Dynamic properties of Na+ ions in models of ion channels: a molecular dynamics study.
We present simulation results for the effective diffusion coefficients of a sodium ion in a series of model ion channels of different diameters and hydrophobicities, including models of alamethicin, a leucine-serine peptide, and the M2 helix bundle of the nicotinic acetylcholine receptor. The diffusion coefficient, which in the simulations has a value of 0.15(2) A2ps-1 in bulk water, is found to be reduced to as little as 0.02(1) A2ps-1 in the narrower channels, and to about 0.10(5) A2ps-1 in wider channels such as the nicotinic acetylcholine receptor. It is anticipated that this work will be useful in connection with calculations of channel conductivity using such techniques as the Poisson-Nernst-Planck equation, Eyring rate theory, or Brownian dynamics.
Smith
G R
GR
Laboratory of Molecular Biophysics, University of Oxford, Oxford OX1 3QU, United Kingdom.
Sansom
M S
MS
D000408:Alamethicin / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D001499:Bayes Theorem; D055592:Biophysical Phenomena; D001703:Biophysics; D004058:Diffusion; D066298:In Vitro Techniques; D007473:Ion Channels / Q000737:chemistry* / Q000378:metabolism*; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011978:Receptors, Nicotinic / Q000737:chemistry / Q000378:metabolism; D012964:Sodium / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity; D013499:Surface Properties; D013816:Thermodynamics
D007473:Ion Channels; D010455:Peptides; D011978:Receptors, Nicotinic; D000408:Alamethicin; D012964:Sodium