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The European Physical Journal Special Topics

, Volume 222, Issue 10, pp 2595–2605 | Cite as

Dynamics of ions in the selectivity filter of the KcsA channel

Towards a coupled Brownian particle description
  • S.M. CossedduEmail author
  • I.A. Khovanov
  • M.P. Allen
  • P.M. Rodger
  • D.G. Luchinsky
  • P.V.E. McClintock
Regular Article Applications in Chemistry, Physics and Engineering

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.

Keywords

Molecular Dynamic Simulation European Physical Journal Special Topic Langevin Equation Brownian Dynamic Fractional Noise 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© EDP Sciences and Springer 2013

Authors and Affiliations

  • S.M. Cosseddu
    • 1
    • 2
    Email author
  • I.A. Khovanov
    • 1
    • 2
  • M.P. Allen
    • 3
  • P.M. Rodger
    • 1
    • 4
  • D.G. Luchinsky
    • 5
    • 6
  • P.V.E. McClintock
    • 6
  1. 1.Centre for Scientific Computing, University of WarwickCoventryUK
  2. 2.School of Engineering, University of WarwickCoventryUK
  3. 3.Department of PhysicsUniversity of WarwickCoventryUK
  4. 4.Department of ChemistryUniversity of WarwickCoventryUK
  5. 5.Mission Critical Technologies Inc., 2041 Rosecrans Ave. Suite 225 El SegundoCAUSA
  6. 6.Physics Department, Lancaster University, LA1 4YB LancasterLancasterUK

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