Journal
CURRENT OPINION IN STRUCTURAL BIOLOGY
Volume 18, Issue 4, Pages 425-431Publisher
CURRENT BIOLOGY LTD
DOI: 10.1016/j.sbi.2008.02.003
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Funding
- Wellcome Trust
- BBSRC
- EPSRC
- Swedish Research Council
- Foundation for Strategic Research
- Carl Trygger foundation
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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 mu s to fully sample their dynamics. One new way this is being addressed is coarse-grained models that enable mesoscopic simulations on multi-mu s 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.
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