The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions
Abstract
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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Golub, G. (2012) · doi:10.56021/9781421407944 · Cited by 34,505
Dynamic personalities of proteins
Henzler-Wildman, K., & Kern, D. (2007) · Nature · doi:10.1038/nature06522 · Cited by 2,545
Separation of a mixture of independent signals using time delayed correlations
Molgedey, L., & Schuster, H. G. (1994) · Physical Review Letters · doi:10.1103/physrevlett.72.3634 · Cited by 882
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BackgroundSchwantes, C. R., & Pande, V. S. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct300878a · Cited by 597
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Bose, S., Lotz, S. D., Deb, I., Shuck, M., Lee, K. S. S., & Dickson, A. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c08940 · Cited by 16
Metadata
- Authors
- Naritomi, Y., & Fuchigami, S.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2011-02-09
- Volume
- 134
- Issue
- 6
- Pages
- 065101-065101
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2091701505
- Cited by
- 299
- References
- 3
- FWCI
- 1.29
- Type
- journal article
- Language
- en
- Open access
- closed
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