, author={Walters, Jad and Schipper, Joshua L. and Swartz, Paul and Mattos, Carla and Clark, A. Clay}, year={2012}, month={Aug}, pages={401–411} }
 @article{holzapfel_buhrman_mattos_2012, title={Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition}, volume={51}, ISSN={["0006-2960"]}, DOI={10.1021/bi300509j}, abstractNote={Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the "on" state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the "ordered off" state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-β. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.}, number={31}, journal={BIOCHEMISTRY}, author={Holzapfel, Genevieve and Buhrman, Greg and Mattos, Carla}, year={2012}, month={Aug}, pages={6114–6126} }
 @article{gagnon_biswas_zhang_brown_wollenzien_mattos_maxwell_2012, title={Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity}, volume={287}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m111.323253}, abstractNote={Background: Box C/D RNPs direct site-specific 2′-O-methylation of rRNA. Results: The Nop56/58 and fibrillarin core proteins establish a very stable dimer with Nop56/58 contributing to methyltransferase activity. Conclusion: The Nop56/58 core protein plays a role not only in RNP assembly, but also methyltransferase activity. Significance: Our observations reveal a novel role for the Nop56/58 core protein in box C/D RNP function. Box C/D RNA-protein complexes (RNPs) guide the 2′-O-methylation of nucleotides in both archaeal and eukaryotic ribosomal RNAs. The archaeal box C/D and C′/D′ RNP subcomplexes are each assembled with three sRNP core proteins. The archaeal Nop56/58 core protein mediates crucial protein-protein interactions required for both sRNP assembly and the methyltransferase reaction by bridging the L7Ae and fibrillarin core proteins. The interaction of Methanocaldococcus jannaschii (Mj) Nop56/58 with the methyltransferase fibrillarin has been investigated using site-directed mutagenesis of specific amino acids in the N-terminal domain of Nop56/58 that interacts with fibrillarin. Extensive mutagenesis revealed an unusually strong Nop56/58-fibrillarin interaction. Only deletion of the NTD itself prevented dimerization with fibrillarin. The extreme stability of the Nop56/58-fibrillarin heterodimer was confirmed in both chemical and thermal denaturation analyses. However, mutations that did not affect Nop56/58 binding to fibrillarin or sRNP assembly nevertheless disrupted sRNP-guided nucleotide modification, revealing a role for Nop56/58 in methyltransferase activity. This conclusion was supported with the cross-linking of Nop56/58 to the target RNA substrate. The Mj Nop56/58 NTD was further characterized by solving its three-dimensional crystal structure to a resolution of 1.7 Å. Despite low primary sequence conservation among the archaeal Nop56/58 homologs, the overall structure of the archaeal NTD domain is very well conserved. In conclusion, the archaeal Nop56/58 NTD exhibits a conserved domain structure whose exceptionally stable interaction with fibrillarin plays a role in both RNP assembly and methyltransferase activity.}, number={23}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Gagnon, Keith T. and Biswas, Shyamasri and Zhang, Xinxin and Brown, Bernard A., II and Wollenzien, Paul and Mattos, Carla and Maxwell, E. Stuart}, year={2012}, month={Jun}, pages={19418–19428} }
 @article{biswas_buhrman_gagnon_mattos_brown_maxwell_2011, title={Comparative Analysis of the 15.5kD Box C/D snoRNP Core Protein in the Primitive Eukaryote Giardia lamblia Reveals Unique Structural and Functional Features}, volume={50}, ISSN={["0006-2960"]}, DOI={10.1021/bi1020474}, abstractNote={Box C/D ribonucleoproteins (RNP) guide the 2'-O-methylation of targeted nucleotides in archaeal and eukaryotic rRNAs. The archaeal L7Ae and eukaryotic 15.5kD box C/D RNP core protein homologues initiate RNP assembly by recognizing kink-turn (K-turn) motifs. The crystal structure of the 15.5kD core protein from the primitive eukaryote Giardia lamblia is described here to a resolution of 1.8 Å. The Giardia 15.5kD protein exhibits the typical α-β-α sandwich fold exhibited by both archaeal L7Ae and eukaryotic 15.5kD proteins. Characteristic of eukaryotic homologues, the Giardia 15.5kD protein binds the K-turn motif but not the variant K-loop motif. The highly conserved residues of loop 9, critical for RNA binding, also exhibit conformations similar to those of the human 15.5kD protein when bound to the K-turn motif. However, comparative sequence analysis indicated a distinct evolutionary position between Archaea and Eukarya. Indeed, assessment of the Giardia 15.5kD protein in denaturing experiments demonstrated an intermediate stability in protein structure when compared with that of the eukaryotic mouse 15.5kD and archaeal Methanocaldococcus jannaschii L7Ae proteins. Most notable was the ability of the Giardia 15.5kD protein to assemble in vitro a catalytically active chimeric box C/D RNP utilizing the archaeal M. jannaschii Nop56/58 and fibrillarin core proteins. In contrast, a catalytically competent chimeric RNP could not be assembled using the mouse 15.5kD protein. Collectively, these analyses suggest that the G. lamblia 15.5kD protein occupies a unique position in the evolution of this box C/D RNP core protein retaining structural and functional features characteristic of both archaeal L7Ae and higher eukaryotic 15.5kD homologues.}, number={14}, journal={BIOCHEMISTRY}, author={Biswas, Shyamasri and Buhrman, Greg and Gagnon, Keith and Mattos, Carla and Brown, Bernard A., II and Maxwell, E. Stuart}, year={2011}, month={Apr}, pages={2907–2918} }
 @article{walters_swartz_mattos_clark_2011, title={Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3}, volume={508}, ISSN={["1096-0384"]}, DOI={10.1016/j.abb.2011.01.011}, abstractNote={Interactions between loops 2, 2′ and 4, known as the loop bundle, stabilize the active site of caspase-3. Loop 4 (L4) is of particular interest due to its location between the active site and the dimer interface. We have disrupted a salt bridge between K242 and E246 at the base of L4 to determine its role in overall conformational stability and in maintaining the active site environment. Stability measurements show that only the K242A single mutant decreases stability of the dimer, whereas both single mutants and the double mutant demonstrate much lower activity compared to wild-type caspase-3. Structural studies of the caspase-3 variants show the involvement of K242 in hydrophobic interactions that stabilize helix 5, near the dimer interface, and the role of E246 appears to be to neutralize the positive charge of K242 within the hydrophobic cluster. Overall, the results suggest E246 and K242 are important in procaspase-3 for their interaction with neighboring residues, not with one another. Conversely, formation of the K242–E246 salt bridge in caspase-3 is needed for an accurate, stable conformation of loop L4 and proper active site formation in the mature enzyme.}, number={1}, journal={ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS}, author={Walters, Jad and Swartz, Paul and Mattos, Carla and Clark, A. Clay}, year={2011}, month={Apr}, pages={31–38} }
 @article{buhrman_kumar_cirit_haugh_mattos_2011, title={Allosteric Modulation of Ras-GTP Is Linked to Signal Transduction through RAF Kinase}, volume={286}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m110.193854}, abstractNote={Ras is a key signal transduction protein in the cell. Mutants of Gly12 and Gln61 impair GTPase activity and are found prominently in cancers. In wild type Ras-GTP, an allosteric switch promotes disorder to order transition in switch II, placing Gln61 in the active site. We show that the “on” and “off” conformations of the allosteric switch can also be attained in RasG12V and RasQ61L. Although both mutants have similarly impaired active sites in the on state, RasQ61L stabilizes an anti-catalytic conformation of switch II in the off state of the allosteric switch when bound to Raf. This translates into more potent activation of the MAPK pathway involving Ras, Raf kinase, MEK, and ERK (Ras/Raf/MEK/ERK) in cells transfected with RasQ61L relative to RasG12V. This differential is not observed in the Raf-independent pathway involving Ras, phosphoinositide 3-kinase (PI3K), and Akt (Ras/PI3K/Akt). Using a combination of structural analysis, hydrolysis rates, and experiments in NIH-3T3 cells, we link the allosteric switch to the control of signaling in the Ras/Raf/MEK/ERK pathway, supporting a GTPase-activating protein-independent model for duration of the Ras-Raf complex.}, number={5}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Buhrman, Greg and Kumar, V. S. Senthil and Cirit, Murat and Haugh, Jason M. and Mattos, Carla}, year={2011}, month={Feb}, pages={3323–3331} }
 @article{buhrman_holzapfel_fetics_mattos_2010, title={Allosteric modulation of Ras positions Q61 for a direct role in catalysis}, volume={107}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0912226107}, abstractNote={
            Ras and its effector Raf are key mediators of the Ras/Raf/MEK/ERK signal transduction pathway. Mutants of residue Q61 impair the GTPase activity of Ras and are found prominently in human cancers. Yet the mechanism through which Q61 contributes to catalysis has been elusive. It is thought to position the catalytic water molecule for nucleophilic attack on the γ-phosphate of GTP. However, we previously solved the structure of Ras from crystals with symmetry of the space group R32 in which switch II is disordered and found that the catalytic water molecule is present. Here we present a structure of wild-type Ras with calcium acetate from the crystallization mother liquor bound at a site remote from the active site and likely near the membrane. This results in a shift in helix 3/loop 7 and a network of H-bonding interactions that propagates across the molecule, culminating in the ordering of switch II and placement of Q61 in the active site in a previously unobserved conformation. This structure suggests a direct catalytic role for Q61 where it interacts with a water molecule that bridges one of the γ-phosphate oxygen atoms to the hydroxyl group of Y32 to stabilize the transition state of the hydrolysis reaction. We propose that Raf together with the binding of Ca
            2+
            and a negatively charged group mimicked in our structure by the acetate molecule induces the ordering of switch I and switch II to complete the active site of Ras.
          }, number={11}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Buhrman, Greg and Holzapfel, Genevieve and Fetics, Susan and Mattos, Carla}, year={2010}, month={Mar}, pages={4931–4936} }
 @article{walters_pop_scott_drag_swartz_mattos_salvesen_clark_2009, title={A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis}, volume={424}, ISSN={["1470-8728"]}, DOI={10.1042/bj20090825}, abstractNote={The caspase-3 zymogen has essentially zero activity until it is cleaved by initiator caspases during apoptosis. However, a mutation of V266E in the dimer interface activates the protease in the absence of chain cleavage. We show that low concentrations of the pseudo-activated procaspase-3 kill mammalian cells rapidly and, importantly, this protein is not cleaved nor is it inhibited efficiently by the endogenous regulator XIAP (X-linked inhibitor of apoptosis). The 1.63 Å (1 Å = 0.1 nm) structure of the variant demonstrates that the mutation is accommodated at the dimer interface to generate an enzyme with substantially the same activity and specificity as wild-type caspase-3. Structural modelling predicts that the interface mutation prevents the intersubunit linker from binding in the dimer interface, allowing the active sites to form in the procaspase in the absence of cleavage. The direct activation of procaspase-3 through a conformational switch rather than by chain cleavage may lead to novel therapeutic strategies for inducing cell death.}, journal={BIOCHEMICAL JOURNAL}, author={Walters, Jad and Pop, Cristina and Scott, Fiona L. and Drag, Marcin and Swartz, Paul and Mattos, Carla and Salvesen, Guy S. and Clark, A. Clay}, year={2009}, month={Dec}, pages={335–345} }
 @article{brenke_kozakov_chuang_beglov_hall_landon_mattos_vajda_2009, title={Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques}, volume={25}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/btp036}, abstractNote={Abstract
               Motivation: The binding sites of proteins generally contain smaller regions that provide major contributions to the binding free energy and hence are the prime targets in drug design. Screening libraries of fragment-sized compounds by NMR or X-ray crystallography demonstrates that such ‘hot spot’ regions bind a large variety of small organic molecules, and that a relatively high ‘hit rate’ is predictive of target sites that are likely to bind drug-like ligands with high affinity. Our goal is to determine the ‘hot spots’ computationally rather than experimentally.
               Results: We have developed the FTMAP algorithm that performs global search of the entire protein surface for regions that bind a number of small organic probe molecules. The search is based on the extremely efficient fast Fourier transform (FFT) correlation approach which can sample billions of probe positions on dense translational and rotational grids, but can use only sums of correlation functions for scoring and hence is generally restricted to very simple energy expressions. The novelty of FTMAP is that we were able to incorporate and represent on grids a detailed energy expression, resulting in a very accurate identification of low-energy probe clusters. Overlapping clusters of different probes are defined as consensus sites (CSs). We show that the largest CS is generally located at the most important subsite of the protein binding site, and the nearby smaller CSs identify other important subsites. Mapping results are presented for elastase whose structure has been solved in aqueous solutions of eight organic solvents, and we show that FTMAP provides very similar information. The second application is to renin, a long-standing pharmaceutical target for the treatment of hypertension, and we show that the major CSs trace out the shape of the first approved renin inhibitor, aliskiren.
               Availability: FTMAP is available as a server at http://ftmap.bu.edu/.
               Contact:  vajda@bu.edu
               Supplementary information:  Supplementary Material is available at Bioinformatics online.}, number={5}, journal={BIOINFORMATICS}, author={Brenke, Ryan and Kozakov, Dima and Chuang, Gwo-Yu and Beglov, Dmitri and Hall, David and Landon, Melissa R. and Mattos, Carla and Vajda, Sandor}, year={2009}, month={Mar}, pages={621–627} }
 @article{dechene_wink_smith_swartz_mattos_2009, title={Multiple solvent crystal structures of ribonuclease A: An assessment of the method}, volume={76}, ISSN={["1097-0134"]}, DOI={10.1002/prot.22393}, abstractNote={AbstractThe multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6‐hexanediol, 70% isopropanol, 50% R,S,R‐bisfuran alcohol, 70% t‐butanol, 50% trifluoroethanol, or 1.0M trimethylamine‐N‐oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor‐bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot‐spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS. Proteins 2009. © 2009 Wiley‐Liss, Inc.}, number={4}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Dechene, Michelle and Wink, Glenna and Smith, Mychal and Swartz, Paul and Mattos, Carla}, year={2009}, month={Sep}, pages={861–881} }
 @misc{mattos_clark_2008, title={Minimizing frustration by folding in an aqueous environment}, volume={469}, number={1}, journal={Archives of Biochemistry and Biophysics}, author={Mattos, C. and Clark, A. C.}, year={2008}, pages={118–131} }
 @article{milam_nicely_feeney_mattos_clark_2007, title={Rapid folding and unfolding of Apaf-1 CARD}, volume={369}, ISSN={["0022-2836"]}, DOI={10.1016/j.jmb.2007.02.105}, abstractNote={Caspase recruitment domains (CARDs) are members of the death domain superfamily and contain six antiparallel helices in an α-helical Greek key topology. We have examined the equilibrium and kinetic folding of the CARD of Apaf-1 (apoptotic protease activating factor 1), which consists of 97 amino acid residues, at pH 6 and pH 8. The results showed that an apparent two state equilibrium mechanism is not adequate to describe the folding of Apaf-1 CARD at either pH, suggesting the presence of intermediates in equilibrium unfolding. Interestingly, the results showed that the secondary structure is less stable than the tertiary structure, based on the transition mid-points for unfolding. Single mixing and sequential mixing stopped-flow studies showed that Apaf-1 CARD folds and unfolds rapidly and suggest a folding mechanism that contains parallel channels with two unfolded conformations folding to the native conformation. Kinetic simulations show that a slow folding phase is described by a third conformation in the unfolded ensemble that interconverts with one or both unfolded species. Overall, the native ensemble is formed rapidly upon refolding. This is in contrast to other CARDs in which folding appears to be dominated by formation of kinetic traps.}, number={1}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Milam, Sara L. and Nicely, Nathan I. and Feeney, Brett and Mattos, Carla and Clark, A. Clay}, year={2007}, month={May}, pages={290–304} }
 @article{buhrman_wink_mattos_2007, title={Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf}, volume={15}, ISSN={["1878-4186"]}, DOI={10.1016/j.str.2007.10.011}, abstractNote={<h2>Summary</h2> Transformation efficiencies of Ras mutants at residue 61 range over three orders of magnitude, but the in vitro GTPase activity decreases 10-fold for all mutants. We show that Raf impairs the GTPase activity of RasQ61L, suggesting that the Ras/Raf complex differentially modulates transformation. Our crystal structures show that, in transforming mutants, switch II takes part in a network of hydrophobic interactions burying the nucleotide and precatalytic water molecule. Our results suggest that Y32 and a water molecule bridging it to the γ-phosphate in the wild-type structure play a role in GTP hydrolysis in lieu of the Arg finger in the absence of GAP. The bridging water molecule is absent in the transforming mutants, contributing to the burying of the nucleotide. We propose a mechanism for intrinsic hydrolysis in Raf-bound Ras and elucidate structural features in the Q61 mutants that correlate with their potency to transform cells.}, number={12}, journal={STRUCTURE}, author={Buhrman, Greg and Wink, Glenna and Mattos, Carla}, year={2007}, month={Dec}, pages={1618–1629} }
 @article{mattos_bellamacina_peisach_pereira_vitkup_petsko_ringe_2006, title={Multiple solvent crystal structures: Probing binding sites, plasticity and hydration}, volume={357}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2006.01.039}, abstractNote={Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design.}, number={5}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Mattos, C and Bellamacina, CR and Peisach, E and Pereira, A and Vitkup, D and Petsko, GA and Ringe, D}, year={2006}, month={Apr}, pages={1471–1482} }
 @article{feeney_pop_swartz_mattos_clark_2006, title={Role of loop bundle hydrogen bonds in the maturation and activity of (pro) caspase-3}, volume={45}, ISSN={["0006-2960"]}, DOI={10.1021/bi0611964}, abstractNote={During maturation, procaspase-3 is cleaved at D175, which resides in a linker that connects the large and small subunits. The intersubunit linker also connects two active site loops that rearrange following cleavage and, in part, form the so-called loop bundle. As a result of chain cleavage, new hydrogen bonds and van der Waals contacts form among three active site loops. The new interactions are predicted to stabilize the active site. One unresolved issue is the extent to which the loop bundle residues also stabilize the procaspase active site. We examined the effects of replacing four loop bundle residues (E167, D169, E173, and Y203) on the biochemical and structural properties of the (pro)caspase. We show that replacing the residues affects the activity of the procaspase as well as the mature caspase, with D169A and E167A replacements having the largest effects. Replacement of D169 prevents caspase-3 autoactivation, and its cleavage at D175 no longer leads to an active enzyme. In addition, the E173A mutation, when coupled to a second mutation in the procaspase, D175A, may alter the substrate specificity of the procaspase. The mutations affected the active site environment as assessed by changes in fluorescence emission, accessibility to quencher, and cleavage by either trypsin or V8 proteases. High-resolution X-ray crystallographic structures of E167A, D173A, and Y203F caspases show that changes in the active site environment may be due to the increased flexibility of several residues in the N-terminus of the small subunit. Overall, the results show that these residues are important for stabilizing the procaspase active site as well as that of the mature caspase.}, number={44}, journal={BIOCHEMISTRY}, author={Feeney, Brett and Pop, Cristina and Swartz, Paul and Mattos, Carla and Clark, A. Clay}, year={2006}, month={Nov}, pages={13249–13263} }
 @article{buhrman_parker_sohn_rudolph_mattos_2005, title={Structural mechanism of oxidative regulation of the phosphatase Cdc25B via an intramolecular disulfide bond}, volume={44}, ISSN={["0006-2960"]}, DOI={10.1021/bi047449f}, abstractNote={Cdc25B phosphatase, an important regulator of the cell cycle, forms an intramolecular disulfide bond in response to oxidation leading to reversible inactivation of phosphatase activity. We have obtained a crystallographic time course revealing the structural rearrangements that occur in the P-loop as the enzyme goes from its apo state, through the sulfenic (Cys-SO(-)) intermediate, to the stable disulfide. We have also obtained the structures of the irreversibly oxidized sulfinic (Cys-SO(2)(-)) and sulfonic (Cys-SO(3)(-)) Cdc25B. The active site P-loop is found in three conformations. In the apoenzyme, the P-loop is in the active conformation. In the sulfenic intermediate, the P-loop partially obstructs the active site cysteine, poised to undergo the conformational changes that accompany disulfide bond formation. In the disulfide form, the P-loop is closed over the active site cysteine, resulting in an enzyme that is unable to bind substrate. The structural changes that occur in the sulfenic intermediate of Cdc25B are distinctly different from those seen in protein tyrosine phosphatase 1B where a five-membered sulfenyl amide ring is generated as the stable end product. This work elucidates the mechanism by which chemistry and structure are coupled in the regulation of Cdc25B by reactive oxygen species.}, number={14}, journal={BIOCHEMISTRY}, author={Buhrman, G and Parker, B and Sohn, J and Rudolph, J and Mattos, C}, year={2005}, month={Apr}, pages={5307–5316} }
 @article{nicely_kosak_serrano_mattos_2004, title={Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap}, volume={12}, ISSN={["1878-4186"]}, DOI={10.1016/j.str.2004.08.011}, abstractNote={RalA is a GTPase with effectors such as Sec5 and Exo84 in the exocyst complex and RalBP1, a GAP for Rho proteins. We report the crystal structures of Ral-GppNHp and Ral-GDP. Disordered switch I and switch II, located away from crystal contacts, are observed in one of the molecules in the asymmetric unit of the Ral-GppNHp structure. In the other molecule in the asymmetric unit, a second Mg(2+) ion is bound to the GppNHp gamma-phosphate in an environment in which switch I is pulled away from the nucleotide and switch II is found in a tight beta turn. Clustering of conserved residues on the surface of Ral-GppNHp identifies two putative sites for protein-protein interaction. One site is adjacent to switch I. The other is modulated by switch II and is obstructed in Ral-GDP. The Ral structures are discussed in the context of the published structures of the Ral/Sec5 complex, Ras, and Rap.}, number={11}, journal={STRUCTURE}, author={Nicely, NI and Kosak, J and Serrano, V and Mattos, C}, year={2004}, month={Nov}, pages={2025–2036} }
 @article{mattos_cohen_green_tidor_karplus_2004, title={X-ray structural and simulation analysis of a protein mutant: The value of a combined approach}, volume={55}, ISSN={["1097-0134"]}, DOI={10.1002/prot.20031}, abstractNote={AbstractThe effect of the mutation Arg 96 to His on the stability of bacteriophage T4 lysozyme has been previously studied by calorimetric experiments, X‐ray crystallography, and free energy simulation techniques. The experimental and calculated values for the difference between the free energy of denaturation of the mutant and the wild type are in reasonable agreement. However, the two approaches led to different explanations for the loss in stability. To analyze the differences, a series of refinements based on the crystallographic data were performed, a number of aspects of the simulations were reexamined, and continuum electrostatic calculations were done to complement the latter. The results of those comparisons provide a better understanding of the origin of the free energy difference in this mutant. Furthermore, they show the importance of the combined use of simulations and crystallography for interpreting the effects of mutations on the energetics of the system. Proteins 2004. © 2004 Wiley‐Liss, Inc.}, number={3}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Mattos, C and Cohen, JD and Green, DF and Tidor, B and Karplus, M}, year={2004}, month={May}, pages={733–742} }
 @article{buhrman_serrano_mattos_2003, title={Organic solvents order the dynamic switch II in Ras crystals}, volume={11}, ISSN={["1878-4186"]}, DOI={10.1016/s0969-2126(03)00128-x}, abstractNote={Room temperature crystal structures of crosslinked H-Ras bound to GMPPNP were solved in 50% 2,2,2-trifluoroethanol, 60% 1,6-hexanediol, and 50% isopropanol. The disordered switch II region of Ras is ordered in the presence of 2,2,2-trifluoroethanol or 1,6-hexanediol. The overall backbone conformation of switch II in these organic solvents is the same as in the Ras-GMPPNP complexes with RalGDS, PI3 kinase, and RasGAP, indicating a biologically relevant form. Key polar interactions that stabilize the ordered switch are enhanced in the presence of hydrophobic cosolvents. These results suggest that hydrophobic solvents can be used in general to order short biologically relevant segments of disordered regions in protein crystals by favoring H-bonding interactions between atoms that are highly solvated and mobile in aqueous solution.}, number={7}, journal={STRUCTURE}, author={Buhrman, G and Serrano, V and Mattos, C}, year={2003}, month={Jul}, pages={747–751} }
 @misc{mattos_2002, title={Protein-water interactions in a dynamic world}, volume={27}, number={4}, journal={Trends in Biochemical Sciences}, author={Mattos, C.}, year={2002}, pages={203–208} }
 @article{mattos_ringe_2001, title={Proteins in organic solvents}, volume={11}, ISSN={["0959-440X"]}, DOI={10.1016/S0959-440X(01)00278-0}, abstractNote={Catalysis in organic solvents and the mapping of protein surfaces using multiple solvent crystal structures are two rapidly developing areas of research. Recent advances include the study of protein folding and stability in different solvents, and the demonstration that it is possible to qualitatively rank the affinities of protein binding sites for a given organic solvent using the multiple solvent crystal structures method.}, number={6}, journal={CURRENT OPINION IN STRUCTURAL BIOLOGY}, author={Mattos, C and Ringe, D}, year={2001}, month={Dec}, pages={761–764} }