Dynamics of ions in the selectivity filter of the KcsA channel

Cosseddu, Salvatore M. and Khovanov, I. A. and Allen, Michael P. and Rodger, P. Mark and Luchinsky, Dmitrii G. and McClintock, Peter V. E. (2013) Dynamics of ions in the selectivity filter of the KcsA channel. European Physical Journal - Special Topics, 222 (10). pp. 2595-2605. ISSN 1951-6355

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Abstract

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force de-rived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.

Item Type:
Journal Article
Journal or Publication Title:
European Physical Journal - Special Topics
Additional Information:
The final publication is available at Springer via http://dx.doi.org/10.1140/epjst/e2013-02040-9
Uncontrolled Keywords:
/dk/atira/pure/subjectarea/asjc/1600/1606
Subjects:
ID Code:
67689
Deposited By:
Deposited On:
25 Nov 2013 11:20
Refereed?:
Yes
Published?:
Published
Last Modified:
29 Feb 2020 02:52