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.

Sega, M., Faccioli, P., Pederiva, F., Garberoglio, G., Orland, H. (2007). Quantitative Protein Dynamics from Dominant Folding Pathways. PHYSICAL REVIEW LETTERS, 99(11) [10.1103/PhysRevLett.99.118102].

Quantitative Protein Dynamics from Dominant Folding Pathways

Faccioli, P
;
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.
Articolo in rivista - Articolo scientifico
Protein folding
English
2007
99
11
118102
none
Sega, M., Faccioli, P., Pederiva, F., Garberoglio, G., Orland, H. (2007). Quantitative Protein Dynamics from Dominant Folding Pathways. PHYSICAL REVIEW LETTERS, 99(11) [10.1103/PhysRevLett.99.118102].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/405652
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