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. Finally, our work provides a key example of howmore »
- Authors:
-
- Univ. of Groningen, Groningen (The Netherlands)
- Univ. of Groningen, Groningen (The Netherlands); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1346131
- Report Number(s):
- LLNL-JRNL-715277
Journal ID: ISSN 0002-7863
- Grant/Contract Number:
- AC52-07NA27344
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Journal of the American Chemical Society
- Additional Journal Information:
- Journal Volume: 139; Journal Issue: 7; Journal ID: ISSN 0002-7863
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Melo, Manuel N., Arnarez, Clement, Sikkema, Hendrik, Kumar, Neeraj, Walko, Martin, Berendsen, Herman J. C., Kocer, Armagan, Marrink, Siewert J., and Ingolfsson, Helgi I. High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating. United States: N. p., 2017.
Web. doi:10.1021/jacs.6b11091.
Melo, Manuel N., Arnarez, Clement, Sikkema, Hendrik, Kumar, Neeraj, Walko, Martin, Berendsen, Herman J. C., Kocer, Armagan, Marrink, Siewert J., & Ingolfsson, Helgi I. High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating. United States. https://doi.org/10.1021/jacs.6b11091
Melo, Manuel N., Arnarez, Clement, Sikkema, Hendrik, Kumar, Neeraj, Walko, Martin, Berendsen, Herman J. C., Kocer, Armagan, Marrink, Siewert J., and Ingolfsson, Helgi I. 2017.
"High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating". United States. https://doi.org/10.1021/jacs.6b11091. https://www.osti.gov/servlets/purl/1346131.
@article{osti_1346131,
title = {High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating},
author = {Melo, Manuel N. and Arnarez, Clement and Sikkema, Hendrik and Kumar, Neeraj and Walko, Martin and Berendsen, Herman J. C. and Kocer, Armagan and Marrink, Siewert J. and Ingolfsson, Helgi I.},
abstractNote = {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. Finally, 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.},
doi = {10.1021/jacs.6b11091},
url = {https://www.osti.gov/biblio/1346131},
journal = {Journal of the American Chemical Society},
issn = {0002-7863},
number = 7,
volume = 139,
place = {United States},
year = {Thu Jan 26 00:00:00 EST 2017},
month = {Thu Jan 26 00:00:00 EST 2017}
}
Web of Science
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Coarse Grained Model for Semiquantitative Lipid Simulations
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The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
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journal, April 2008
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Lateral Pressures in Cell Membranes: A Mechanism for Modulation of Protein Function
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Mechanosensitive ion channels of E. coli activated by amphipaths
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A large-conductance mechanosensitive channel in E. coli encoded by mscL alone
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Synthesis and utilization of reversible and irreversible light-activated nanovalves derived from the channel protein MscL
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Physical principles underlying the transduction of bilayer deformation forces during mechanosensitive channel gating
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Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS
journal, May 2012
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- Proceedings of the National Academy of Sciences, Vol. 109, Issue 22
Pressure-sensitive ion channel in Escherichia coli.
journal, April 1987
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- Proceedings of the National Academy of Sciences, Vol. 84, Issue 8
Perspectives on How to Drug an Ion Channel
journal, April 2008
- Andersen, Olaf Sparre
- Journal of General Physiology, Vol. 131, Issue 5
The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension‐induced gating
journal, June 2014
- Mukherjee, Nobina; Jose, Mac Donald; Birkner, Jan Peter
- The FASEB Journal, Vol. 28, Issue 10
Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes
journal, July 2009
- Lundbæk, Jens A.; Collingwood, Shemille A.; Ingólfsson, Helgi I.
- Journal of The Royal Society Interface, Vol. 7, Issue 44
Structure of the MscL Homolog from Mycobacterium tuberculosis: A Gated Mechanosensitive Ion Channel
journal, December 1998
- Chang, G.; Spencer, R. H.; Lee, A. T.
- Science, Vol. 282, Issue 5397
Bilayer Thickness and Membrane Protein Function: An Energetic Perspective
journal, June 2007
- Andersen, Olaf S.; Koeppe, Roger E.
- Annual Review of Biophysics and Biomolecular Structure, Vol. 36, Issue 1
Molecular Basis of Mechanotransduction in Living Cells
journal, April 2001
- Hamill, Owen P.; Martinac, Boris
- Physiological Reviews, Vol. 81, Issue 2
Computational ‘microscopy’ of cellular membranes
journal, January 2016
- Ingólfsson, Helgi I.; Arnarez, Clément; Periole, Xavier
- Journal of Cell Science, Vol. 129, Issue 2
Force Transduction and Lipid Binding in MscL: A Continuum-Molecular Approach
journal, December 2014
- Vanegas, Juan M.; Arroyo, Marino
- PLoS ONE, Vol. 9, Issue 12
The Influence of Short-Chain Alcohols on Interfacial Tension, Mechanical Properties, Area/Molecule, and Permeability of Fluid Lipid Bilayers
journal, August 2004
- Ly, Hung V.; Longo, Marjorie L.
- Biophysical Journal, Vol. 87, Issue 2
Lipid Bilayer Pressure Profiles and Mechanosensitive Channel Gating
journal, June 2004
- Gullingsrud, Justin; Schulten, Klaus
- Biophysical Journal, Vol. 86, Issue 6
How Alcohol Chain-Length and Concentration Modulate Hydrogen Bond Formation in a Lipid Bilayer
journal, April 2007
- Dickey, Allison N.; Faller, Roland
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