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Régis Pomès

Computational Biophysics:
Biomacromolecular Structure, Function, and Dynamics

Hospital for Sick Children

Senior Scientist, Molecular Structure & Function (department website)

University of Toronto

Associate Professor, Department of Biochemistry (department website) (lab website)

Canada Research Chair

Proteomics, Bioinformatics & Functional Genomics

Research Interests
  • Protein folding, solvation, and self-assembly
  • Structure-based drug design
  • Proton transport across biomembranes
Research Activities

Understanding the physical principles that govern the structure and function of biological molecules is paramount to predict and rationalize biological activity. To this end, we use computer simulations to study biological systems at the molecular level. Currently the laboratory is engaged in three main directions of research.

  • We are studying the solvation, folding, and self-aggregation of peptides and proteins.
  • We are developing novel computational methods for the prediction of protein-ligand binding affinities to help in the discovery of new therapeutic agents (rational drug design).
  • We are studying the molecular mechanism of proton transport across biological membranes, a process which is essential to life itself (respiration, metabolism).
External Funding
Selected Recent Publications
  • S. Rauscher, R. Pomès, "Molecular simulations of protein disorder", Biochem. Cell Biol., 88(2):269-90 (2010).
  • N. Chakrabarti, C. Neale, J. Payandeh, E. F. Pai, and R. Pomès, "An Iris-Like Mechanism of Pore Dilation in the CorA Magnesium Transport System", Biophys. J., 98(5):784-792 (2010).
  • A. Nikolic, S. Baud, S. Rauscher, and R. Pomès, "Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces", Proteins, accepted (2010).
  • S. Rauscher, C. Neale, and R. Pomès, "Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling", J. Chem. Theory Comput., 5(10):2640-2662 (2009).
  • R. M. Henry, C-H. Yu, T. Rodinger, and R. Pomès, "Functional Hydration and Conformational Gating of Proton Uptake in Cytochrome c Oxidase", J. Mol. Bio., 387, 1165-1185 (2009).
  • C. Neale, T. Rodinger, and Régis Pomès, "Equilibrium exchange enhances the convergence rate of umbrella sampling", Chemical Physics Letters 460:375-381 (2008).
  • E. Fadda, C.-H. Yu, R. Pomès. "Electrostatic Contron of Proton Pumping in Cytochrome c Oxidase", Biophys. Biochim. Acta, Bioenergetics 1777:277-284 (2008).
  • T. Rodinger, P. L. Howell, and R. Pomès, "Calculation of absolute protein-ligand binding free energy using distributed replica sampling", J. Chem. Phys. 129, 155102 (2008).
  • S. Rauscher, S. Baud, M. Miao, F.W. Keeley, and R. Pomès, "Proline and glycine control protein self-organization into elastomeric or amyloid fibrils," Structure 11:1667-76 (2006).
  • T. Rodinger, P.L. Howell, and R. Pomès, "Distributed Replica Sampling" J. Chem. Theory Comput., 2:725 (2006).
  • E. Fadda, N. Chakrabarti, and R. Pomès, "Acidity of a Cu-Bound Histidine in the Binuclear Center of Cytochrome c Oxidase," J. Phys. Chem. B 109:22629 (2005).
  • T. Rodinger, P.L. Howell, and R. Pomès, "Absolute Free Energy Calculations by Thermodynamic Integration in Four Spatial Dimensions," J. Chem. Phys. 123:34104 (2005).
  • T. Rodinger and R. Pomès, "Enhancing the Accuracy, the Efficiency, and the Scope of Free Energy Simulations," Curr. Opin. Struct. Biol. 15:164-170 (2005). (Review)
  • N. Chakrabarti, B. Roux, and R. Pomès, "Structural Determinants of Proton Blockage in Aquaporins," J. Mol. Biol. 343:493-510 (2004).
  • N. Chakrabarti, E. Tajkhorshid, B. Roux, and R. Pomès, "Molecular Basis of Proton Blockage in Aquaporins," Structure 12:65-74 (2004).
  • C.H. Yu and R. Pomès, "Functional Dynamics of Ion Channels: Modulation of Proton Movement by Conformational Switches," J. Amer. Chem. Soc. 125:13890-13894 (2003).
  • C.H. Yu, S. Cukierman, and R. Pomès, "Theoretical Study of the Structure and Dynamic Fluctuations of Dioxolane-Linked Gramicidin Channels," Biophys. J. 84: 816-831 (2003).