Quantitative Protein Dynamics from Dominant Folding Pathways

M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio, and H. Orland
Phys. Rev. Lett. 99, 118102 – Published 12 September 2007

Abstract

We develop a theoretical approach to the protein-folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps are removed, and simulating the entire reaction in atomistic details using existing computers becomes feasible. We discuss how to determine the most probable folding pathway, identify configurations representative of the transition state, and compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine dipeptide, within an all-atom model based on the empiric GROMOS96 force field.

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  • Received 30 January 2007

DOI:https://doi.org/10.1103/PhysRevLett.99.118102

©2007 American Physical Society

Authors & Affiliations

M. Sega1, P. Faccioli2,3, F. Pederiva4, G. Garberoglio1, and H. Orland5

  • 1C.N.R./I.N.F.M. and Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento), I-38050 Italy
  • 2Dipartimento di Fisica Università degli Studi di Trento e I.N.F.N, Via Sommarive 14, Povo (Trento), I-38050 Italy
  • 3European Centre for Theoretical Studies in Nuclear Physics and Related Areas (E.C.T.), Strada delle Tabarelle 284, Villazzano (Trento), I-38050 Italy
  • 4Dipartimento di Fisica and C.N.R./I.N.F.M.-DEMOCRITOS National Simulation Center, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento), I-38050 Italy
  • 5Service de Physique Théorique, Centre d’Etudes de Saclay, F-91191 Gif-sur-Yvette Cedex, France

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Issue

Vol. 99, Iss. 11 — 14 September 2007

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