publication . Article . Preprint . 2013

Dynamics of ions in the selectivity filter of the KcsA channel: Towards a coupled Brownian particle description

Cosseddu, Salvatore M.; Khovanov, I. A.; Allen, Michael P.; Rodger, P. Mark; Luchinsky, Dmitrii G.; McClintock, Peter V. E.;
Open Access English
  • Published: 01 Oct 2013
  • Publisher: Springer
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 ...
Subjects
arxiv: Quantitative Biology::Subcellular Processes
free text keywords: QC, Quantitative Biology - Biomolecules, Physics - Biological Physics
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publication . Article . Preprint . 2013

Dynamics of ions in the selectivity filter of the KcsA channel: Towards a coupled Brownian particle description

Cosseddu, Salvatore M.; Khovanov, I. A.; Allen, Michael P.; Rodger, P. Mark; Luchinsky, Dmitrii G.; McClintock, Peter V. E.;