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Appointments:
Professor
Department of Biochemistry and
Molecular Biology
Department of Pediatrics
Institute of Molecular Pediatric Sciences
Committee on Cancer Biology
Committee on Molecular Medicine/MPMM
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Education:
Ph.D. Harvard
University, 1990
M.Sc. University of
Montreal, 1984
B.Sc. University of
Montreal, 1981
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Contact:
Phone: (773) 834-3557
Fax:
(773) 834-1917
E-Mail:
roux@uchicago.edu
Address:
The University of Chicago
GCIS W323B
929 East 57th Street
Chicago, IL 60637
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Related Research Interests:
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Benoit Roux, Ph.D.
Theoretical and Computational Studies of the Structure,
Dynamics and Function of Biological Macromolecular Systems
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
Jogini V, Roux B. (2005). Electrostatics of the intracellular vestibule
of K+ channels. J Mol Biol.
354(2):272-88. Epub 2005 Sep 30. PMID: 16242718 [PubMed - indexed for
MEDLINE]
Banavali NK, Roux B. (2005). The N-terminal end of the catalytic domain
of SRC
kinase Hck is a conformational switch implicated in long-range
allosteric regulation. Structure.
2005 Nov;13(11):1715-23. PMID: 16271895 [PubMed - in process]
Lague P, Roux B, Pastor RW. (2005). Molecular dynamics simulations of
the influenza
hemagglutinin fusion peptide in micelles and bilayers: conformational
analysis of peptide and lipids. J Mol Biol.
354(5):1129-41. Epub 2005 Nov 8. PMID: 16297931 [PubMed - indexed for
MEDLINE]
Faraldo-Gomez JD, Kutluay E, Jogini V, Zhao Y, Heginbotham L, Roux B.
(2006). Mechanism of Intracellular Block of the KcsA K(+)
Channel by Tetrabutylammonium: Insights from X-ray Crystallography,
Electrophysiology and Replica-exchange Molecular Dynamics Simulations. J Mol Biol. [Epub ahead of
print] PMID: 17070844 [PubMed - as supplied by publisher]
Roux B. (2006). Dissecting the Coupling between the Voltage Sensor and
Pore Domains. Neuron. 52(4):568-9. PMID:
17114039 [PubMed - in process]
Roux B. (2006). Extracellular Blockade of Potassium Channels by TEA+:
The Tip of the Iceberg? J
Gen Physiol. 128(6):635-6. No abstract available. PMID: 17130517
[PubMed - in process]
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Faculty and Research
Programs
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