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Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations
KTH, School of Engineering Sciences (SCI), Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Engineering Sciences (SCI), Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-0828-3899
2018 (English)In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1860, no 4, p. 909-926Article, review/survey (Refereed) Published
Abstract [en]

The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables.

Place, publisher, year, edition, pages
ELSEVIER SCIENCE BV , 2018. Vol. 1860, no 4, p. 909-926
Keyword [en]
Molecular dynamics simulations, Membrane protein, Ion channel, Transporter, G-protein coupled receptor, Free energy landscape
National Category
Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-225283DOI: 10.1016/j.bbamem.2017.10.033ISI: 000426027600012PubMedID: 29113819Scopus ID: 2-s2.0-85035114873OAI: oai:DiVA.org:kth-225283DiVA, id: diva2:1194714
Note

QC 20180403

Available from: 2018-04-03 Created: 2018-04-03 Last updated: 2018-04-03Bibliographically approved

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