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Arieh Warshel

Distinguished Professor of Chemistry, Biochemistry and Chemical Engineering and Dana and David Dornsife Chair in Chemistry and Biochemistry
Distinguished Professor

Contact Information
E-mail: warshel@usc.edu
Phone: (213) 740-4114
Office: SGM 406

LINKS
Curriculum Vitae
Faculty Profile on Departmental Website
 

Education

Ph.D. , Weizmann Institute, Israel, 1/1969
M.S. , Weizmann Institute, Israel, 1/1967
B.S. , Technion, Haifa, Israel, 1/1966
 

Description of Research

Summary Statement of Research Interests

Professor Warshel researches problems in modern biophysical chemistry. He and his coworkers have pioneered several of the most effective models for computer simulations of biological molecule. His early works paved the way for quantitative theoretical studies of enzymatic reactions. He also studies the energetics and dynamics of chemical processes in solution, which include the use and development of various QM/MM approaches and related models for quantitative simulations of chemical reactions in solutions.
 

Funded Research

Contracts and Grants Awarded

Structural basis of Large T Helicase (NIH), Xiaojiang Chen, $1,992,000, 07/01/2009-06/30/2014  
Computer Simulations of Enzymatic Reactions (NIH), Arieh Warshel, $1,680,000, 04/01/2010-03/31/2014  
Computer Simulation of Elctron Transfer and Proton Transfer (NIH), Arieh Warshel, $1,320,000, 08/01/2009-07/31/2013  
The origin of the fidelity of DNA polymerase-Fidelity Mechanism: Theory and Experiment (NCI), Myron Goodman, Arieh Warshel, Sam Wilson, $3,350,186, 09/26/2008-07/31/2013  
Structure function correlation of G-Proteins (NSF), Arieh Warshel, $780,000, 04/01/2009-03/30/2013  
Computer Simulation of Enzymatic Reactions (NIH), Arieh Warshel, $1,513,050, 04/01/2006-03/31/2010  
Computer Stimulation Of Electron And Proton Transfer (Nat Inst of General Medical Sciences (NIGMS)), Warshel, Arieh, $946,227, 08/01/2005-07/31/2009  
Structure Function Correlation of G-Proteins (NSF), Arieh Warshel, $710,000, 07/01/2004-06/30/2009  
The Origin of the Fidelity of DNA Polymerase-Fidelity Mechanism: Theory and Experiment (NCI), Myron Goodman, Arieh Warshel, Sam Wilson, $3,577,717, 01/08/2004-07/31/2008  
 

Conferences and Other Presentations

Conference Presentations

"How Do Enzymes Work and How Do They Not Work: Advances in Simulations and Computer Aided Enzyme Design", IUPAC Symposium on Enzyme Catalysis , Talk/Oral Presentation, Puerto Rico, Invited, Fall 2011   
"Reference Potentials and CG Approaches for Simulations of Biological Systems", WATOC 2011, Talk/Oral Presentation, Santiago de Compostela, Spain, Invited, Fall 2011   
"Coarse Grained renormalization studies of the functions of membrane proteins", ACS symposium on "Membrane Proteins, Structure and Function", Talk/Oral Presentation, Anaheim, CA, Invited, Spring 2011   
"Renormalization and Other CG Approaches For Long Time Simulations of Biological Systems ", ThioBio 2011 , Talk/Oral Presentation, Madeira, Portugal , Invited, Spring 2011   
"Renormalization and other CG approaches for long time simulations of biological systems ", Stanford-Sweden Workshop, Lecture/Seminar, Uppsala, Sweden, Invited, Spring 2011   
"The Constraints on the Efficiency of Coupled Electron Transfer /Proton Transfer Biological Pumps, and What Does it Take to Relate the Structure of Cytochrome c Oxidase to its Actual Function", Royal Swedish Academy Symposium on "Proton Transport Across Biological Membranes, Talk/Oral Presentation, Stockholm, Sweden, Invited, Spring 2011   
"Challenges and Advances in QM/MM Methods and Multi Scale modeling for studies of biological functions", Pacifichem 2010 , Talk/Oral Presentation, Honolulu, Hawaii, Invited, Fall 2010   
"Multiscale Modeling in Chemistry and Biology", The Quantum Systems in Chemistry and Physics (QSCP) XV conference , Meeting, Cambridge, England, Invited, Fall 2010   
"The role of water in biological systems", Workshop on Water in Biology , Talk/Oral Presentation, Chicago, IL, Invited, Fall 2010   
"Using Consistent Simulations to Examine Proposals About The Origin of Enzyme Catalysis", The XVth QAMTS Conference , Meeting, Darmstadt , Germany , Invited, Fall 2010   
"What Does it Take to Simulate Reliably and Effectively Proton Transfer Processes in Membrane Proteins", Telluride Workshop on Proton Transfer in Biology , Talk/Oral Presentation, Telluride, CO, Invited, Fall 2010   
"Computer Simulations of Biological Functions", National Academy Of Science, Section 29, Talk/Oral Presentation, Washington, DC, Invited, Spring 2010   
"Computer Simulations of the Functions of Biological Systems; What Has Been Accomplished and Where we are Going", The Lifson Memorial Lecture, Lecture/Seminar, The Wiezmann Institute, Israel, Invited, Spring 2010   
"Electrostatic basis of Biological Functions", The Chevy Goldstein Distinguished Lecture in Chemistry, Meeting, Cal Poly Pomona, CA, USA, Invited, Spring 2010   
"Multiscale Modeling of Biological Functions", Conference on Computational Molecular Science (CMS) 2010 , Meeting, Royal Agricultural College, Cirencester, Invited, Spring 2010   
"Multiscale Modeling of Biological Functions", Invited Lecture, Lecture/Seminar, Department of Chemistry, Oxford University, Invited, Spring 2010   
"Multiscale Simulations of Complex Biological Systems ; Exploring Problematic Dynamical Proposals and Quantifying Enzyme catalysis ", Invited Lecture, Lecture/Seminar, Department of Chemistry California Institute of Technology, Invited, Spring 2010   
"Coarse graining approaches in studying proton transport and ion transport ", Multiscale Modeling and Simulations in Science, Lecture/Seminar, Stockholm, Sweden, Invited, Fall 2009   
"Computer Simulations of the Functions of Biological Molecules , What has Been Accomplished and Where we are Going", Symposium on Protein Structure and Function , Lecture/Seminar, Shanghai, People's Republic of China , Invited, Fall 2009   
"Dynamical effects are important in ultrafast reactions but not in enzyme catalysis: Advances in modeling long time enzyme dynamics", ACS National Meeting, Symposium on Protein Dynamics and Functions, Lecture/Seminar, Washington, Invited, Fall 2009   
"How do Enzymes Really Work and How They do Not Work; What Has Been Learned From Computer Simulations ", Lecture/Seminar, Frankfurt, Germany, Invited, Fall 2009   
"How to Study Electrostaic Energies in Proteins", Workshop on Electrostatics in Proteins, Lecture/Seminar, Telluride, Colorado , Invited, Fall 2009   
"Multi scale modeling of protein functions on long time scale ", Multiscale Modeling and Simulations in Science, Lecture/Seminar, Stockholm, Sweden, Invited, Fall 2009   
"Multiscale Modeling of Biological Functions", Model(l)ing09 , Lecture/Seminar, Erlangen, Germany, Invited, Fall 2009   
"Multiscale strategies in QM/MM modeling", Multiscale Modeling and Simulations in Science, Lecture/Seminar, Stockholm, Sweden, Invited, Fall 2009   
"Simulating Proton Transfer and Electron Transfer in Biology", Protein-Cofactor Interactions in Biological Processes , Lecture/Seminar, Berlin, Germany , Invited, Fall 2009   
"The EVB as a quantitative tool for Simulating and Analyzing Biological and Chemical Reactions ", Faraday Discussion on Physical Organic Chemistry, Lecture/Seminar, Cardiff, UK, Invited, Fall 2009   
"Dynamical Coupling Between Conformational and Chemical Motions Does not Contribute to Catalysis", A Symposium on Functional Motions in Enzyme Catalysis (ACS National meeting), Lecture/Seminar, Salt Lake City, Invited, Spring 2009   
"How Do Enzymes Really Work and How Do They Not Work: What Has Been Learnt From Computer Simulation Studies?", The CUSO lecture series , Lecture/Seminar, Lausanne, Switzerland, Invited, Spring 2009   
"How Do Enzymes Work and How Do They Not Work: What Has Been Learnt From Computer Simulation Studies?", Isotopes 2009 , Lecture/Seminar, Cluj-Napoca, Romania , Invited, Spring 2009   
"How do Enzymes Really Work and How They do Not Work; What Has Been Learned From Computer Simulations", The R.B Woodward Lectures in Chemical Science, Lecture/Seminar, Harvard University, Boston, Invited, Spring 2009   
"Modeling Proton Transfer and Electron Transfer Reactions in Chemistry and Biology", The CUSO lecture series , Lecture/Seminar, Bern, Switzerland, Invited, Spring 2009   
"Multilevel Modeling in Biophysics and Chemistry: Modeling Light Induced Photochemical and Photobiological Reactions", The CUSO lecture series , Lecture/Seminar, Geneva, Switzerland, Invited, Spring 2009   
"On the Nature of Proton Transport in Biological Systems", The CUSO lecture series , Lecture/Seminar, Switzerland, Invited, Spring 2009   
"What Can Be Learned From Consistent Simulation Studies and Who is Grotthuss Anyhow?, ", The CUSO lecture series , Lecture/Seminar, Basel, Switzerland, Invited, Spring 2009   
"Computer Simulations of Biological Functions", WATOC Congress, Lecture/Seminar, Sydney, Australia, Invited, Fall 2008   
"Hidden Principles of Enzyme Design", ESF-EMBO Symposium on Protein Design and Evolution For Biocatalysis, Lecture/Seminar, San Feliu, Spain, ESF-EMBO , Invited, Fall 2008   
"Computer Simulations can Bridge Between Experimental Studies of Enzymes and Their Interpretation: Recent Confirmations of the Electrostatic Idea an Additional Evidences That Enzyme Catalysis Does not Involve Dynamical Effects", Gordon Research Conference on Isotopes in biological and Chemical Sciences, Lecture/Seminar, ventura, Invited, Spring 2008   
"Computer Simulations of Biological Functions", Wenner-Gren Foundation Symposium on Theoretical Biochemistry, Lecture/Seminar, Stockholm, Wenner-Gren Foundation , Invited, Spring 2008   
"Electrostatic basis For Structure –Function Correlation in Proteins: Examples, validations and Challenges", Workshop on protein Electrostatics, Lecture/Seminar, Telluride, Colorado, Invited, Spring 2008   
"Electrostatic basis of Biological Energy Conversion and the fuel of Biological Motors", Molecular Frontiers Symposium, Royal Swedish Academy of science, Lecture/Seminar, Stockholm, Royal Swedish Academy of science, Invited, Spring 2008   
"Consistent and Effective Sampling in ab initio QM/MM Simulations", ACS National Meeting, Lecture/Seminar, Boston, MA, Invited, Fall 2007   
"Modeling Enzyme Catalysis ", Symposium on 40 Year of Structural Molecular Biology ( Levitt 60 Birthday ) , Lecture/Seminar, Stanford, Invited, Fall 2007   
"Challenges in Calculations of Electrostatic Energies in Macromolecules", ACS National Meeting, Lecture/Seminar, Chicago, IL, Invited, Spring 2007   
"Computer Simulations of Photobiological Reactions: ADvances and Problems", ACS National Meeting, Talk/Oral Presentation, Boston, MA, Invited, Spring 2007   
"Effective Strategies for Unraveling Microscopic Energetic adn Dynamics of Proton Transport in Complex Systems: From QM/MM to Monte Carlo EVB Based Mod", ICTP Workshop, Lecture/Seminar, Trieste, Italy, Invited, Spring 2007   
"How Do Enzymes REally Work?", John Stauffer Symposium, USC, Talk/Oral Presentation, Los Angeles, CA, Invited, Spring 2007   
"Looking for Key Factors in Enzyme Catalysis; Some Recent Confirmation of the Electrostatic Idea", Isotopes 2007, Lecture/Seminar, Benicassim, Spain, Invited, Spring 2007   
"Looking for Key Factors in Enzyme Catalysis; Some Recent Confirmation of the Electrostatic Idea and Additional Advances that Enzyme Catalysis Does not", EMBO Workshop, Lecture/Seminar, Hamburg, Germany, Invited, Spring 2007   
"Modeling Enzyme Catalysis", Symposium on 40 Year of Structural Molecular Biology, Talk/Oral Presentation, Stanford, CA, Invited, Spring 2007   
"On Accuracy and Reliability in Simulations of Enzyme Catalysis", ACS National Meeting, Lecture/Seminar, Chicago, IL, Invited, Spring 2007   
"Quantitative Results in QM/MM Calculations of Biological Systems", APS National Meeting, Talk/Oral Presentation, Bolder, CO, Invited, Spring 2007   
"Simulating Drug Resistance", Gordon Research Conference on Computer Aided Drug Design, Talk/Oral Presentation, Tilton, Invited, Spring 2007   
"Simulating Proton Transport and Ion Transport", Molecular Dymanics Conference on Conductance in Molecules, Lecture/Seminar, Fritz Haber Center, HUJI, Israel, Invited, Spring 2007   
"Computer Simulations as a Powerful Tool for Probing the Origin of Enzyme Catalysis", A Symposium on Enzyme Catalysis of the SFBM, Lecture/Seminar, Uppsala, Sweden, Invited, Fall 2006   
"Computer Simulations of the Action of Metalloenzymes; Methods and Insights", Urobic8, Lecture/Seminar, Avero, Protugal, Invited, Fall 2006   
"From Macroscopic to Microscopic Descriptions of Electron Transfer and Proton Transfer Reactions: Quantifying Marcus Parabolas", ACS National Meeting, Lecture/Seminar, San FRancisco, CA, Invited, Fall 2006   
"Recent Advances in Simulation of Biological Functions", Gordon Conference on Computational Chemistry, Lecture/Seminar, Les Diablerets, Switzerland, Invited, Fall 2006   
"Capturing the Nature of Biochemical Processes by Molecular Simulations ", Seventh Meeting of the Swedish Theoretical Chemists , Keynote Lecture, Stockholm, Sweden , Invited, Spring 2006   
"Computer Simulations of Proton Transport in Proteins ", Gordon Research Conference on Protons and Membrane Reactions , Lecture/Seminar, Ventura, CA , Invited, Spring 2006   
"Computer Simulations of the Function of Biological Molecules; What has been Accomplished and Where are We Going?", ISQBP President's Meeting: The 2006 President's Award Lecture, Keynote Lecture, Strasburg, France, Invited, Spring 2006   
 

Other Presentations

"Computer simulations of phosphate hydrolysis in biology: Facts fictions and open questions", talk, Departement of Biology Uppsala University, Uppsala University, Sweden, Spring 2008   
"Dynamical Contributions to Enzyme Catalysis: Critical Tests of a problematic Hypothesis", lecture, Department of Computational Biology, University of Pittsburg Scholl of Medicine, Pittsburg,USA, Spring 2008   
"Dynamical Contributions to Enzyme Catalysis: Critical Tests of a problematic Hypothesis", talk, Department of Chemistry, University of California, Davis,, Davis,USA, Spring 2008   
"Electrostatic Control of Bioenergetics", lecture, Department of Chemistry Chalmers University, Gothenburg, Sweden, Spring 2008   
"On the Nature of Proton Transport in Cytochrome c Oxidase and Other Biological Systems; What Can Be Learned From Consistent Simulation Studies].", lecture, Department of Biophysics, Johns Hopkins University, Baltimore,USA, Spring 2008   
"on The control of Proton Transport and Ion Transport in Biology: What Can be Learned From Consistent Simulations", lecture, California Institute of Quantitative Biomedical research (invitational Speakers Series), San Francisco, USA, Spring 2008   
"on the Nature of Proton Transport in Cytochrome c Oxidase and Other Biological Systems; What Can Be Learned From Consistent Simulation Studies", lecture, Stockholm University, Stockholm, Sweden, Spring 2008   
"on the Nature of Proton Transport in Cytochrome c Oxidase and other Biological Systems; What Can Be Learned From Consistent Simulation Studies].", lecture, Max Planck Institute for Biophysics, Frankfurt, Germany, Spring 2008   
"Computer Simulation of Biological Functions ", lecture, Department of Biochemistry and Biophysics, University of Pennsylvania , Pennsylvania, USA , Fall 2007   
"Computer Simulations of Enzymatic Reactions ", Talk, Department of Chemistry, University of Zurich , Zurich, Switzerland , Spring 2007   
"Computer Simulations of Very Fast and Extremely Slow Biological Processes ", Talk, ETH Colloquium Fur Physicalische Chemie , Zurich, Switzerland , Spring 2007   
"Simulating Enzyme Catalysis ", Talk, Department of Chemistry , Lublijana, Slovenia , Spring 2007   
"Computer Simulations of Enzymatic Reactions ; finding Out what are the catalytic principles that really Work?", Talk, Department of Chemistry, University of Wisconsin, Wisconsin, Madison, Spring 2006   
"Computer Simulations of Enzymatic Reactions ; finding Out what are the catalytic principles that really Work?] ", Talk, Department of Chemistry, University of Alberta, Edmonton, Canada, Spring 2006   
"Computer Simulations of Enzymatic Reactions: Finding Out What are the Catalytic Principles that Really Work ", Talk, Department of Chemistry, University of Calgary, Calgary, Canada , Spring 2006   
"Molecular Dynamics Simulations of Biological Functions: Finding Out What Dynamical Effects Where Actually Optimized by Evolution? ", Talk, Chalmers University , Chalmers, Sweden , Spring 2006   
"Molecular dynamics simulations of biological functions: Finding out what dynamical effects where actually optimized by evolution?", Talk, Lund University, Lund, Sweden, Spring 2006   
"Molecular dynamics simulations of biological functions: Finding out what dynamical effects where actually optimized by evolution?", Talk, Uppsala University, Uppsala, Sweden, Spring 2006   
 

Other Research

Sabbatical, Spring 2007   
 

Publications

Book

Kato, M., Warshel, A., Braun-Sand, S. (2008). Challenges and Progresses in Calculations of Binding Free Energies – What Does it Take to Quantify Electrostatic Contributions to Protein–Ligand Interactions?. (Stroud, R. M., Finer –Moore, J., Ed.). Computational and Structural Approaches to Drug DiscoveryRSC Publishing.
Parson, W. W., Warshel, A. (2008). Calculations of Electrostatic Energies in Proteins: Using Microscopic, Semimicroscopic and Macroscopic Models and Free Energy Perturbation Approaches. (Aartmas, J., Matysik, J., Ed.). Biophysical Techniques in Photosystem IISpringer.
 

Book Chapter

Liu, H., Warshel, A. (2009). Tunneling Does Not Contribute Significantly to Enzyme Catalysis, But Studying Temperature Dependence of Isotope Effects is Useful. pp. 242-267. RSC Biomolecular Sciences, Quantum Tunnelling in Enzyme-Catalysed Reactions.
Braun-Sand, S., Warshel, A. (2005). Electrostatics of Protein: Principles, Models and Applications. pp. p.N/A. Weinheim: Protein Folding Handbook, Part I.
 

Journal Article

Johansson, A., Chakrabarty, S., Berthold, C. L., Högbom, M., Warshel, A., Brzezinski, P. (2011). Proton-Transport Mechanisms in Cytochrome c Oxidase Revealed by Studies of Kinetic Isotope Effects. Biochimica et Biophysica Acta (BBA) - Bioenergetics. Vol. 1807 (9), pp. 1083-1094. PubMed Web Address
Prasad, B. R., Warshel, A. (2011). Prechemistry versus preorganization in DNA replication fidelity. Proteins: Structure, Function, and Bioinformatics. Vol. 79 (10), pp. 2900–2919. PubMed Web Address
Adamczyk, A. J., Cao, J., Kamerlin, S. C., Warshel, A. (2011). Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proceedings of the National Academcy of Sciences. Vol. 108 (34), pp. 14115-14120. PubMed Web Address
Dryga, A., Chakrabarty, S., Vicatos, S., Warshel, A. (2011). Coarse grained model for exploring voltage dependent ion channels. Biochimica et Biophysica Acta (BBA) - Biomembranes.
Adamczyk, A. J., Warshel, A. (2011). Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome. Proceedings of the National Academcy of Sciences. Vol. 108 (24), pp. 9827–9832. PubMed Web Address
Kamerlin, S. C., Vicatos, S., Dryga, A., Warshel, A. (2011). Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems. Ann. Rev. Phys. Chem. Vol. 62, pp. 41-64. PubMed Web Address
Plotnikov, N. V., Kamerlin, S. C., Warshel, A. (2011). Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks. Journal of Physical Chemistry B. Vol. 115 (24), pp. 7950–7962. PubMed Web Address
Chakrabarty, S., Namslauer, I., Brzezinski, P., Warshel, A. (2011). Exploration of the Cytochrome c Oxidase Pathway Puzzle and Examination of the Origin of Elusive Mutational Effects. Biochimica et Biophysica Acta (BBA) - Bioenergetics. Vol. 1807 (4), pp. 413-426. PubMed Web Address
Kamerlin, S. C., Warshel, A. (2011). Multiscale modeling of biological functions. Phys. Chem. Chem. Phys.. Vol. 13, pp. 10401-10411. PubMed Web Address
Frushicheva, M. P., Cao, J., Warshel, A. (2011). Challenges and Advances in Validating Enzyme Design Proposals: The Case of the Kemp Eliminase Catalysis. Biochemistry. Vol. 50 (18), pp. 3849–3858. PubMed Web Address
Kamerlin, S. C., Warshel, A. (2011). The empirical valence bond model: theory and applications. Wiley Interdisciplinary Reviews: Computational Molecular Science. Vol. 1 (1), pp. 30-45.
Rychkova, A., Vicatos, S., Warshel, A. (2010). On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes. Proc. Acad. Natl. Sci., USA. Vol. 107 (41), pp. 17598–17603.
Frushicheva, M., Cao, J., Chu, Z. T., Warshel, A. (2010). Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase. Proc. Acad. Natl. Sci., USA. Vol. 107 (39), pp. 16869-16874.
Dryga, A., Warshel, A. (2010). Renormalizing SMD: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated PMF Calculations of Macromolecules. J. Phys. Chem. B. (American Chemical Society). Vol. 114 (39), pp. 12720–12728.
Kamerlin, S. C., Chu, Z. T., Warshel, A. (2010). On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models. Journal of Organic Chemistry (John Wiley & Sons Inc.). Vol. 75 (19), pp. 6391–6401. PubMed Web Address
Kamerlin, S. C., Mavri, J., Warshel, A. (2010). Examining the Case for the Effect of Barrier Compression on Tunneling, Vibrationally Enhanced Catalysis, Catalytic Entropy and Related Issues. FEBS Letters. Vol. 584 (13), pp. 2759-2766. PubMed Web Address
Kamerlin, S. C., Warshel, A. (2010). An analysis of all the relevant facts and arguments indicates that enzyme catalysis does not involve large contributions from nuclear tunneling. Journal of Physical Organic Chemistry (John Wiley & Sons Inc.). Vol. 23 (7), pp. 677-684.
Kamerlin, S. C., Warshel, A. (2010). At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?. PROTEINS: Structure, Function, and Bioinformatics. Vol. 78 (6), pp. 1339-1375.
Singh, N., Warshel, A. (2010). Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions. PROTEINS: Structure, Function, and Bioinformatics. Vol. 78 (7), pp. 1705-1723.
Singh, N., Warshel, A. (2010). A comprehensive examination of the contributions to the binding entropy of protein–ligand complexes. PROTEINS: Structure, Function, and Bioinformatics. Vol. 78 (7), pp. 1724-1735.
Messer, B. M., Roca, M., Chu, Z. T., Vicatos, S., Kilshtain, A. V., Warshel, A. (2010). Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models. PROTEINS: Structure, Function, and Bioinformatics. Vol. 78 (5), pp. 1212-1227. PubMed Web Address
Kamerlin, S. C., Warshel, A. (2010). Reply to Karplus: Conformational Dynamics Have no Role in The Chemical Step. Proc. Acad. Natl. Sci., USA. Vol. 107 (17), pp. E72.
Kamerlin, S. C., Sharma, P. K., Chu, Z. T., Warshel, A. (2010). Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization. Proc. Acad. Natl. Sci., USA. Vol. 107 (9), pp. 4075-4080.
Rucker, R., Oelschlaeger, P., Warshel, A. (2010). A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases. Proteins: Structure, Function, and Bioinformatics. Vol. 78 (3), pp. 671–680. PubMed Web Address
Kamerlin, S. C., Warshel, A. (2010). The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions. Faraday Discuss. Vol. 145, pp. 71-106.
Alkherraz, A., Kamerlin, S. C., Feng, G., Sheikh, Q. I., Warshel, A., Williams, N. H. (2010). Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer. Faraday Discuss. Vol. 145, pp. 281-299.
Kamerlin, S. C., Warshel, A. (2009). On the Energetics of ATP Hydrolysis in Solution. J. Phys. Chem. B. Vol. 113 (47), pp. 15692–15698.
Pisliakov, A. V., Cao, J., Kamerlin, S. C., Warshel, A. (2009). Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proceedings of the National Academy of Sciences,USA. Vol. 106 (41), pp. 17359-17364.
Rucker, R., Oelschlaeger, P., Warshel, A. (2009). A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases. Proteins: Structure, Function, and Bioinformatics.
Kamerlin, S. C., Cao, J., Rosta, E., Warshel, A. (2009). On Unjustifiably Misrepresenting the EVB Approach While Simultaneously Adopting It. J. Phys. Chem. B. Vol. 113 (31), pp. 10905–10915.
Singh, N., Warshel, A. (2009). Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects. J. Phys. Chem. B. Vol. 113 (20), pp. 7372-7382.
Liu, H., Shi, Y., Chen, X. S., Warshel, A. (2009). Simulating the Electrostatic Guidance of the Vectorial Translocations in Hexameric Helicases and Translocases. Proceedings of the National Academy of Sciences,USA. Vol. 106 (18), pp. 7449-7454.
Warshel, A., Kamerlin, S. C., Haranczyk, M. (2009). Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models. ChemPhysChem. Vol. 10 (7), pp. 1125-1134.
Vicatos, S., Roca, M., Warshel, A. (2009). Effective approach for calculations of absolute stability of proteins using focused dielectric constants. Proteins: Structure, Function, and Bioinformatics. Vol. 77 (3), pp. 670-684.
Vardi-Kilshtain, A., Roca, M., Warshel, A. (2009). The Empirical Valence Bond as an Effective Strategy for Computer-Aided Enzyme Design. Biotechnol. J. , 4,495-500 (2009).. Vol. 4 (4), pp. 495-500.
Kamerlin, S. C., McKenna, C. E., Goodman, M. F., Warshel, A. (2009). A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases. Biochemistry. Vol. 48 (25), pp. 5963–5971.
Warshel, A., Vardi-Kilshtain, A. (2009). On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes. Proteins: Structure, Function, and Bioinformatics. Vol. 77 (3), pp. 536-550.
Roca, M., Vardi-Kilshtain, A., Warshel, A. (2009). Toward Accurate Screening in Computer-Aided Enzyme Design. Biochemistry. Vol. 48 (14), pp. 3046-3056.
Kamerlin, S. C., Williams, N. H., Warshel, A. (2008). Dineopentyl phosphate hydrolysis: evidence for stepwise water attack. J Org Chem. Vol. 73 (18), pp. 6960-9.
Roca, M., Messer, B., Hilvert, D., Warshel, A. (2008). On the relationship between folding and chemical landscapes in enzyme catalysis. Proc Natl Acad Sci U S A. Vol. 105 (37), pp. 13877-82.
Haranczyk, M., Gutowski, M., Warshel, A. (2008). Solvation free energies of molecules. The most stable anionic tautomers of uracil. Phys Chem Chem Phys. Vol. 10 (30), pp. 4442-8.
Pisliakov, A. V., Sharma, P. K., Chu, Z. T., Haranczyk, M., Warshel, A. (2008). Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A. Vol. 105 (22), pp. 7726-31.
Kamerlin, S. C., Florian, J., Warshel, A. (2008). Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies. Chemphyschem. Vol. 9 (12), pp. 1767-73.
Rosta, E., Haranczyk, M., Chu, Z. T., Warshel, A. (2008). Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution. J Phys Chem B. Vol. 112 (18), pp. 5680-92.
Sucato, C. A., Upton, T. G., Kashemirov, B. A., Osuna, J., Oertell, K., Beard, W. A., Wilson, S. H., Florian, J., Warshel, A., McKenna, C. E., Goodman, M. F. (2008). DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Biochemistry. Vol. 47 (3), pp. 870-9.
Rosta, E., Kamerlin, S. C., Warshel, A. (2008). On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution. Biochemistry. Vol. 47 (12), pp. 3725-35.
Braun-Sand, S., Sharma, P. K., Chu, Z. T., Pisliakov, A. V., Warshel, A. (2008). The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. Biochim Biophys Acta. Vol. 1777 (5), pp. 441-52.
Ishikita, H., Warshel, A. (2008). Predicting drug-resistant mutations of HIV protease. Angew Chem Int Ed Engl. Vol. 47 (4), pp. 697-700.
Warshel, A., Jacob, C. R., Visscher, L. (2008). A subsystem density-functional theory approach for the quantum chemical treatment of proteins. J Chem Phys. Vol. 128 (15), pp. 155102.
Mavri, J., Liu, H., Olsson, M. H., Warshel, A. (2008). Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase. J Phys Chem B. Vol. 112 (19), pp. 5950-4.
Xiang, Y., Goodman, M. F., Beard, W. A., Wilson, S. H., Warshel, A. (2008). Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins. Vol. 70 (1), pp. 231-47.
Xiang, Y., Warshel, A. (2008). Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping. J Phys Chem B. Vol. 112 (3), pp. 1007-15.
Roca, M., Liu, H., Messer, B., Warshel, A. (2007). On the relationship between thermal stability and catalytic power of enzymes. Biochemistry. Vol. 46 (51), pp. 15076-88.
Liu, H., Warshel, A. (2007). Origin of the temperature dependence of isotope effects in enzymatic reactions: The case of dihydrofolate reductase. Journal of Physical Chemistry B. Vol. 111, pp. 7852-7861.
Liu, H., Warshel, A. (2007). Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase. J Phys Chem B. Vol. 111 (27), pp. 7852-61.
Liu, H., Warshel, A. (2007). The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry. Vol. 46, pp. 6011-6025.
Roca, M., Messer, B., Warshel, A. (2007). Electrostatic contributions to protein stability and folding energy. FEBS Letters. Vol. 581, pp. 2065-2071.
Sharma, P. K., Chu, Z. T., Olsson, M. H., Warshel, A. (2007). A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes. Proceedings of the National Academy of Sciences of the United States of America. Vol. 104, pp. 9661-9666.
Sharma, P. K., Chu, Z. T., Olsson, M. H., Warshel, A. (2007). A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes. Proc Natl Acad Sci U S A. Vol. 104 (23), pp. 9661-6.
Oelschlaeger, P., Klahn, M., Beard, W. A., Wilson, S. H., Warshel, A. (2007). Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: Improved accuracy in studies of structural features and mutational effects. Journal of Molecular Biology. Vol. 366 (2), pp. 687-701.
Liu, H., Warshel, A. (2007). The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry. Vol. 46 (20), pp. 6011-25.
Oelschlaeger, P., Klahn, M., Beard, W. A., Wilson, S. H., Warshel, A. (2007). Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects. J Mol Biol. Vol. 366 (2), pp. 687-701.
Olsson, M. H., Slegbahn, P. E., Blomberg, M. R., Warshel, A. (2007). Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: A general framework for examining energetics and mechanistic alternatives. Biochimica Et Biophysica Acta-Bioenergetics. Vol. 1767, pp. 244-260.
Warshel, A., Sharma, P. K., Chu, Z. T., Aqvist, J. (2007). 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 isomerase. Biochemistry. Vol. 46 (6), pp. 1466-76.
Martínek, V., Bren, U., Goodman, M. F., Warshel, A., Florián, J. (2007). DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. FEBS Letters. Vol. 581, pp. 775-780.
Sucato, C. A., Upton, T. G., Kashemirov, B. A., Batra, V. K., Martinek, V., Xiang, Y., Beard, W. A., Pedersen, L. C., Wilson, S. H., McKenna, C. E., Florian, J., Goodman, M. F., Warshel, A. (2007). Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Biochemistry. Vol. 46, pp. 461-471.
Warshel, A., Sharma, P. K., Chu, Z. T., Aqvist, J. (2007). 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 isomerase. Biochemistry. Vol. 46, pp. 1466-1476.
Olsson, M. H., Siegbahn, P. E., Blomberg, M. R., Warshel, A. (2007). Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives. Biochim Biophys Acta. Vol. 1767 (3), pp. 244-60.
Roca, M., Messer, B., Warshel, A. (2007). Electrostatic contributions to protein stability and folding energy. FEBS Lett. Vol. 581 (10), pp. 2065-71.
Sucato, C. A., Upton, T. G., Kashemirov, B. A., Batra, V. K., Martinek, V., Xiang, Y., Beard, W. A., Pedersen, L. C., Wilson, S. H., McKenna, C. E., Florian, J., Warshel, A., Goodman, M. F. (2007). Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Biochemistry. Vol. 46 (2), pp. 461-71.
Klähn, M., Rosta, E., Warshel, A. (2006). On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins. Journal of the American Chemical Society. Vol. 128, pp. 15310-15323.
Warshel, A., Sharma, P. K., Kato, M., Parson, W. W. (2006). Modeling electrostatic effects in proteins. Biochimica Et Biophysica Acta-Proteins and Proteomics. Vol. 1764, pp. 1647-1676.
Kato, M., Pisliakov, A. V., Warshel, A. (2006). The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations. Proteins - Structure Function and Bioinformatics. Vol. 64 (4), pp. 829-844.
Warshel, A., Sharma, P. K., Kato, M., Xiang, Y., Liu, H. B., Olsson, M. H. (2006). Electrostatic basis for enzyme catalysis. Chemical Reviews. Vol. 106, pp. 3210-3235.
Hong, G., Rosta, E., Warshel, A. (2006). Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases. Journal of Physical Chemistry B. Vol. 110, pp. 19570-19574.
Olsson, M. H., Mavri, J., Warshel, A. (2006). Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems. Philosophical Transactions of the Royal Society B-Biological Sciences. Vol. 361, pp. 1417-1432.
Xiang, Y., Oelschlaeger, P., Florian, J., Goodman, M. F., Warshel, A. (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 beta. Biochemistry. Vol. 45, pp. 7036-7048.
Olsson, M. H., Parson, W. W., Warshel, A. (2006). Dynamical contributions to enzyme catalysis: Critical tests of a popular hypothesis. Chemical Reviews. Vol. 106 (5), pp. 1737-1756.
Burykin, A., Warshel, A. (2006). Membranes assembled from narrow carbon nanotubes block proton transport and can form effective nano-filtration devices. Journal of Computational and Theoretical Nanoscience. Vol. 3, pp. 237-242.
Kato, M., Warshel, A. (2006). Using a charging coordinate in studies of ionization induced partial unfolding. Journal of Physical Chemistry B. Vol. 110, pp. 11566-11570.
Olsson, M. H., Warshel, A. (2006). Monte Carlo simulations of proton pumps: On the working principles of the biological valve that controls proton pumping in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. Vol. 103, pp. 6500-6505.
Warshel, A. (2006). Towards Accurate Ab Initio QM/MM Calculations of Free-Energy Profiles of Enzymatic Reactions. J. Phys. Chem. B. Vol. 110, pp. 2934-2941.
Kato, M., Warshel, A. (2005). Through the Channel and around the Channel: Validating and Comparing Microsxopic Approaches for the Evaluation of Free Engergy Profiles for Ion Penetration through Ion Channels. J. Phys. Chem. B. Vol. 109 (41), pp. 19516-19522.
Sharma, P. K., Xiang, Y., Kato, M., Warshel, A. (2005). What Are the Roles of Substrate-Assisted Catalysis and Proximity Effects in Peptide Bond Formation by the Ribosome. Biochemistry. Vol. 44 (34), pp. 11307-11314.
Klahn, M., Braun-Sand, S., Rosta, E., Warshel, A. (2005). On Possible Pitfalls in ab Initio Quantum Mechanics/Molecular Mechanics Minimization Approaches for Studies of Enzymatic Reactions. J. Phys. Chem. B. Vol. 109, pp. 15645-15650.
Olsson, M. H., Sharma, P. K., Warshel, A. (2005). Simulating Redox Coupled Proton Transfer in Cytochrome c Oxidase: Looking for the Proton Bottleneck. FEBS Letters. Vol. 579 (10), pp. 2026-2034.
Florián, J., Goodman, M. F., Warshel, A. (2005). Computer simulations of Protein Functions: Searching for the Molecular Orgin of the Replication Fidelity of DNA Polymerases. Proc. Natl. Acad. Sci. USA.. Vol. 102 (19), pp. p.1026819-6824.
Warshel, A. (2005). Inverting the selectivity of aquaporin 6: Gating versus direct electrostatic interaction. Proc. Natl. Acad. Sci. USA. Vol. 102, pp. 1812-1813.
Braun-Sand, S., Burykin, A., Chu, Z. T., Warshel, A. (2005). Realistic Simulations of Proton Transport Along the Gramicidin Channel: Demostrating the Inportance of Solvation Effects. J. Phys. Chem. B.. Vol. 109, pp. 583-592.
Braun-Sand, S., Olsson, M. H., Warshel, A. (2005). Computer Modeling of Enzyme Catalysis and its Relationship to Concepts in Physical Organic Chemistry. Advances in Physical Organic Chemistry. Vol. 40, pp. 201.
Shurki, A., Warshel, A. (2004). Why does the Ras Switch 'Break' By Oncogenic Mutations?. PROTEINS: Structure, Function and Genetics. Vol. 55, pp. 1-10.
Strajbl, M., Shurki, A., Warshel, A. (2003). Converting conformational changes to electrostatic energy in molecular motors: Thge energetics of ATP synthase. Proc. Natl. Acad. Sci. USA.. Vol. 100, pp. 14834-14839.
Warshel, A. (2003). Computer Simulations of Enzyme Catalysis: Methods, Progress and Insights. Annu. Rev. Biophys. Biomol. Struct.. Vol. 32, pp. 425-443.
Burykin, A., Kato, M., Warshel, A. (2003). Exploring the origiin of the ion selectivity of the KcsA potassium channel. PROTEINS: Structure, Function and Genetics. Vol. 52, pp. 412-426.
 

Guest Lectures in Courses

549: Protein Chemistry Gave lecture on Enzymes Catalysis in a course tought by Langen and Qin, Spring 2006   
 

New Courses Developed

Enzyme Modeling, School of Biotechnology, and Stockholm, Special Course on Modeling Enzyme Reactions in the Royal Institute of Technology ,School of Biotechnology, and Stockholm., Spring 2006   
 

Honors and Awards

Nobel Prize Recipients, Nobel Prize in Chemistry, 10/9/2013-  
National Academy Member, Elected Member of The National Academy of Sceince, 2009-  
Elected Fellow of the Royal Society of Chemistry (FRSC) , 2008-  
Elected fellow of the Biophysical Society , 2000-  
Very High Citations (H-Idex of 94 and more than 30,000 citations, 2010-2011   
2006 ISQBP President's award in compuational biology, 2006-2007   
Tolman Medal, top award given by the Southern California Section of the American Chemical Society in recognition of excellence in research, 2003  
 

Service to the University

Committees

Member, High Performance Computations, 2002-  
Member of the University Committee on Appointments, Promotions and Tenure, 2010-2013  
Member, Faculty Tenure & Privileges Appeals, 2007-2010  
Sabbatical, Spring 2007   
Member, Research Comittee, 2002-2005  
 

Service to the Profession

Committees

Member, Faculty Tenure & Privileges Appeals, 09/2007-09/2010  
 

Conferences Organized

Chair , ACS Symposiuom on Enzymes , 2004-2005   
 

Editorships and Editorial Boards

Associated Editor, Journal of Computational and Theoretical Nanoscience, 2002-  
Associated Editor, Thoretical Chemistry accounts, 2000-  
Associated Editor, PROTEINS, 1998-  
 

Review Panels

European Research Council, ERC-STG, 2010-2014  
National Academy of Science, NAS Review committee of molecular dynamics proposals, Fall 2010   
European Research Council, RTD-ER-EXPERTS, 2007-2008  
NIH, ZRG1 BCMB-Q study section, 2006-2007  
NIH, National center for biocomputing, 05/2004  
NIH, Special review panel on a program project on ikb/NF kB recognition, 03/2004  
 
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