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Membrane proteins: molecular dynamics simulations
Stockholm University.ORCID iD: 0000-0002-2734-2794
Oxford University.
2008 (English)In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 18, no 4, 425-431 p.Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics simulations of membrane proteins are making rapid progress, because of new high-resolution structures, advances in computer hardware and atomistic simulation algorithms, and the recent introduction of coarse-grained models for membranes and proteins. In addition to several large ion channel simulations, recent studies have explored how individual amino acids interact with the bilayer or snorkel/anchor to the headgroup region, and it has been possible to calculate water/membrane partition free energies. This has resulted in a view of bilayers as being adaptive rather than purely hydrophobic solvents, with important implications, for example, for interaction between lipids and arginines in the charged S4 helix of voltage-gated ion channels. However, several studies indicate that the typical current simulations fall short of exhaustive sampling, and that even simple protein-membrane interactions require at least ca. 1 micros to fully sample their dynamics. One new way this is being addressed is coarse-grained models that enable mesoscopic simulations on multi-micros scale. These have been used to model interactions, self-assembly and membrane perturbations induced by proteins. While they cannot replace all-atom simulations, they are a potentially useful technique for initial insertion, placement, and low-resolution refinement.

Place, publisher, year, edition, pages
2008. Vol. 18, no 4, 425-431 p.
National Category
Biophysics Bioinformatics and Systems Biology Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-82621DOI: 10.1016/j.sbi.2008.02.003ISI: 000259556000005PubMedID: 18406600OAI: oai:DiVA.org:kth-82621DiVA: diva2:498468
Note
QC 20120227Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2017-12-07Bibliographically approved

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Lindahl, Erik

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