Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 105, Issue 50, Pages 19708-19713Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0810679105
Keywords
alpha/beta protein; beta-sheet polypeptide; anomalous diffusion; detrended-fluctuations analysis; power law
Categories
Funding
- National Institutes of Health [GM-14312]
- National Science Foundation [MCB05-41633]
- Conseil Regional de Bourgogne
- Universite de Bourgogne
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Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein ( crambin) and a beta-sheet polypeptide (BS2) in their native'' states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C-alpha atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.
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