Liquid-like and solid-like motions in proteins - Archive ouverte HAL
Article Dans Une Revue Journal of Molecular Liquids Année : 2002

Liquid-like and solid-like motions in proteins

Résumé

Recent analyses of molecular dynamics simulations of hydrated C-phycocyanin suggest that the internal single-particle dynamics of this protein can be decomposed into four almost decoupled motion types: (1) diffusion of residues ("beads") in an effective harmonic potential, (2) corresponding vibrations in a local potential well, (3) purely rotational rigid side-chain diffusion, and (4) residue deformations. Each residue bead is represented by the corresponding C[α] carbon atom on the main chain. The effective harmonic residue potential can be imagined as the envelope of many local wells which are separated by small energy barriers. The residue friction matrix is assumed diagonal and the individual friction constants can be related to the density of the surrounding atoms. In this article we show that our model can be applied to lysozyme in solution as well, the only difference being that the side-chain deformations are more important and seem to be strongly correlated with the side-chain rotations. Comparing the simulated coherent scattering function of C-phycocyanin to a neutron spin-echo spectrum we show that our model can also describe collective motions in proteins at the residue level.

Dates et versions

hal-00114769 , version 1 (17-11-2006)

Identifiants

Citer

K. Hinsen, A.J. Petrescu, S. Dellerue, M.C. Bellissent-Funel, Kneller Gr.. Liquid-like and solid-like motions in proteins. Journal of Molecular Liquids, 2002, 98-99, pp.383-400. ⟨10.1016/S0167-7322(01)00341-5⟩. ⟨hal-00114769⟩
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