%0 Journal Article %1 Lindahl2008MembraneProteinMD %A Lindahl, Erik %A Sansom, Mark SP %D 2008 %J Current Opinion in Structural Biology %K computational-biology membrane-proteins molecular-dynamics %N 4 %P 425 - 431 %R http://dx.doi.org/10.1016/j.sbi.2008.02.003 %T Membrane proteins: molecular dynamics simulations %U http://www.sciencedirect.com/science/article/pii/S0959440X08000304 %V 18 %X 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 μs to fully sample their dynamics. One new way this is being addressed is coarse-grained models that enable mesoscopic simulations on multi-μs 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.

@article{Lindahl2008MembraneProteinMD, abstract = {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 μs to fully sample their dynamics. One new way this is being addressed is coarse-grained models that enable mesoscopic simulations on multi-μs 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. }, added-at = {2016-02-04T00:28:02.000+0100}, author = {Lindahl, Erik and Sansom, Mark SP}, biburl = {https://www.bibsonomy.org/bibtex/2dabc67cea4cc8f0948c075bf4cb8666e/salotz}, description = {Membrane proteins: molecular dynamics simulations}, doi = {http://dx.doi.org/10.1016/j.sbi.2008.02.003}, interhash = {b35f12ed4eb9b9571505b31d8c2fa34a}, intrahash = {dabc67cea4cc8f0948c075bf4cb8666e}, issn = {0959-440X}, journal = {Current Opinion in Structural Biology }, keywords = {computational-biology membrane-proteins molecular-dynamics}, note = {Membranes / Engineering and design }, number = 4, pages = {425 - 431}, timestamp = {2016-02-04T00:28:02.000+0100}, title = {Membrane proteins: molecular dynamics simulations }, url = {http://www.sciencedirect.com/science/article/pii/S0959440X08000304}, volume = 18, year = 2008 }