PMID: 15244845Jul 13, 2004Paper

Dynamics of the minimally frustrated helices determine the hierarchical folding of small helical proteins

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Mario CompianiR Casadio

Abstract

In this paper we aim at determining the key residues of small helical proteins in order to build up reduced models of the folding dynamics. We start by arguing that the folding process can be dissected into concurrent fast and slow dynamics. The fast events are the quasiautonomous coil-to-helix transitions occurring in the minimally frustrated initiation sites of folding in the early stages of the process. The slow processes consist in the docking of the fluctuating helices formed in these critical sites. We show that a neural network devised to predict native secondary structures from sequence can be used to estimate the probabilities of formation of these helical traits as they are embedded in the protein. The resulting probabilities are shown to correlate well with the experimental helicities measured in the same isolated peptides. The relevance of this finding to the hierarchical character of folding is confirmed within the framework of a diffusion-collision-like mechanism. We demonstrate that thermodynamic and topological features of these critical helices allow accurate estimation of the folding times of five proteins that have been kinetically studied. This suggests that these critical helices determine the fundamental e...Continue Reading

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Citations

Feb 18, 2010·Journal of Micromechanics and Microengineering : Structures, Devices, and Systems·David J FilipiakDavid H Gracias
Dec 17, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Pedro G LindHans J Herrmann
Nov 6, 2013·Biochemistry·Mario Compiani, Emidio Capriotti
Jul 21, 2006·The Journal of Physical Chemistry. B·Alberto StizzaMario Compiani

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