Membrane models for molecular simulations of peripheral membrane proteins

Autor: Mahmoud Moqadam, Thibault Tubiana, Emmanuel E. Moutoussamy, Nathalie Reuter
Jazyk: angličtina
Rok vydání: 2021
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Zdroj: Advances in Physics: X, Vol 6, Iss 1 (2021)
Druh dokumentu: article
ISSN: 2374-6149
23746149
DOI: 10.1080/23746149.2021.1932589
Popis: Peripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their interfacial-binding site with membrane lipids remain difficult to observe directly. Their binding and unbinding mechanism, the conformational changes of the PMPs and their influence on the membrane structure are notoriously challenging to study experimentally. Molecular dynamics simulations are particularly useful to fill some knowledge-gaps and provide hypothesis that can be experimentally challenged to further our understanding of PMP-membrane recognition. Because of the time-scales of PMP-membrane binding events and the computational costs associated with molecular dynamics simulations, membrane models at different levels of resolution are used and often combined in multiscale simulation strategies. We here review membrane models belonging to three classes: atomistic, coarse-grained and implicit. Differences between models are rooted in the underlying theories and the reference data they are parameterized against. The choice of membrane model should therefore not only be guided by its computational efficiency. The range of applications of each model is discussed and illustrated using examples from the literature.
Databáze: Directory of Open Access Journals
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