Quantitative protein dynamics from dominant folding pathways

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 existin...

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Bibliographic Details
Published in:Physical review letters 2007-09, Vol.99 (11), p.118102-118102, Article 118102
Main Authors: Sega, M, Faccioli, P, Pederiva, F, Garberoglio, G, Orland, H
Format: Article
Language:English
Subjects:
Biophysical Phenomena
Biophysics
Models, Molecular
Protein Conformation
Protein Folding
Proteins - chemistry
Stochastic Processes
Thermodynamics
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Summary: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.
ISSN:0031-9007
1079-7114
DOI:10.1103/PhysRevLett.99.118102