Ionic permeation free energy in gramicidin: a semimicroscopic perspective.

ABSTRACT: Ion permeation through the gramicidin channel is studied using a model that circumvents two major difficulties inherent to standard simulational methods. It exploits the timescale separation between electronic and structural contributions to dielectric stabilization, accounting for the influence of electronic polarization by embedding the channel in a dielectric milieu that describes this polarization in a mean sense. The explicit mobile moieties are the ion, multipolar waters, and the carbonyls and amides of the peptide backbone. The model treats the influence of aromatic residues and the membrane dipole potential. A new electrical geometry is introduced that treats long-range electrostatics exactly and avoids problems related to periodic boundary conditions. It permits the translocating

SUBMITTER: Dorman VL 

PROVIDER: S-EPMC1304257 | biostudies-literature | 2004 Jun

REPOSITORIES: biostudies-literature