个人简介

B.Sc. Physics, University of Montreal, 1981 M.Sc. Physics, University of Montreal, 1984 Ph.D. Biophysics, Harvard University, 1990

研究领域

Physical Chemistry/Biophysics/Theoretical

We use theoretical and computational methods to advance our understanding of the structure, dynamics and function of biological macromolecular systems at the atomic level. We are particularly interested in issues concerning the function of ion channels and other membrane transport proteins such as ion permeation, ion selectivity, and gating. Most of our work on ion channels is computational though we have recently started to add an experimental component to our research with electrophysiological measurements and protein crystallography. The computational approach called "molecular dynamics" (MD) is central to our work. It consists of constructing detailed atomic models of the macromolecular system and, having described the microscopic forces with a potential function, using Newton's classical equation, F=MA, to literally "simulate" the dynamical motions of all the atoms as a function of time. The calculated trajectory, though an approximation to the real world, provides detailed information about the time course of the atomic motions, which is nearly impossible to access experimentally. We use such all-atom MD simulations to rigorously compute conformational free energies, and binding free energies. In addition, other computational approaches, at different level of complexity and sophistication, can be very useful. In particular, Poisson Boltzmann (PB) continuum electrostatic models, in which the influence of the solvent is incorporated implicitly, plays an increasingly important role in estimating the solvation free energy of macromolecular assemblies. We are also spending efforts in the development of new computational approaches (polarizable force field, solvent boundary potentials, efficient sampling methods) for studying biological macromolecular systems.

近期论文

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Gan, W. X., and B. Roux. 2009. Binding specificity of SH2 domains: Insight from free energy simulations. Proteins-Structure Function and Bioinformatics 74:996-1007. Gan, W., S. Yang, and B. Roux. 2009. Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories. Biophys J 97:L8-L10. Harder, E., A. D. Mackerell, and B. Roux. 2009. Many-Body Polarization Effects and the Membrane Dipole Potential. J Am Chem Soc 131:2760-2761. Harder, E., D. E. Walters, Y. D. Bodnar, R. S. Faibish, and B. Roux. 2009. Molecular Dynamics Study of a Polymeric Reverse Osmosis Membrane. The journal of physical chemistry 113:10177-10182. Jiang, W., M. Hodoscek, and B. Roux. 2009. Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics J. Chem. Theory Comput. 5:2583-2588. Lopes, P. E. M., B. Roux, and A. D. M. Jr. 2009. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications Theor. Chem. Acc. 124:11-28. Maragliano, L., E. Vanden-Eijnden, and B. Roux. 2009. Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials. . J. Chem. Theo. Comp. 5:2594-2589. Numano, R., S. Szobota, A. Y. Lau, P. Gorostiza, M. Volgraf, B. Roux, D. Trauner, and E. Y. Isacoff. 2009. Nanosculpting reversed wavelength sensitivity into a photoswitchable iGluR. Proc Natl Acad Sci U S A 106:6814-6819. Park, S., J. P. Bardhan, B. Roux, and L. Makowski. 2009. Simulated x-ray scattering of protein solutions using explicit-solvent models. The Journal of chemical physics 130:134114. Sezer, D., J. H. Freed, and B. Roux. 2009. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J Am Chem Soc 131:2597-2605. Shivakumar, D., Y. Q. Deng, and B. Roux. 2009. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. Journal of Chemical Theory and Computation 5:919-930. Tan, K., A. Sather, J. L. Robertson, S. Moy, B. Roux, and A. Joachimiak. 2009. Structure and electrostatic property of cytoplasmic domain of ZntB transporter. Protein Sci 18:2043-2052. Truchon, J. F., A. Nicholl's, J. A. Grant, R. I. Iftimie, B. Roux, and C. I. Bayly. 2009. Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions. J Comput Chem. 31:811-824. Yang, S., N. K. Banavali, and B. Roux. 2009. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci U S A 106:3776-3781. Yang, S., S. Park, L. Makowski, and B. Roux. 2009. A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys J 96:4449-4463. Yu, H., S. Y. Noskov, and B. Roux. 2009. Hydration number, topological control, and ion selectivity. The journal of physical chemistry 113:8725-8730. Yu, H., and B. Roux. 2009. On the utilization of energy minimization to the study of ion selectivity. Biophys J 97:L15-17. Baker, C. M., P. E. Lopes, X. Zhu, B. Roux, and A. D. Mackerell. 2010. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput 6:1181-1198. Chakrapani, S., P. Sompornpisut, P. Intharathep, B. Roux, and E. Perozo. 2010. The activated state of a sodium channel voltage sensor in a membrane environment. Proc Natl Acad Sci U S A 107:5435-5440. Egwolf, B., Y. Luo, D. E. Walters, and B. Roux. 2010. Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter. II. Multi-ion effects studied with grand canonical Monte Carlo/Brownian dynamics simulations. The journal of physical chemistry 114:2901-2909. Ge, X., and B. Roux. 2010. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials. J Mol Recognit 23:128-141. Khalili-Araghi, F., V. Jogini, V. Yarov-Yarovoy, E. Tajkhorshid, B. Roux, and K. Schulten. 2010. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J 98:2189-2198. Luo, Y., B. Egwolf, D. E. Walters, and B. Roux. 2010. Ion selectivity of alpha-hemolysin with a beta-cyclodextrin adapter. I. Single ion potential of mean force and diffusion coefficient. The journal of physical chemistry 114:952-958. Luo, Y., and B. Roux. 2010. Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions J. Phys. Chem. Letters 1:183-189. Roux, B. 2010. Exploring the ion selectivity properties of a large number of simplified binding site models. Biophys J 98:2877-2885. Roux, B., and H. Yu. 2010. Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory. The Journal of chemical physics 132:234101. Yu, H., T. W. Whitfield, E. Harder, G. Lamoureux, I. Vorobyov, V. M. Anisimov, A. D. Mackerell, and B. Roux. 2010. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J Chem Theory Comput 6:774-786.