Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations

Hunenberger, PH, Mark, AE and Vangunsteren, WF (1995) Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. Journal of Molecular Biology, 252 4: 492-503. doi:10.1006/jmbi.1995.0514


Author Hunenberger, PH
Mark, AE
Vangunsteren, WF
Title Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations
Journal name Journal of Molecular Biology   Check publisher's open access policy
ISSN 0022-2836
Publication date 1995-01-01
Year available 1995
Sub-type Article (original research)
DOI 10.1006/jmbi.1995.0514
Open Access Status Not yet assessed
Volume 252
Issue 4
Start page 492
End page 503
Total pages 12
Place of publication LONDON
Publisher ACADEMIC PRESS (LONDON) LTD
Language eng
Subject 2406 Virology
1312 Molecular Biology
Abstract Nanosecond molecular dynamics simulations of bovine pancreatic trypsin inhibitor and lysozyme in water are analyzed in terms of backbone atomic positional fluctuations and dynamical cross-correlations. It is found that although the molecular systems are stable, B-factors calculated over a time period as long as 500 ps are not representative for the motions within the proteins. This is especially true for the most mobile residues. On a nanosecond time-scale, the B-factors calculated from the simulations of the proteins in solution are considerably larger than. those obtained by structure refinement of the proteins in crystals, based on X-ray data. The time evolution of the atomic fluctuations shows that for large portions of the proteins under study atomic positional fluctuations are not yet converged after a nanosecond. Cross-correlations do not converge faster than the fluctuations themselves. Most display very erratic behavior if the sampling covers less than about 200 ps. It is also shown that inclusion of mobile atoms into the procedure used to remove rigid-body motion from the simulation can lead to spurious correlations between the motions of the atoms at the surface of the protein. (C) 1995 Academic Press Limited
Keyword Atomic fluctuations
B-factors
Computer simulation
Molecular dynamics
Protein dynamics
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: Scopus Import - Archived
 
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