Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.
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) atoms (n, n + 1) and the bonds joining these C(α) atoms to their respective C(β) atoms] was analyzed. The motions of SCs (δ(n)) and MC (γ(n)) over time occur on similar free-energy profiles and were found to be subdiffusive. The fluctuations of the SCs (δ(n)) and those of the MC (γ(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 δ(n)(t) and γ(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 [δ(t) and γ(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.
Laboratoire Interdisciplinaire Carnot de Bourgogne, Unité Mixte de Recherche 6303 Centre National de la Recherche Scientifique-Université de Bourgogne, 9 Avenue A Savary, BP 47 870, F-21078 Dijon Cedex, France.
Yoann
Y
Cote
Patrick
P
Senet
Patrice
P
Delarue
Gia G
GG
Maisuradze
Harold A
HA
Scheraga
D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins