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Article Dans Une Revue Proceedings of the National Academy of Sciences of the United States of America Année : 2012

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

Résumé

Structural fluctuations of a protein are essential for a protein to function and fold. By using molecular dynamics (MD) simulations of the model alpha/beta protein VA3 in its native state, the coupling between the main-chain (MC) motions [represented by coarse-grained dihedral angles (CGDAs) gamma(n) based on four successive C-alpha atoms (n - 1, n, n + 1, n + 2) along the amino acid sequence] and its side-chain (SC) motions [represented by CGDAs delta(n) formed by the virtual bond joining two consecutive C-alpha atoms (n, n + 1) and the bonds joining these C-alpha atoms to their respective C-beta atoms] was analyzed. The motions of SCs (delta(n)) and MC (gamma(n)) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (delta(n)) and those of the MC (gamma(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 (delta(n))t and gamma(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 [delta(t) and gamma(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.

Dates et versions

hal-00761194 , version 1 (05-12-2012)

Identifiants

Citer

Yoann Cote, Patrick Senet, Patrice Delarue, Gia G. Maisuradze, Harold A. Scheraga. Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109, pp.10346--10351. ⟨10.1073/pnas.1207083109⟩. ⟨hal-00761194⟩
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