From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
Coarse-grained molecular dynamics provides a means for simulating the assembly and the interactions of membrane protein/lipid complexes at a reduced level of representation, allowing longer and larger simulations. We describe a fragment-based protocol for converting membrane simulation systems, comp...
| Váldodahkkit: | , |
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| Materiálatiipa: | Journal article |
| Giella: | English |
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2011
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| _version_ | 1826297890087108608 |
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| author | Stansfeld, P Sansom, M |
| author_facet | Stansfeld, P Sansom, M |
| author_sort | Stansfeld, P |
| collection | OXFORD |
| description | Coarse-grained molecular dynamics provides a means for simulating the assembly and the interactions of membrane protein/lipid complexes at a reduced level of representation, allowing longer and larger simulations. We describe a fragment-based protocol for converting membrane simulation systems, comprising a membrane protein embedded in a phospholipid bilayer, from coarse-grained to atomistic resolution, for further refinement and analysis via atomistic simulations. Overall, this provides a method for generating an accurate and well equilibrated membrane protein/lipid complex. We exemplify the protocol using the acid-sensing/amiloride-sensitive ion channel protein (ASIC) channel protein, a trimeric integral membrane protein. The method is further evaluated using a test set of 10 different membrane proteins of differing size and complexity. Simulations are assessed in terms of protein conformational drift, lipid/protein interactions, and lipid dynamics. © 2011 American Chemical Society. |
| first_indexed | 2024-03-07T04:38:31Z |
| format | Journal article |
| id | oxford-uuid:d0d02f81-e919-4988-8472-a48c74b401e8 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:38:31Z |
| publishDate | 2011 |
| record_format | dspace |
| spelling | oxford-uuid:d0d02f81-e919-4988-8472-a48c74b401e82022-03-27T07:52:39ZFrom Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein SimulationsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:d0d02f81-e919-4988-8472-a48c74b401e8EnglishSymplectic Elements at Oxford2011Stansfeld, PSansom, MCoarse-grained molecular dynamics provides a means for simulating the assembly and the interactions of membrane protein/lipid complexes at a reduced level of representation, allowing longer and larger simulations. We describe a fragment-based protocol for converting membrane simulation systems, comprising a membrane protein embedded in a phospholipid bilayer, from coarse-grained to atomistic resolution, for further refinement and analysis via atomistic simulations. Overall, this provides a method for generating an accurate and well equilibrated membrane protein/lipid complex. We exemplify the protocol using the acid-sensing/amiloride-sensitive ion channel protein (ASIC) channel protein, a trimeric integral membrane protein. The method is further evaluated using a test set of 10 different membrane proteins of differing size and complexity. Simulations are assessed in terms of protein conformational drift, lipid/protein interactions, and lipid dynamics. © 2011 American Chemical Society. |
| spellingShingle | Stansfeld, P Sansom, M From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations |
| title | From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations |
| title_full | From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations |
| title_fullStr | From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations |
| title_full_unstemmed | From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations |
| title_short | From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations |
| title_sort | from coarse grained to atomistic a serial multiscale approach to membrane protein simulations |
| work_keys_str_mv | AT stansfeldp fromcoarsegrainedtoatomisticaserialmultiscaleapproachtomembraneproteinsimulations AT sansomm fromcoarsegrainedtoatomisticaserialmultiscaleapproachtomembraneproteinsimulations |