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Insights into membrane protein–lipid interactions from free energy calculations

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Corey, Robin A., Vickery, Owen N., Sansom, Mark S. P. and Stansfeld, Phillip J. (2019) Insights into membrane protein–lipid interactions from free energy calculations. Journal of Chemical Theory and Computation, 15 (10). pp. 5727-5736. doi:10.1021/acs.jctc.9b00548

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Official URL: http://dx.doi.org/10.1021/acs.jctc.9b00548

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Abstract

Integral membrane proteins are regulated by specific interactions with lipids from the surrounding bilayer. The structures of protein–lipid complexes can be determined through a combination of experimental and computational approaches, but the energetic basis of these interactions is difficult to resolve. Molecular dynamics simulations provide the primary computational technique to estimate the free energies of these interactions. We demonstrate that the energetics of protein–lipid interactions may be reliably and reproducibly calculated using three simulation-based approaches: potential of mean force calculations, alchemical free energy perturbation, and well-tempered metadynamics. We employ these techniques within the framework of a coarse-grained force field and apply them to both bacterial and mammalian membrane protein–lipid systems. We demonstrate good agreement between the different techniques, providing a robust framework for their automated implementation within a pipeline for annotation of newly determined membrane protein structures.

Item Type: Journal Article
Subjects: Q Science > QP Physiology
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Membrane proteins, Lipids, Membrane lipids, Protein binding, Lipoproteins, Molecular dynamics -- Computer simulation
Journal or Publication Title: Journal of Chemical Theory and Computation
Publisher: American Chemical Society
ISSN: 1549-9618
Official Date: 2 September 2019
Dates:
DateEvent
2 September 2019Published
2 September 2019Accepted
Volume: 15
Number: 10
Page Range: pp. 5727-5736
DOI: 10.1021/acs.jctc.9b00548
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
208361/Z/17/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
BB/P01948X/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
MR/S009213/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
BB/S003339/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
BB/R002517/1 [BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
EP/L000253/1[EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266

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