Paper Citing NAMD - Abstract
Pezeshki, Soroosh; Chimerel, Catalin; Bessonov, Andrey N.; Winterhalter, Mathias; Kleinekathoefer, Ulrich
Understanding Ion Conductance on a Molecular Level: An All-Atom Modeling of the Bacterial Porin OmpF
BIOPHYSICAL JOURNAL, 97:1898-1906, OCT 7 2009
All-atom molecular dynamics simulations of the ion current through OmpF, the major porin in the outer membrane of Escherichia coli, were performed. Starting from the crystal structure, the all-atom modeling allows us to calculate a parameter-free ion conductance in semiquantitative agreement with experiment. Discrepancies between modeling and experiment occur, e.g., at salt concentrations above 1 M KCl or at high temperatures. At lower salt concentrations, the ions have separate pathways along the channel surface. The constriction zone in the channel contains, on one side, a series of positively charges (R42, R82, R132), and on the opposite side, two negatively charged residues (D113, E117). Mutations generated in the constriction zone by removing cationic residues enhance the otherwise small cation selectivity, whereas removing the anionic residues reverses the selectivity. Reduction of the negatively charged residues decreases the conductance by half, whereas cationic residues enhance the conductance. Experiments on mutants confirm the results of the molecular-level simulations.
