A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells
Amadei A, de Groot BL, Ceruso MA, Paci M, Di Nola A, Berendsen HJC
PROTEINS-STRUCTURE FUNCTION AND GENETICS
35 (3): 283-292 MAY 15 1999

FULL TEXT

Abstract:

The dynamics of collective protein motions derived from Molecular Dynamics simulations have been studied for two small model proteins: initiation factor I and the B1 domain of Protein G. First, we compared the structural fluctuations, obtained by local harmonic approximations in different energy minima, with the ones revealed by large scale molecular dynamics (MD) simulations. It was found that a limited set of harmonic wells can be used to approximate the configurational fluctuations of these proteins, although any single harmonic approximation cannot properly describe their dynamics. Subsequently, the kinetics of the main (essential) collective protein motions were characterized. A dual-diffusion behavior was observed in which a fast type of diffusion switches to a much slower type in a typical time of about 1-3 ps, From these results, the large backbone conformational fluctuations of a protein may be considered as "hopping" between multiple harmonic wells on a basically flat free energy surface.

Author Keywords:

collective motions, conformational fluctuations, molecular dynamics, essential dynamics

KeyWords Plus:

RETINOL-BINDING PROTEIN, MOLECULAR-DYNAMICS, COLLECTIVE MOTIONS, TRYPSIN-INHIBITOR, ESCHERICHIA-COLI, GLOBULAR PROTEIN, NATIVE PROTEIN, WATER, SIMULATIONS, SOLVENT

Addresses:

Berendsen HJC, Univ Groningen, Dept Biophys Chem, Groningen Biomol Sci & Biotechnol Inst, Nijenborgh 4, NL-9747 AG Groningen, Netherlands
Univ Groningen, Dept Biophys Chem, Groningen Biomol Sci & Biotechnol Inst, NL-9747 AG Groningen, Netherlands
Univ Rome La Sapienza, Dept Chem, I-00185 Rome, Italy
Univ Rome Tor Vergata, Dipartimento Sci & Tecnol Chim, Rome, Italy