Education

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

Accolades

• Medical Research Council of Canada, Doctoral Fellow 1983-1987
• Research Fellow of the Fond pour la Recherche en Sante du Quebec (FRSQ) 1993-1996
• Research Fellow of the Medical Research Council (MRC) of Canada 1996-1999
• Noranda Lecture Award, The Chemical Institute of Canada 1998
• Rutherford Medal, The Royal Society of Canada 1998
• Enseignant Chercheur Invité, École Normal Supérieure, Paris 2009

Courses Taught

Simulation, Modeling and Computation in Biophysics

Comprehensive General Chemistry

BPHYS Students

David Medovoy, PhD

Ernesto Vargas, PhD

Kevin Song, PhD

Christopher Boughter, PhD

Nabil Faruk

Young Hoon Koh

Andrew Molina

Research Summary

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.

Selected Papers

F. Villa, A.D. MacKerell, Jr., B. Roux, T. Simonson. Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg(2+)". J Phys Chem A. 2019;123(2):629.

S. Jekhmane, J. Medeiros-Silva, J. Li, F. Kummerer, C. Muller-Hermes, M. Baldus, B. Roux, M. Weingarth. Shifts in the selectivity filter dynamics cause modal gating in K(+) channels. Nature communications. 2019;10(1):123.

F. Villa, A.D. MacKerell, Jr., B. Roux, T. Simonson. Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg(2). J Phys Chem A. 2018;122(29):6147-55.

D. Suh, B.K. Radak, C. Chipot, B. Roux. Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator. J Chem Phys. 2018;148(1):014101.

C.R. Rupakheti, B. Roux, F. Dehez, C. Chipot. Modeling induction phenomena in amino acid cation-pi interactions. Theoretical Chemistry Accounts. 2018;137(12).

H. Ramezani-Dakhel, M. Rahimi, J. Pendery, Y.K. Kim, S. Thayumanavan, B. Roux, N.L. Abbott, J.J. de Pablo. Amphiphile-Induced Phase Transition of Liquid Crystals at Aqueous Interfaces. App Mat Inter. 2018;10(43):37618-24.

B.K. Radak, D. Suh, B. Roux. A generalized linear response framework for expanded ensemble and replica exchange simulations. J Chem Phys. 2018;149(7):072315.

 B.K. Radak, C. Chipot, D. Suh, S. Jo, W. Jiang, J.C. Phillips, K. Schulten, B. Roux. Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theo Comp. 2018.

M.P. Pond, L. Blachowicz, B. Roux. (1)H, (15)N, and (13)C resonance assignments of the intrinsically disordered SH4 and Unique domains of Hck. Biomol NMR Ass. 2018.

Y. Meng, C. Gao, D.K. Clawson, S. Atwell, M. Russell, M. Vieth, B. Roux. Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models. J Chem Theo Comp. 2018;14(5):2721-32.

Y. Meng, L.G. Ahuja, A.P. Kornev, S.S. Taylor, B. Roux. Corrigendum to "A Catalytically-Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation." J. Mol. Biol. 430(6) (Mar 16 2018), 881-889. J Mol Biol. 2018;430(21):4439.

Y. Meng, L.G. Ahuja, A.P. Kornev, S.S. Taylor, B. Roux. A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation. J Mol Biol. 2018;430(6):881-9.

 H.H. Loeffler, S. Bosisio, G. Duarte Ramos Matos, D. Suh, B. Roux, D.L. Mobley, J. Michel. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages. J Chem Theo Comp. 2018;14(11):5567-82.

.F.Y. Lin, P.E.M. Lopes, E. Harder, B. Roux, A.D. MacKerell, Jr. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. J Chem Inf Mod. 2018;58(5):993-1004.

J. Li, J. Ostmeyer, L.G. Cuello, E. Perozo, B. Roux. Rapid constriction of the selectivity filter underlies C-type inactivation in the KcsA potassium channel. J Gen Physiol. 2018;150(10):1408-20.

W. Jiang, J. Thirman, S. Jo, B. Roux. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. J Phys Chem B. 2018;122(41):9435-42.

K. Han, R.M. Venable, A.M. Bryant, C.J. Legacy, R. Shen, H. Li, B. Roux, A. Gericke, R.W. Pastor. Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions. J Phys Chem B. 2018;122(4):1484-94.

K.M. Callahan, B. Roux. Molecular Dynamics of Ion Conduction through the Selectivity Filter of the NaVAb Sodium Channel. J Phys Chem B. 2018;122(44):10126-42.

E. Boulanger, L. Huang, C. Rupakheti, A.D. MacKerell, Jr., B. Roux. Optimized Lennard-Jones Parameters for Druglike Small Molecules. J Chem Theo Comp. 2018;14(6):3121-31.

A. Aleksandrov, F.Y. Lin, B. Roux, A.D. MacKerell, Jr. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. J Comp Chem. 2018;39(22):1707-19.