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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
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 | |||||||||||||||||||||
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| Subjects: | Q Science > QP Physiology | |||||||||||||||||||||
| Divisions: | Faculty of 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: |
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| 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: |
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