Modeling of Ion Channels

Modeling of biological ion channels has a long history, going back more then 100 yr ([Hille 1984][1]). In the old, premolecular biology era, interpretation of these simple models provided the primary source of information about channel structure. As molecular biology and, now, x-ray diffraction have

[1]  E. Mccleskey,et al.  Ion Channel Selectivity through Stepwise Changes in Binding Affinity , 1998, The Journal of general physiology.

[2]  E. Jakobsson,et al.  Brownian dynamics study of a multiply-occupied cation channel: application to understanding permeation in potassium channels. , 1994, Biophysical journal.

[3]  S. Chung,et al.  Brownian dynamics study of ion transport in the vestibule of membrane channels. , 1998, Biophysical journal.

[4]  D. Levitt.  General continuum theory for multiion channel. II. Application to acetylcholine channel. , 1991, Biophysical journal.

[5]  M. Klein,et al.  Molecular dynamics simulation of a synthetic ion channel. , 1998, Biophysical journal.

[6]  D. Levitt.  Interpretation of biological ion channel flux data--reaction-rate versus continuum theory. , 1986, Annual review of biophysics and biophysical chemistry.

[7]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[8]  Y. Komeiji,et al.  Computational Observation of an Ion Permeation Through a Channel Protein , 1998, Bioscience reports.

[9]  D C Rees,et al.  Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. , 1998, Science.

[10]  Shin-Ho Chung,et al.  Study of ionic currents across a model membrane channel using Brownian dynamics. , 1998, Biophysical journal.

[11]  E Jakobsson,et al.  Using theory and simulation to understand permeation and selectivity in ion channels. , 1998, Methods.

[12]  D. Levitt.  General continuum theory for multiion channel. I. Theory. , 1991, Biophysical journal.

[13]  H. Berendsen,et al.  A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. , 1998, Biophysical journal.

[14]  K. Diederichs,et al.  Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide. , 1998, Science.

[15]  Peter C. Jordan,et al.  A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity. , 1996, Biophysical journal.

[16]  A. Nitzan,et al.  A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel. , 1999, Biophysical journal.

[17]  G. R. Smith,et al.  Modelling and simulation of ion channels: applications to the nicotinic acetylcholine receptor. , 1998, Journal of structural biology.

[18]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[19]  R.,et al.  Ion Channels , 1996, Ion Channels.

[20]  B. Eisenberg,et al.  Ion permeation and glutamate residues linked by Poisson-Nernst-Planck theory in L-type calcium channels. , 1998, Biophysical journal.

[21]  B. Hille.  Ionic channels of excitable membranes , 2001 .

[22]  G. R. Smith,et al.  Dynamic properties of Na+ ions in models of ion channels: a molecular dynamics study. , 1998, Biophysical journal.

[23]  D. Levitt.  Exact continuum solution for a channel that can be occupied by two ions. , 1987, Biophysical journal.

[24]  M Karplus,et al.  Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. , 1995, Biophysical journal.

[25]  G. Schulz,et al.  Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus. , 1994, Journal of molecular biology.

[26]  B. Roux,et al.  The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data. , 1997, Biophysical journal.