| Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions. | |
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MedLine Citation:
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PMID: 21322734 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
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Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins. |
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Authors:
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Yusuke Naritomi; Sotaro Fuchigami |
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Publication Detail:
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Type: Journal Article |
Journal Detail:
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Title: The Journal of chemical physics Volume: 134 ISSN: 1089-7690 ISO Abbreviation: J Chem Phys Publication Date: 2011 Feb |
Date Detail:
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Created Date: 2011-02-16 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0375360 Medline TA: J Chem Phys Country: United States |
Other Details:
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Languages: eng Pagination: 065101 Citation Subset: IM |
Affiliation:
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Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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