focus of our laboratory is the understanding of the structure
and function of ion channels. We are particularly interested
in issues about ion permeation, ion selectivity, gating, and
channel inhibitors. We are currently working on the KcsA
channel, the OmpF porin, and the gramicidin A>
channel. We are also spending our efforts in the development
of new computational approaches for studying biological macromolecular
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 impossible to access experimentally.
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.
The determination of the structure of the KcsA K+ channel
from Streptomyces lividan has made it possible
to investigate the function of a biological channel at the
( Doyle et al, 1998 ).
Because of its structural similarity with
eukaryotic K-channels, investigations of KcsA are expected
to help understand a large class of biologically important
channels. We are currently working on several fundamental
aspect of the function of the KcsA channel such as, electrostatics, muti-ion
permeation, channel gating, and inhibition by various blocking agents (see
Roux and MacKinnon, 1999 ;
Berneche and Roux, 2000;
Roux et al., 2000;
Crouzy, et al, 2001; ;
Berneche and Roux, 2001).
The outer membrane of Escherichia coli protects the
cell against hostile agents and facilitates the uptake of
nutrients. This activity is mediated by macromolecular structures
called porins. Porins are not very selective and have only
some specificity towards cations or anions.
The porins represent ideal systems for addressing the fundamental
electrostatics principles governing ion flow in molecular
pores. Because high resolution well-characterized structures
are available for outer membrane porins of E coli,
they provide excellent model channel systems for computations
based on detailed atomic models. We are currently
working on the cation-selective matrixporin (OmpF) which
is a major component of the E. coli outer membrane.
Brownian dynamics provides an attractive computational approach
for simulating the permeation of ions over long time-scales
without having to treat all the solvent molecules explicitly.
The approach consists in integrating stochastic equation
of motions with some effective potential which incorporates
the systematic influence of the environment. To account
for non-equilibrium boundary conditions found in ion channel
systems (asymetric ion concentration and transmembrane potential)
we have developed a method combining the Grand Canonical
Monte Carlo algorithm with Brownian dynamics,
GCMC/BD (Im et al, 2000).
Implicit solvation methods
MD simulations with explicit solvent molecules are computationally
expensive and important properties such as solvation free
energies may often converge slowly. Other computational
approaches in which the influence of the solvent is incorporated
implicitly are needed (see
Roux and Simonson, 1999). Those include continuum electrostatics
based on the Poisson-Boltzmann (PB) equations (Nina et al., 1997),
stochastic Brownian Dynamics
(Im et al., 2000), and mean-field theories based on statistical
mechanical integral equations.
Polarizable force field
The potential function is one of the most important ingredients
in MD calculations. Many of the current simulations of biomolecular
systems are based on a potential function representing the
interactions between non-bonded atoms in terms of a Lennard-Jones
6-12 potential and fixed atomic partial charge coulomb electrostatics.
In our group we normally use the potential function of the
biomolecular simulation program. Other
similar potential functions are
AMBER , and
We think that such simple models, which ignore electronic
polarization effects, will be insufficient for understanding
the microscopic basis of ion selectivity in biological channels.
We are currently developing a force
field which will include induced polarization (see
Lamoureux et al, 2003,
Lamoureux et al, 2005,
Harder et al, 2009).
Free energy simulations
By and large, microscopic processes such as ion permeation,
macromolecular conformational changes, ligand binding specificity,
and protein-protein association are driven thermodynamically
by the free energy (or potential of mean force) in diverse
and complex environments such as bulk aqueous solution,
the active site of an enzyme, the interior of an ion channel,
or a bilayer membrane. A quantitative determination of free
energies is thus a problem of central importance in theoretical
biophysics. We are currently developing and extending current methodologies
to allow precise and computationally inexpensive free energy calculations
(see Pomes et al, 1999,
Shobana et al, 2000,
Wang et al, 2006,
Deng and Roux, 2009).
Our group includes a fully-equiped experimental lab, performing expression and purification of proteins such as Hck tyrosine kinase and OmpF Porin. These proteins are characterized using X-ray diffractio and SAXS scattering (see Yang et al, 2010, Dhakshnamoorthy et al, 2010).