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How main-chains of proteins explore the free-energy landscape in native states.

ABSTRACT: 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.

SUBMITTER: Senet P

PROVIDER: S-EPMC2604949 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

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How main-chains of proteins explore the free-energy landscape in native states.

Senet Patrick P Maisuradze Gia G GG Foulie Colette C Delarue Patrice P Scheraga Harold A HA

Proceedings of the National Academy of Sciences of the United States of America 20081210 50

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) ...[more]

PMID: 19073932

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Dataset Information

How main-chains of proteins explore the free-energy landscape in native states.

Publications

How main-chains of proteins explore the free-energy landscape in native states.

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