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. (C) 1999 Wiley-Liss, Inc.

Amadei, A., De Groot, B., Ceruso, M., Paci, M., Di Nola, A., Berendsen, H. (1999). A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells. PROTEINS, 35(3), 283-292 [10.1002/(SICI)1097-0134(19990515)35:3<283::AID-PROT2>3.0.CO;2-R].

A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells

AMADEI, ANDREA;PACI, MAURIZIO;
1999-01-01

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. (C) 1999 Wiley-Liss, Inc.
1999
Pubblicato
Rilevanza internazionale
Articolo
Sì, ma tipo non specificato
Settore CHIM/02 - CHIMICA FISICA
English
Collective motions; Conformational fluctuations; Essential dynamics; Molecular dynamics
Amadei, A., De Groot, B., Ceruso, M., Paci, M., Di Nola, A., Berendsen, H. (1999). A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells. PROTEINS, 35(3), 283-292 [10.1002/(SICI)1097-0134(19990515)35:3<283::AID-PROT2>3.0.CO;2-R].
Amadei, A; De Groot, B; Ceruso, M; Paci, M; Di Nola, A; Berendsen, H
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/44810
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