Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations

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Standard

Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. / Liu, Yang; de Vries, Alex H.; Pezeshkian, Weria; Marrink, Siewert J.

I: Journal of Chemical Theory and Computation, Bind 17, Nr. 9, 14.09.2021, s. 5876-5884.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Liu, Y, de Vries, AH, Pezeshkian, W & Marrink, SJ 2021, 'Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations', Journal of Chemical Theory and Computation, bind 17, nr. 9, s. 5876-5884. https://doi.org/10.1021/acs.jctc.1c00151

APA

Liu, Y., de Vries, A. H., Pezeshkian, W., & Marrink, S. J. (2021). Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 17(9), 5876-5884. https://doi.org/10.1021/acs.jctc.1c00151

Vancouver

Liu Y, de Vries AH, Pezeshkian W, Marrink SJ. Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 2021 sep. 14;17(9):5876-5884. https://doi.org/10.1021/acs.jctc.1c00151

Author

Liu, Yang ; de Vries, Alex H. ; Pezeshkian, Weria ; Marrink, Siewert J. / Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations. I: Journal of Chemical Theory and Computation. 2021 ; Bind 17, Nr. 9. s. 5876-5884.

Bibtex

@article{7d997696ae4543aa8a4c8b1eed8d8cdf,
title = "Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations",
abstract = "Understanding the lateral organization in plasma membranes remains an open problem and is of great interest to many researchers. Model membranes consisting of coexisting domains are commonly used as simplified models of plasma membranes. The coarse-grained (CG) Martini force field has successfully captured spontaneous separation of ternary membranes into a liquid-disordered and a liquid-ordered domain. With all-atom (AA) models, however, phase separation is much harder to achieve due to the slow underlying dynamics. To remedy this problem, here, we apply the virtual site (VS) hybrid method on a ternary membrane composed of saturated lipids, unsaturated lipids, and cholesterol to investigate the phase separation. The VS scheme couples the two membrane leaflets at CG and AA resolution. We found that the rapid phase separation reached by the CG leaflet can accelerate and guide this process in the AA leaflet.",
keywords = "FORCE-FIELD, LIPID RAFTS, MODEL, MARTINI, CHOLESTEROL, ALGORITHM, PROTEINS, EQUILIBRIA, ACTIVATION, MOBILITY",
author = "Yang Liu and {de Vries}, {Alex H.} and Weria Pezeshkian and Marrink, {Siewert J.}",
year = "2021",
month = sep,
day = "14",
doi = "10.1021/acs.jctc.1c00151",
language = "English",
volume = "17",
pages = "5876--5884",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "American Chemical Society",
number = "9",

}

RIS

TY - JOUR

T1 - Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations

AU - Liu, Yang

AU - de Vries, Alex H.

AU - Pezeshkian, Weria

AU - Marrink, Siewert J.

PY - 2021/9/14

Y1 - 2021/9/14

N2 - Understanding the lateral organization in plasma membranes remains an open problem and is of great interest to many researchers. Model membranes consisting of coexisting domains are commonly used as simplified models of plasma membranes. The coarse-grained (CG) Martini force field has successfully captured spontaneous separation of ternary membranes into a liquid-disordered and a liquid-ordered domain. With all-atom (AA) models, however, phase separation is much harder to achieve due to the slow underlying dynamics. To remedy this problem, here, we apply the virtual site (VS) hybrid method on a ternary membrane composed of saturated lipids, unsaturated lipids, and cholesterol to investigate the phase separation. The VS scheme couples the two membrane leaflets at CG and AA resolution. We found that the rapid phase separation reached by the CG leaflet can accelerate and guide this process in the AA leaflet.

AB - Understanding the lateral organization in plasma membranes remains an open problem and is of great interest to many researchers. Model membranes consisting of coexisting domains are commonly used as simplified models of plasma membranes. The coarse-grained (CG) Martini force field has successfully captured spontaneous separation of ternary membranes into a liquid-disordered and a liquid-ordered domain. With all-atom (AA) models, however, phase separation is much harder to achieve due to the slow underlying dynamics. To remedy this problem, here, we apply the virtual site (VS) hybrid method on a ternary membrane composed of saturated lipids, unsaturated lipids, and cholesterol to investigate the phase separation. The VS scheme couples the two membrane leaflets at CG and AA resolution. We found that the rapid phase separation reached by the CG leaflet can accelerate and guide this process in the AA leaflet.

KW - FORCE-FIELD

KW - LIPID RAFTS

KW - MODEL

KW - MARTINI

KW - CHOLESTEROL

KW - ALGORITHM

KW - PROTEINS

KW - EQUILIBRIA

KW - ACTIVATION

KW - MOBILITY

U2 - 10.1021/acs.jctc.1c00151

DO - 10.1021/acs.jctc.1c00151

M3 - Journal article

C2 - 34165988

VL - 17

SP - 5876

EP - 5884

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 9

ER -

ID: 316752331