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Dynamics of ions in the selectivity filter of the KcsA channel

Research output: Contribution to Journal/Magazine › Journal article › peer-review

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Dynamics of ions in the selectivity filter of the KcsA channel. / Cosseddu, Salvatore M.; Khovanov, I. A.; Allen, Michael P. et al.
In: European Physical Journal - Special Topics, Vol. 222, No. 10, 10.2013, p. 2595-2605.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Harvard

Cosseddu, SM, Khovanov, IA, Allen, MP, Rodger, PM, Luchinsky, DG & McClintock, PVE 2013, 'Dynamics of ions in the selectivity filter of the KcsA channel', European Physical Journal - Special Topics, vol. 222, no. 10, pp. 2595-2605. https://doi.org/10.1140/epjst/e2013-02040-9

APA

Cosseddu, S. M., Khovanov, I. A., Allen, M. P., Rodger, P. M., Luchinsky, D. G., & McClintock, P. V. E. (2013). Dynamics of ions in the selectivity filter of the KcsA channel. European Physical Journal - Special Topics, 222(10), 2595-2605. https://doi.org/10.1140/epjst/e2013-02040-9

Vancouver

Cosseddu SM, Khovanov IA, Allen MP, Rodger PM, Luchinsky DG, McClintock PVE. Dynamics of ions in the selectivity filter of the KcsA channel. European Physical Journal - Special Topics. 2013 Oct;222(10):2595-2605. doi: 10.1140/epjst/e2013-02040-9

Author

Cosseddu, Salvatore M. ; Khovanov, I. A. ; Allen, Michael P. et al. / Dynamics of ions in the selectivity filter of the KcsA channel. In: European Physical Journal - Special Topics. 2013 ; Vol. 222, No. 10. pp. 2595-2605.

Bibtex

@article{82c5da123e9e4d5781e8ed42dac8419f,
title = "Dynamics of ions in the selectivity filter of the KcsA 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{\textquoteright}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.",
author = "Cosseddu, {Salvatore M.} and Khovanov, {I. A.} and Allen, {Michael P.} and Rodger, {P. Mark} and Luchinsky, {Dmitrii G.} and McClintock, {Peter V. E.}",
note = "The final publication is available at Springer via http://dx.doi.org/10.1140/epjst/e2013-02040-9",
year = "2013",
month = oct,
doi = "10.1140/epjst/e2013-02040-9",
language = "English",
volume = "222",
pages = "2595--2605",
journal = "European Physical Journal - Special Topics",
issn = "1951-6355",
publisher = "EDP SCIENCES S A",
number = "10",

}

RIS

TY - JOUR

T1 - Dynamics of ions in the selectivity filter of the KcsA channel

AU - Cosseddu, Salvatore M.

AU - Khovanov, I. A.

AU - Allen, Michael P.

AU - Rodger, P. Mark

AU - Luchinsky, Dmitrii G.

AU - McClintock, Peter V. E.

N1 - The final publication is available at Springer via http://dx.doi.org/10.1140/epjst/e2013-02040-9

PY - 2013/10

Y1 - 2013/10

N2 - 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.

AB - 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.

U2 - 10.1140/epjst/e2013-02040-9

DO - 10.1140/epjst/e2013-02040-9

M3 - Journal article

VL - 222

SP - 2595

EP - 2605

JO - European Physical Journal - Special Topics

JF - European Physical Journal - Special Topics

SN - 1951-6355

IS - 10

ER -