We present a method to investigate the kinetics of protein folding and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. By writing the solution of the Fokker-Planck equation in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is applied to the folding of the Villin headpiece subdomain simulated using a Go model. An initial collapsing phase driven by the initial configuration is followed by a rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This completely general method does not require the prior knowledge of any reaction coordinate and is an efficient tool to perform simulations of the entire folding process with available computers.

Faccioli, P., Sega, M., Pederiva, F., H., O. (2006). Dominant pathways in protein folding. PHYSICAL REVIEW LETTERS, 97(10), 1-4 [10.1103/PhysRevLett.97.108101].

Dominant pathways in protein folding

Faccioli, Pietro;
2006

Abstract

We present a method to investigate the kinetics of protein folding and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. By writing the solution of the Fokker-Planck equation in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is applied to the folding of the Villin headpiece subdomain simulated using a Go model. An initial collapsing phase driven by the initial configuration is followed by a rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This completely general method does not require the prior knowledge of any reaction coordinate and is an efficient tool to perform simulations of the entire folding process with available computers.
Articolo in rivista - Articolo scientifico
Biophysics; Diffusion; Kinetics; Microfilament Proteins; Models, Molecular; Models, Statistical; Models, Theoretical; Normal Distribution; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Time Factors
English
2006
97
10
1
4
108101
none
Faccioli, P., Sega, M., Pederiva, F., H., O. (2006). Dominant pathways in protein folding. PHYSICAL REVIEW LETTERS, 97(10), 1-4 [10.1103/PhysRevLett.97.108101].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/405610
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