1. Dynamics of ions in the selectivity filter of the KcsA channel
- Author
-
P. .. . M. .. Rodger, Peter V. E. McClintock, Igor A. Khovanov, Michael P. Allen, S. .. . M. .. Cosseddu, and Dmitri G. Luchinsky
- Subjects
Physics ,010304 chemical physics ,KcsA potassium channel ,FOS: Physical sciences ,General Physics and Astronomy ,Biomolecules (q-bio.BM) ,White noise ,01 natural sciences ,Ion ,Quantitative Biology::Subcellular Processes ,Langevin equation ,Molecular dynamics ,Quantitative Biology - Biomolecules ,Biological Physics (physics.bio-ph) ,Chemical physics ,FOS: Biological sciences ,0103 physical sciences ,Brownian dynamics ,General Materials Science ,Physics - Biological Physics ,Statistical physics ,Physical and Theoretical Chemistry ,Umbrella sampling ,010306 general physics ,Ion channel - 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., to appear in Eur. Phys. J. Spec. Top
- Published
- 2013