title: Semimicroscopic modeling of permeation energetics in ion channels.
abstract: The semimicroscopic (SMC) approach to modeling the energetics of ion permeation through biological channels provides an alternative perspective to standard molecular dynamics methods. It exploits the timescale separation between electronic and structural contributions to dielectric stabilization and accounts for electronic polarization by embedding the channel in a milieu that, on average, describes this polarization. Ions, water, and selected peptide moieties are mobile and comprise the reorganizational contribution to dielectric stabilization. The conceptual advantages and limitations of the technique are described. Methodological details are outlined, stressing three convenient electrical geometries. Practical aspects of the SMC procedure are explained, highlighting the areas ripe for further development. Finally, some specific applications are considered.
authors.affiliation: Department of Chemistry, Brandeis University, Waltham, MA 02454-9110, USA. jordan@brandeis.edu
authors.forename: Peter C
authors.initials: PC
authors.lastname: Jordan
mesh_terms: D002462:Cell Membrane / Q000737:chemistry* / Q000502:physiology*; D002463:Cell Membrane Permeability / Q000502:physiology*; D003198:Computer Simulation; D015640:Ion Channel Gating / Q000502:physiology*; D007473:Ion Channels / Q000737:chemistry / Q000502:physiology*; D008564:Membrane Potentials / Q000502:physiology; D008954:Models, Biological; D008956:Models, Chemical; D013329:Structure-Activity Relationship
chemical_list: D007473:Ion Channels