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| A WarshelSummaryAffiliation: University of Southern California Country: USA Publications
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Publications
Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional propertiesArieh Warshel
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
Proteins 79:3469-84. 2011..We also emphasize recent advances in coarse grained models with a physically based electrostatic treatment and provide some examples including further directions in treating voltage activated ion channels...
Inverting the selectivity of aquaporin 6: gating versus direct electrostatic interactionArieh Warshel
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
Proc Natl Acad Sci U S A 102:1813-4. 2005- Exploring the role of large conformational changes in the fidelity of DNA polymerase betaYun Xiang
Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
Proteins 70:231-47. 2008..The generation of free energy surfaces for R and W also allow us to analyze proposals about the relationship between induced fit and fidelity... 
Modeling electrostatic effects in proteinsArieh Warshel
University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
Biochim Biophys Acta 1764:1647-76. 2006....- Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomeraseArieh Warshel
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
Biochemistry 46:1466-76. 2007..It seems to us that this work provides an excellent example of the need for computational studies in analyzing key experimental findings about enzyme catalysis... - Electrostatic basis for enzyme catalysisArieh Warshel
Department of Chemistry, University of Southern California, SGM Building 418, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
Chem Rev 106:3210-35. 2006 - Protein control of iron-sulfur cluster redox potentialsR Langen
Department of Chemistry, University of Southern California, Los Angeles 90089 0482
J Biol Chem 267:25625-7. 1992..Our calculations provide the first successful quantitative modeling of the protein control of iron-sulfur cluster redox potentials... - Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mappingYun Xiang
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
J Phys Chem B 112:1007-15. 2008..Our results point out that the present implementation of the FDFT approach provides a very promising approach for evaluating QM(ai)/MM free energy surfaces... - Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerasesJan Florian
Department of Chemistry, Loyola University, Chicago, IL 60626, USA
Proc Natl Acad Sci U S A 102:6819-24. 2005..The calculations demonstrate the potential for further integration of theoretical and experimental studies to analyze high- and low-fidelity DNA polymerases... - The empirical valence bond as an effective strategy for computer-aided enzyme designAlexandra Vardi-Kilshtain
Department of Chemistry, University of Southern California, Los Angeles, USA
Biotechnol J 4:495-500. 2009..The ability of the model to predict quantitatively the catalytic power of enzymes should augment the capacity of current approaches for enzyme design... - Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progressA Shurki
Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
Adv Protein Chem 66:249-313. 2003 - Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductaseHanbin Liu
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
J Phys Chem B 111:7852-61. 2007.... - Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based modelsSonja Braun-Sand
Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
Biophys J 87:2221-39. 2004.... - The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energiesHanbin Liu
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
Biochemistry 46:6011-25. 2007..Thus, as far as catalysis is concerned, the change in the activation barrier is due to the change in the electrostatic preorganization energy... - On the origin of the electrostatic barrier for proton transport in aquaporinAnton Burykin
Department of Chemistry, University of Southern California, 3620 McClintock Ave. SGM 418, Los Angeles, CA 90089-1062, USA
FEBS Lett 570:41-6. 2004..Using this definition and "mutating" the NPA residues to their non-polar analogues establishes that these residues do not provide the major contribution to the solvation barrier... - Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systemsMats H M Olsson
Department of Chemistry, University of Southern California, 3620 South McClintock Avenue, Los Angeles, CA 90089-1062, USA
Philos Trans R Soc Lond B Biol Sci 361:1417-32. 2006.... - Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase betaChristopher A Sucato
Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
Biochemistry 46:461-71. 2007..The results are addressed theoretically in terms of the energetics of successive primer 3'-O addition (bond forming) and pyrophosphate analogue elimination (bond breaking) reaction energy barriers... - How much do enzymes really gain by restraining their reacting fragments?A Shurki
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
J Am Chem Soc 124:4097-107. 2002..This solvent-induced effect is quite different from the traditional picture of balance between the repulsive interaction of the reactive fragments and the steric force of the protein... - DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strengthVaclav Martinek
Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
FEBS Lett 581:775-80. 2007..This finding is consistent with the view that enzyme preorganization plays a major role in controlling DNA polymerase specific activity... - DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition stateChristopher A Sucato
Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
Biochemistry 47:870-9. 2008..Solvent pH and deuterium isotope-effect data are also used to evaluate mechanistic differences between correct and mispaired incorporation... - Predicting drug-resistant mutations of HIV proteaseHiroshi Ishikita
Department of Chemistry, University of Southern California, 418 SGM Building, Los Angeles, CA 90089, USA
Angew Chem Int Ed Engl 47:697-700. 2008 - What are the dielectric "constants" of proteins and how to validate electrostatic models?C N Schutz
Department of Chemistry, University of Southern California, Los Angeles, California, USA
Proteins 44:400-17. 2001..These include the effect of water penetration and the effect of the protein reorganization. Finally, we show that the optimal dielectric constant for self-energies is not the optimal constant for charge-charge interactions... - The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculationsMitsunori Kato
Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
Proteins 64:829-44. 2006..Such calculations also help to clarify the crucial role of solvation energies in establishing the barrier in aquaporins... - Effective approach for calculations of absolute stability of proteins using focused dielectric constantsSpyridon Vicatos
Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
Proteins 77:670-84. 2009..8 kcal/mole compared to the observed values, making our method very promising for estimating protein stability. It also provides valuable insight into the complex electrostatic phenomena taking place in folded proteins... - Enzyme millisecond conformational dynamics do not catalyze the chemical stepAndrei V Pisliakov
Department of Chemistry SGM 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089, USA
Proc Natl Acad Sci U S A 106:17359-64. 2009..Nevertheless, the precise nature of this coupling is a question of great importance... - What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposalsAnton Burykin
Department of Chemistry, University of Southern California, Los Angeles, California, USA
Biophys J 85:3696-706. 2003..However, in cases of biological channels, the actual PT mechanism is much less important than the energetics of transferring the proton charge from water to different regions in the channels... - On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactionsMarco Klahn
Department of Chemistry, University of Southern California, 3620 South McClintock Avenue, Los Angeles, California 90089 1062, USA
J Phys Chem B 109:15645-50. 2005..The possible relevance of our conclusion with regard to a recent study of the RasGAP reaction is discussed... - On the origin of the catalytic power of carboxypeptidase A and other metalloenzymesAlexandra Vardi Kilshtain
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
Proteins 77:536-50. 2009..This and earlier studies show that the catalytic effect of the metal is not some constant electrostatic effect, that can be assessed from gas phase studies, but a reflection of the dielectric effect of the specific environment... - Dineopentyl phosphate hydrolysis: evidence for stepwise water attackShina C L Kamerlin
Department of Chemistry, SGM 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA
J Org Chem 73:6960-9. 2008..Our data show that the substrate-as-base mechanism is viable for phosphate ester hydrolysis, which may have important implications for the studies of phosphate ester hydrolysis by enzymes... - On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme modelsShina C L Kamerlin
Department of Chemistry SGM418, University of Southern California, 3620 McClintock Avenue, Los Angeles California 90089, USA
J Org Chem 75:6391-401. 2010..Simply calculating interaction energies with relatively fixed species cannot capture this crucial point, and considering it may help in advancing rational enzyme design... - Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issuesShina Caroline Lynn Kamerlin
Department of Chemistry SGM418, University of Southern California, Los Angeles, CA 90089, USA
FEBS Lett 584:2759-66. 2010..Finally, the temperature dependence of the entropy change in hydride transfer reactions is shown to reflect simple electrostatic effects... - Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effectsPeter Oelschlaeger
University of Southern California, Department of Chemistry, Los Angeles, CA 90089 1062, USA
J Mol Biol 366:687-701. 2007..The model should also have broad applicability to the modeling of other magnesium-containing proteins... - Coarse-grained (multiscale) simulations in studies of biophysical and chemical systemsShina C L Kamerlin
Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
Annu Rev Phys Chem 62:41-64. 2011.... - Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidaseAndrei V Pisliakov
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
Proc Natl Acad Sci U S A 105:7726-31. 2008.... - Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternativesMats H M Olsson
University of Southern California, 3620 McClintock Avenue, Department of Chemistry, SGM 418, Los Angeles, CA 90089 1062, USA
Biochim Biophys Acta 1767:244-60. 2007.... - Electrostatic contributions to protein stability and folding energyMaite Roca
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
FEBS Lett 581:2065-71. 2007..Although this description should be examined by further microscopic studies, the practical use of the current approach seems to offer a powerful tool for protein design and for studies of the energetics of protein folding... - Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit modelsBenjamin M Messer
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
Proteins 78:1212-27. 2010..Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed... - On the relationship between thermal stability and catalytic power of enzymesMaite Roca
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
Biochemistry 46:15076-88. 2007..Thus, the optimized catalysts are less stable. This trend is clearly observed in the DHFR case... - Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation modelsShina C L Kamerlin
Department of Chemistry, University of Southern California, 3620 McClintock Ave, Los Angeles, CA 90089, USA
Chemphyschem 10:1125-34. 2009..Thus, our analysis indicates that this approach provides an unreliable way for modelling phosphate hydrolysis in solution... - On the relationship between folding and chemical landscapes in enzyme catalysisMaite Roca
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA, 90089 1062, USA
Proc Natl Acad Sci U S A 105:13877-82. 2008..This work provides insight into the relationship between folding landscapes and catalysis. The computational approach used here may also provide a powerful strategy for modeling single-molecule experiments and designing enzymes... - Solvation free energies of molecules. The most stable anionic tautomers of uracilMaciej Haranczyk
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
Phys Chem Chem Phys 10:4442-8. 2008..We found that in water solution three of the recently identified anionic tautomers are 6.5-3.6 kcal mol(-1) more stable than the anion of the canonical tautomer... - Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distributionEdina Rosta
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
J Phys Chem B 112:5680-92. 2008..This approach should provide a very powerful tool for QM(ai)/MM evaluation of solvation free energies in aqueous solutions and proteins... - Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymesMats H M Olsson
Chemistry Department, SGM 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
J Biol Inorg Chem 9:96-9. 2004..The simulation reproduces quite well the experimental kinetic information and the corresponding difference between the classical and quantum mechanical activation free energies for the H and D transfer reactions... - Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmarkMats H M Olsson
University of Southern California, 3620 McClintock Avenue, Department of Chemistry, SGM418, Los Angeles, California 90089 1062, USA
J Am Chem Soc 126:15167-79. 2004..It is also shown that the effect of the difference in the relaxation time of the solvent coordinate in the enzyme and solution reaction is rather trivial relative to the effect of the corresponding changes in reorganization free energy... - Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneckMats H M Olsson
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
FEBS Lett 579:2026-34. 2005..Although further studies are clearly needed, we believe that our approach offers a general and effective tool for correlating the structure of COX with its function... - Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenaseMats H M Olsson
Chemistry Department, University of Southern California, Los Angeles, California 90089 1062, USA
J Am Chem Soc 126:2820-8. 2004..We also reached similar conclusions in studies of other enzymes... - Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyaninMats H M Olsson
Chemistry Department, University of Southern California, 3620 McClintock Avenue, SGM 418, Los Angeles, California 90089 0047, USA
J Am Chem Soc 125:5025-39. 2003..This electrostatic environment, which is the major effect determining the reduction potential, is a property of the entire protein and solvent system and cannot be ascribed to any particular single interaction... - Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymeraseJan Florian
Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, USA
J Am Chem Soc 125:8163-77. 2003..The relative height of these barriers comparing right and wrong dNTP substrates should therefore be a primary focus of future computational studies of the fidelity of DNA polymerases... - Computer simulation studies of the fidelity of DNA polymerasesJan Florian
Department of Chemistry, University of Southern California, Los Angeles, CA 90089 1062, USA
Biopolymers 68:286-99. 2003.... - Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesisMats H M Olsson
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
Chem Rev 106:1737-56. 2006 - Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol betaYun Xiang
Department of Chemistry, University of Southern California, Seeley G. Mudd 418, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
Biochemistry 45:7036-48. 2006..We discuss the potential of direct calculations of binding energy of the TS in a rational design of TS analogues and in drug design... - Computer simulations of enzyme catalysis: methods, progress, and insightsArieh Warshel
Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
Annu Rev Biophys Biomol Struct 32:425-43. 2003..Finally, it is pointed out that although some of the issues are likely to remain controversial for some time, computer modeling approaches can provide a powerful tool for understanding enzyme catalysis... - Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effectsSonja Braun-Sand
University of Southern California, Los Angeles, California 90089, USA
J Phys Chem B 109:583-92. 2005..This finding has clear consequences with regards to PTR processes in biological systems... - Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilizationMarek Strajbl
Department of Chemistry, University of Southern California, Los Angeles, California 90098-1062, USA
J Am Chem Soc 125:10228-37. 2003..However, since the charge distribution of the transition state and the reactant state is similar, the stabilization of the transition state leads to reduction in the distance between the reacting atoms in the reactant state... - Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthaseMarek Strajbl
Department of Chemistry, University of Southern California, Los Angeles, CA 90098-1062, USA
Proc Natl Acad Sci U S A 100:14834-9. 2003..It is found that the conformational changes are converted to changes in the electrostatic interaction between the protein and its ligands, which drives the ATP synthesis... - Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidaseMats H M Olsson
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM418, Los Angeles, CA 90089 1062, USA
Proc Natl Acad Sci U S A 103:6500-5. 2006.... - The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteasesClaudia N Schutz
Department of Chemistry, University of Southern California, Los Angeles 90089-1062, USA
Proteins 55:711-23. 2004..The present study provides a support to the idea that enzymes work by creating a preorganized polar environment... - A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerasesShina C L Kamerlin
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA
Biochemistry 48:5963-71. 2009..An understanding of the mechanism of this reaction in solution could thereby provide a steppingstone for understanding the factors governing the fidelity of DNA polymerases... - Electrostatic effects in macromolecules: fundamental concepts and practical modelingA Warshel
Department of Chemistry, University of Southern California, Los Angeles 90089, USA
Curr Opin Struct Biol 8:211-7. 1998.... - Computer simulations of enzyme catalysis: finding out what has been optimized by evolutionA Warshel
Department of Chemistry, University of Southern California, Los Angeles, CA 90089 1062, USA
Proc Natl Acad Sci U S A 95:5950-5. 1998..Apparently, the catalytic power of enzymes is stored in their folding energy in the form of the preorganized polar environment... - Why does the Ras switch "break" by oncogenic mutations?Avital Shurki
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
Proteins 55:1-10. 2004..This "allosteric" effect causes a major reduction in the electrostatic stabilization of the TS. Our findings have general relevance to other proteins that control signal transduction processes... - On unjustifiably misrepresenting the EVB approach while simultaneously adopting itShina C L Kamerlin
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA
J Phys Chem B 113:10905-15. 2009..which where presented as verification of the unreliability of the EVB model were in fact obtained by the use of incorrect parameters, without comparing to the correct surface obtained by our program... - Toward accurate screening in computer-aided enzyme designMaite Roca
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
Biochemistry 48:3046-56. 2009.... - Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminaseMaria P Frushicheva
Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
Proc Natl Acad Sci U S A 107:16869-74. 2010.... - Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energiesShina C L Kamerlin
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
J Phys Chem B 113:1253-72. 2009.... - A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymesPankaz K Sharma
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
Proc Natl Acad Sci U S A 104:9661-6. 2007..The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design... - On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteinsMarco Klahn
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
J Am Chem Soc 128:15310-23. 2006.... - Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactionsNidhi Singh
Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
Proteins 78:1705-23. 2010..Overall, the PDLD/S-LRA/beta appears to offer an appealing option for the final stages of massive screening approaches... - Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactionsEdina Rosta
Department of Chemistry, University of Southern California, 3620 South McClintock Avenue, Los Angeles, California 90089-1062, USA
J Phys Chem B 110:2934-41. 2006..Our advance allows one to explore consistently various mechanistic and catalytic proposals while using ab initio (ai) QM/MM approaches... - Advances in methods and algorithms in a modern quantum chemistry program packageYihan Shao
Department of Chemistry, University of California, Berkeley, CA 94720, USA
Phys Chem Chem Phys 8:3172-91. 2006.... - Calculation of the redox potentials of iron-sulfur proteins: the 2-/3-couple of [Fe4S*4Cys4] clusters in Peptococcus aerogenes ferredoxin, Azotobacter vinelandii ferredoxin I, and Chromatium vinosum high-potential iron proteinG M Jensen
Department of Chemistry, University of Southern California, Los Angeles 90089
Biochemistry 33:10911-24. 1994..In contrast, the results for Cluster II differ substantially; for reasons not yet clear, the recently revised structure leads to results in worse agreement with experiment... - Simulations of ion current in realistic models of ion channels: the KcsA potassium channelA Burykin
Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
Proteins 47:265-80. 2002..The ability to simulate the current in realistic models of ion channels should provide a powerful tool for studies of the biologic function of such systems, including the analysis of the effect of mutations, pH, and electric potentials... - Molecular dynamics simulations of biological reactionsArieh Warshel
Department of Chemistry, University of Southern California, University Park Campus, Los Angeles, California 90089-1062, USA
Acc Chem Res 35:385-95. 2002..The resulting insight is crucial in studies of fast photobiological reactions and instructive in cases of slower processes... - Electrostatic basis for bioenergeticsAvital Shurki
Department of Chemistry, University of Southern California, Los Angeles 90089, USA
Methods Enzymol 380:52-84. 2004 - Exploring the origin of the ion selectivity of the KcsA potassium channelAnton Burykin
Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
Proteins 52:412-26. 2003.... - What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?Pankaz K Sharma
University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
Biochemistry 44:11307-14. 2005..The nature of these effects and their relationship to catalytic factors in modern enzymes is analyzed and discussed... - Using a charging coordinate in studies of ionization induced partial unfoldingMitsunori Kato
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
J Phys Chem B 110:11566-70. 2006.... - Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phasesGongyi Hong
Department of Chemistry, University of Southern California, 3620 S. McClintock Ave, Los Angeles, 90089-1062, USA
J Phys Chem B 110:19570-4. 2006..It is found that, at least for the test case of S(N)()2 reactions, the off diagonal element does not change significantly upon moving from the gas phase to solutions and thus the EVB assumption is valid and extremely useful... - Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenaseJanez Mavri
National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
J Phys Chem B 112:5950-4. 2008..In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction... - Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channelsMitsunori Kato
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
J Phys Chem B 109:19516-22. 2005.... - On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solutionEdina Rosta
Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
Biochemistry 47:3725-35. 2008..We demonstrate that when this factor is taken into account, it is possible to reproduce the experimental LFER for this system with reasonable accuracy... - The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after allSonja Braun-Sand
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
Biochim Biophys Acta 1777:441-52. 2008..This provides the driving force for the subsequent PT steps... - On the generation of catalytic antibodies by transition state analoguesMontserrat Barbany
Computational Structural Biology Laboratory, , Spain
Chembiochem 4:277-85. 2003..The general implications of our findings and the difficulties in designing a perfect TSA are discussed. Finally, the possible use of our approach in screening for an optimal TSA is pointed out...
Research Grants
- Computer Simulation of Electron and Proton TransferArieh Warshel; Fiscal Year: 2010..This should assist in the development of effective drugs that will help to fight diseases that are associated with defective charge transport proteins. ..
- COMPUTER SIMULATION OF ENZYMATIC REACTIONSArieh Warshel; Fiscal Year: 2001....
- COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONSArieh Warshel; Fiscal Year: 2000....
- COMPUTER SIMULATION OF ENZYMATIC REACTIONSArieh Warshel; Fiscal Year: 2010..1 ..
- COMPUTER SIMULATION OF ENZYMATIC REACTIONSArieh Warshel; Fiscal Year: 2009..This study will also explore the reason for the difference between the activities of catalytic antibodies and enzymes that catalyze similar reactions. ..
- Computer Simulation of Electron and Proton TransferArieh Warshel; Fiscal Year: 2007..iv) Continuing our studies of the bacterial RCs. (v) Continuing fundamental studies of electrostatic energies in proteins and, (vi) continue our studies of the selectivity of biological ion channels. ..
- COMPUTER SIMULATION OF ENZYMATIC REACTIONSArieh Warshel; Fiscal Year: 2007..This study will also explore the reason for the difference between the activities of catalytic antibodies and enzymes that catalyze similar reactions. ..
- COMPUTER SIMULATION OF ENZYMATIC REACTIONSArieh Warshel; Fiscal Year: 2005..abstract_text> ..
- Computer Simulation of Electron and Proton TransferArieh Warshel; Fiscal Year: 2004....
- THEORETICAL STUDIES OF ENZYMATIC REACTIONSArieh Warshel; Fiscal Year: 1980....
- COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONSArieh Warshel; Fiscal Year: 1992..v) The redox potential of electron transfer proteins will be evaluated by free energy perturbation methods. This study will include calculations of the effects of genetic modifications on redox potentials...
- COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONSArieh Warshel; Fiscal Year: 1993..vi) Simulation of ET in solution, using an explicit representation of donor and acceptor, trying to reproduce experimental results of well defined test cases...
- THEORETICAL STUDIES OF ENZYMATIC REACTIONSArieh Warshel; Fiscal Year: 1993..In parallel to our fundamental studies we will start to explore the predictive power of our models by simulating the effect of site-directed mutagenesis on rate enhancement of enzymatic reactions...