| Download | - View accepted manuscript: Towards coarse-grained modeling of proteins (PDF, 794 KiB)
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| DOI | Resolve DOI: https://doi.org/10.5488/CMP.10.3.441 |
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| Author | Search for: Stepanova, Maria1 |
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| Affiliation | - National Research Council Canada. National Institute for Nanotechnology
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| Format | Text, Article |
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| Subject | protein dynamics; conformational changes; theory and modelling; projection operator; principal component analysis |
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| Abstract | This paper introduces a basic theoretical background to the description of conformational dynamics of proteins through a system of interacting domains. The essential collective degrees of freedom derived by principal component analysis of a molecular dynamics trajectory are used as dynamic variables defining the projection operator technique that underlies the formalism suggested. The explicit form of the corresponding projection operator is obtained, and the projection method is employed to derive systems of coupled generalized Langevin equations for both individual atomic degrees of freedom and essential collective degrees of freedom in a protein. A definition of correlated domains in proteins is introduced based on the analysis of the essential dynamics. Examples of identification of such domains are presented. A system of coupled generalized Langevin equations is derived representing the protein through a few interacting domains embedded into a dissipative medium. Further developments and potential applications of the formalism are outlined. |
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| Publication date | 2007 |
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| In | |
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| Language | English |
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| Peer reviewed | Yes |
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| NRC number | 481 |
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| NPARC number | 8926185 |
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| Export citation | Export as RIS |
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| Report a correction | Report a correction (opens in a new tab) |
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| Record identifier | 3c54bcf4-ca86-481a-abb4-a720f408b790 |
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| Record created | 2009-04-23 |
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| Record modified | 2020-05-10 |
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