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Dynamics of ions in the selectivity filter of the KcsA channel
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Cosseddu, Salvatore M., Khovanov, I. A., Allen, M. P., Rodger, P. Mark, Luchinsky, Dmitri G. and McClintock, P. V. E. (2013) Dynamics of ions in the selectivity filter of the KcsA channel. European Physical Journal - Special Topics, Volume 222 (Number 10). pp. 2595-2605. doi:10.1140/epjst/e2013-02040-9 ISSN 1951-6355.
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Official URL: http://dx.doi.org/10.1140/epjst/e2013-02040-9
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 derived 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 | ||||
|---|---|---|---|---|---|
| Subjects: | Q Science > QC Physics | ||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Chemistry Faculty of Science, Engineering and Medicine > Engineering > Engineering Faculty of Science, Engineering and Medicine > Science > Physics Faculty of Science, Engineering and Medicine > Science > Centre for Scientific Computing |
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| Library of Congress Subject Headings (LCSH): | Molecular dynamics, Ions, Langevin equations | ||||
| Journal or Publication Title: | European Physical Journal - Special Topics | ||||
| Publisher: | Springer | ||||
| ISSN: | 1951-6355 | ||||
| Official Date: | October 2013 | ||||
| Dates: |
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| Volume: | Volume 222 | ||||
| Number: | Number 10 | ||||
| Page Range: | pp. 2595-2605 | ||||
| DOI: | 10.1140/epjst/e2013-02040-9 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access | ||||
| Funder: | Engineering and Physical Sciences Research Council (EPSRC) | ||||
| Grant number: | EP/G070660/1 (EPSRC), EP/K000128/1 (EPSRC) | ||||
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