Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.

ABSTRACT: A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradien

SUBMITTER: Khalili-Araghi F 

PROVIDER: S-EPMC3787774 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature