http://www.cnr.it/ontology/cnr/individuo/prodotto/ID2452

Quantitative protein dynamics from dominant folding pathways (Articolo in rivista)

Type

Label

Quantitative protein dynamics from dominant folding pathways (Articolo in rivista) (literal)

Anno

Alternative label

Sega, M; Faccioli, P; Pederiva, F; Garberoglio, G; Orland, H (2007)
Quantitative protein dynamics from dominant folding pathways
in Physical review letters (Print)
(literal)

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Rivista

Note

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Univ Trent, CNR, Ist Nazl Fis Nucl, Dipartimento Fis, I-38050 Trento, Italy; Univ Trent, Ist Nazl Fis Nucl, Dipartimento Fis, I-38050 Trento, Italy; European Ctr Theoret Studies Nucl Phys & Related, I-38050 Trento, Italy; Univ Trent, Democritos Natl Simulat Ctr, CNR, Ist Nazl Fis Nucl,Dipartimento Fis, I-38050 Trento, Italy; Ctr Etud Saclay, Serv Phys Theor, F-91191 Gif Sur Yvette, France (literal)

Titolo

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. (literal)

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