Benoît T. Roux, Ph.D.
Amgen Professor of Biochemistry and Molecular Biology Department of Biochemistry and Molecular Biology
Biographical Info
Research Interest
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 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 differing levels 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 developing new computational approaches (polarizable force field, solvent boundary potentials, efficient sampling methods) for studying biological macromolecular systems.
Honors and Awards
Featured Publications
- Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis
- Long Non-coding RNAs Are Central Regulators of the IL-1β-Induced Inflammatory Response in Normal and Idiopathic Pulmonary Lung Fibroblasts
- Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages
- Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response
- Transcriptional profiling identifies differential expression of long non-coding RNAs in Jo-1 associated and inclusion body myositis
- Ion channels and ion selectivity
Training
- Ph.D., 1980, Harvard University, Biophysics
- M.Sc, 1984, University of Montreal, Physics
- B.Sc., 1981, University of Montreal, Physics
