Publication

High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating

Melo, M. N., Arnarez, C., Sikkema, H., Kumar, N., Walko, M., Berendsen, H. J. C., Kocer, A., Marrink, S. J. & Ingólfsson, H. I., 22-Feb-2017, In : Journal of the American Chemical Society. 139, 7, p. 2664-2671 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

APA

Melo, M. N., Arnarez, C., Sikkema, H., Kumar, N., Walko, M., Berendsen, H. J. C., Kocer, A., Marrink, S. J., & Ingólfsson, H. I. (2017). High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. Journal of the American Chemical Society, 139(7), 2664-2671. https://doi.org/10.1021/jacs.6b11091

Author

Melo, Manuel N ; Arnarez, Clement ; Sikkema, Hendrik ; Kumar, Neeraj ; Walko, Martin ; Berendsen, Herman J C ; Kocer, Armagan ; Marrink, Siewert J ; Ingólfsson, Helgi I. / High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. In: Journal of the American Chemical Society. 2017 ; Vol. 139, No. 7. pp. 2664-2671.

Harvard

Melo, MN, Arnarez, C, Sikkema, H, Kumar, N, Walko, M, Berendsen, HJC, Kocer, A, Marrink, SJ & Ingólfsson, HI 2017, 'High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating', Journal of the American Chemical Society, vol. 139, no. 7, pp. 2664-2671. https://doi.org/10.1021/jacs.6b11091

Standard

High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. / Melo, Manuel N; Arnarez, Clement; Sikkema, Hendrik; Kumar, Neeraj; Walko, Martin; Berendsen, Herman J C; Kocer, Armagan; Marrink, Siewert J; Ingólfsson, Helgi I.

In: Journal of the American Chemical Society, Vol. 139, No. 7, 22.02.2017, p. 2664-2671.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Melo MN, Arnarez C, Sikkema H, Kumar N, Walko M, Berendsen HJC et al. High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. Journal of the American Chemical Society. 2017 Feb 22;139(7):2664-2671. https://doi.org/10.1021/jacs.6b11091


BibTeX

@article{5aeb6ad2fd944870b83eb8f01d516f79,
title = "High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating",
abstract = "The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe osmotic downshock. Sensing bilayer tension, MscL channels are sensitive to changes in the bilayer environment and are, therefore, an ideal test case for exploring membrane protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gating kinetics in different bilayer environments under the influence of alcohols. We performed over five hundred simulations to obtain sufficient statistics to reveal the subtle effects of changes in the membrane environment on MscL gating. MscL opening times were found to increase with the addition of the straight chain alcohols ethanol, octanol, and to some extent dodecanol but not with hexadecanol. Increasing concentration of octanol increased the impeding effect, but only up to 10-20 mol %. Our in silico predictions were experimentally confirmed using reconstituted MscL in a liposomal fluorescent efflux assay. Our combined data reveal that the effect of alcohols on MscL gating arises not through specific binding sites but through a combination of the alcohol-induced changes to a number of bilayer properties and their alteration of the MscL bilayer interface. Our work provides a key example of how extensive molecular simulations can be used to predict the functional modification of membrane proteins by subtle changes in their bilayer environment.",
keywords = "MOLECULAR-DYNAMICS SIMULATIONS, MECHANOSENSITIVE ION-CHANNEL, LATERAL PRESSURE PROFILES, COARSE-GRAINED MODEL, SHORT-CHAIN ALCOHOLS, PROTEIN FUNCTION, LIPID-BILAYER, MYCOBACTERIUM-TUBERCULOSIS, ESCHERICHIA-COLI, FORCE-FIELD",
author = "Melo, {Manuel N} and Clement Arnarez and Hendrik Sikkema and Neeraj Kumar and Martin Walko and Berendsen, {Herman J C} and Armagan Kocer and Marrink, {Siewert J} and Ing{\'o}lfsson, {Helgi I}",
year = "2017",
month = feb,
day = "22",
doi = "10.1021/jacs.6b11091",
language = "English",
volume = "139",
pages = "2664--2671",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "AMER CHEMICAL SOC",
number = "7",

}

RIS

TY - JOUR

T1 - High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating

AU - Melo, Manuel N

AU - Arnarez, Clement

AU - Sikkema, Hendrik

AU - Kumar, Neeraj

AU - Walko, Martin

AU - Berendsen, Herman J C

AU - Kocer, Armagan

AU - Marrink, Siewert J

AU - Ingólfsson, Helgi I

PY - 2017/2/22

Y1 - 2017/2/22

N2 - The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe osmotic downshock. Sensing bilayer tension, MscL channels are sensitive to changes in the bilayer environment and are, therefore, an ideal test case for exploring membrane protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gating kinetics in different bilayer environments under the influence of alcohols. We performed over five hundred simulations to obtain sufficient statistics to reveal the subtle effects of changes in the membrane environment on MscL gating. MscL opening times were found to increase with the addition of the straight chain alcohols ethanol, octanol, and to some extent dodecanol but not with hexadecanol. Increasing concentration of octanol increased the impeding effect, but only up to 10-20 mol %. Our in silico predictions were experimentally confirmed using reconstituted MscL in a liposomal fluorescent efflux assay. Our combined data reveal that the effect of alcohols on MscL gating arises not through specific binding sites but through a combination of the alcohol-induced changes to a number of bilayer properties and their alteration of the MscL bilayer interface. Our work provides a key example of how extensive molecular simulations can be used to predict the functional modification of membrane proteins by subtle changes in their bilayer environment.

AB - The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe osmotic downshock. Sensing bilayer tension, MscL channels are sensitive to changes in the bilayer environment and are, therefore, an ideal test case for exploring membrane protein coupling. Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gating kinetics in different bilayer environments under the influence of alcohols. We performed over five hundred simulations to obtain sufficient statistics to reveal the subtle effects of changes in the membrane environment on MscL gating. MscL opening times were found to increase with the addition of the straight chain alcohols ethanol, octanol, and to some extent dodecanol but not with hexadecanol. Increasing concentration of octanol increased the impeding effect, but only up to 10-20 mol %. Our in silico predictions were experimentally confirmed using reconstituted MscL in a liposomal fluorescent efflux assay. Our combined data reveal that the effect of alcohols on MscL gating arises not through specific binding sites but through a combination of the alcohol-induced changes to a number of bilayer properties and their alteration of the MscL bilayer interface. Our work provides a key example of how extensive molecular simulations can be used to predict the functional modification of membrane proteins by subtle changes in their bilayer environment.

KW - MOLECULAR-DYNAMICS SIMULATIONS

KW - MECHANOSENSITIVE ION-CHANNEL

KW - LATERAL PRESSURE PROFILES

KW - COARSE-GRAINED MODEL

KW - SHORT-CHAIN ALCOHOLS

KW - PROTEIN FUNCTION

KW - LIPID-BILAYER

KW - MYCOBACTERIUM-TUBERCULOSIS

KW - ESCHERICHIA-COLI

KW - FORCE-FIELD

U2 - 10.1021/jacs.6b11091

DO - 10.1021/jacs.6b11091

M3 - Article

C2 - 28122455

VL - 139

SP - 2664

EP - 2671

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 7

ER -

ID: 39288479