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Short-range coherence of internal protein dynamics revealed by high-precision in silico study



Short-range coherence of internal protein dynamics revealed by high-precision in silico study



Journal of the American Chemical Society 131(41): 14610-1



Correlated internal dynamics of proteins, which is believed to be important for their function, is analyzed at unprecedented precision using explicit-solvent submicrosecond molecular dynamics simulations of ubiquitin and calbindin D(9k). Without exception, all of the mobile dihedral angle pairs in ubiquitin with sizable dynamics correlations (R(2) >or= 0.1) are at short-range distance. In rare cases, they involve sequentially remote dihedral angles that form sparse clusters, suggesting a structural-dynamic propagation mechanism via soft torsional couplings that act over short distances with a rapid loss of coherence over longer distances.

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Accession: 055759648

Download citation: RISBibTeXText

PMID: 19780553

DOI: 10.1021/ja905340s


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