Membrane proteins: molecular dynamics simulations.
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 i...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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2008
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| _version_ | 1797055452539781120 |
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| author | Lindahl, E Sansom, MS |
| author_facet | Lindahl, E Sansom, MS |
| author_sort | Lindahl, E |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-06T19:10:56Z |
| format | Journal article |
| id | oxford-uuid:16bec046-02e6-4e4d-b4d4-f7bee116bcc2 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T19:10:56Z |
| publishDate | 2008 |
| record_format | dspace |
| spelling | oxford-uuid:16bec046-02e6-4e4d-b4d4-f7bee116bcc22022-03-26T10:33:07ZMembrane proteins: molecular dynamics simulations.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:16bec046-02e6-4e4d-b4d4-f7bee116bcc2EnglishSymplectic Elements at Oxford2008Lindahl, ESansom, MSMolecular 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. |
| spellingShingle | Lindahl, E Sansom, MS Membrane proteins: molecular dynamics simulations. |
| title | Membrane proteins: molecular dynamics simulations. |
| title_full | Membrane proteins: molecular dynamics simulations. |
| title_fullStr | Membrane proteins: molecular dynamics simulations. |
| title_full_unstemmed | Membrane proteins: molecular dynamics simulations. |
| title_short | Membrane proteins: molecular dynamics simulations. |
| title_sort | membrane proteins molecular dynamics simulations |
| work_keys_str_mv | AT lindahle membraneproteinsmoleculardynamicssimulations AT sansomms membraneproteinsmoleculardynamicssimulations |