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Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.

ABSTRACT: Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model ?/? protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-grained dihedral angles (CGDAs) ?(n) based on four successive C(?) atoms (n - 1, n, n + 1, n + 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs ?(n) formed by the virtual bond joining two consecutive C(?) atoms (n, n + 1) and the bonds joining these C(?) atoms to their respective C(?) atoms] was analyzed. The motions of SCs (?(n)) and MC (?(n)) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (?(n)) and those of the MC (?(n)) are generally poorly correlated on a ps time-scale with a correlation increasing with time to reach a maximum value at about 10 ns. This maximum value is close to the correlation between the ?(n)(t) and ?(n)(t) time-series extracted from the entire duration of the MD runs (400 ns) and varies significantly along the amino acid sequence. High correlations between the SC and MC motions [?(t) and ?(t) time-series] were found only in flexible regions of the protein for a few residues which contribute the most to the slowest collective modes of the molecule. These results are a possible indication of the role of the flexible regions of proteins for the biological function and folding.

SUBMITTER: Cote Y

PROVIDER: S-EPMC3387131 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

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Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.

Cote Yoann Y Senet Patrick P Delarue Patrice P Maisuradze Gia G GG Scheraga Harold A HA

Proceedings of the National Academy of Sciences of the United States of America 20120611 26

Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model α/β protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-grained dihedral angles (CGDAs) γ(n) based on four successive C(α) atoms (n - 1, n, n + 1, n + 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs δ(n) formed by the virtual bond joining two consecutive C(α) at ...[more]

PMID: 22689963

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Project description:Protein interactions play a key role in life processes. Characterization of conformational properties of protein-protein interactions is important for understanding the mechanisms of protein association. The rapidly increasing amount of experimentally determined structures of proteins and protein-protein complexes provides foundation for research on protein interactions and complex formation. The knowledge of the conformations of the surface side chains is essential for modeling of protein complexes. The purpose of this study was to analyze and compare dihedral angle distribution functions of the side chains at the interface and non-interface areas in bound and unbound proteins.To calculate the dihedral angle distribution functions, the configuration space was divided into grid cells. Statistical analysis showed that the similarity between bound and unbound interface and non-interface surface depends on the amino acid type and the grid resolution. The correlation coefficients between the distribution functions increased with the grid spacing increase for all amino acid types. The Manhattan distance showing the degree of dissimilarity between the distribution functions decreased accordingly. Short residues with one or two dihedral angles had higher correlations and smaller Manhattan distances than the longer residues. Met and Arg had the slowest growth of the correlation coefficient with the grid spacing increase. The correlations between the interface and non-interface distribution functions had a similar dependence on the grid resolution in both bound and unbound states. The interface and non-interface differences between bound and unbound distribution functions, caused by biological protein-protein interactions or crystal contacts, disappeared at the 70° grid spacing for interfaces and 30° for non-interface surface, which agrees with an average span of the side-chain rotamers.The two-fold difference in the critical grid spacing indicates larger conformational changes upon binding at the interface than at the rest of the surface. At the same time, transitions between rotamers induced by interactions across the interface or the crystal packing are rare, with most side chains having local readjustments that do not change the rotameric state. The analysis is important for better understanding of protein interactions and development of flexible docking approaches.

Dataset Information

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.

Publications

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.

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