Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease.

ABSTRACT: Understanding collective motions in protein crystals is likely to furnish insight into functional protein dynamics and will improve models for refinement against diffraction data. Here, four 10 ns molecular dynamics simulations of crystalline Staphylococcal nuclease are reported and analyzed in terms of fluctuations and correlations in atomic motion. The simulation-derived fluctuations strongly correlate with, but are slightly higher than, the values derived from the experimental B-factors. Approximately 70% of the atomic fluctuations are due to internal protein motion. For 65% of the protein atoms the internal fluctuations converge on the nanosecond timescale. Convergence is much slower for the elements of the interatomic displacement correlation matrix--of these, >80% converge within 1 n

SUBMITTER: Meinhold L 

PROVIDER: S-EPMC1305352 | biostudies-literature | 2005 Apr

REPOSITORIES: biostudies-literature