Complex network analysis of free-energy landscapes.

Détails

ID Serval
serval:BIB_F498BCD12D3C
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Complex network analysis of free-energy landscapes.
Périodique
Proceedings of the National Academy of Sciences of the United States of America
Auteur⸱e⸱s
Gfeller D., De Los Rios P., Caflisch A., Rao F.
ISSN
0027-8424 (Print)
ISSN-L
0027-8424
Statut éditorial
Publié
Date de publication
2007
Peer-reviewed
Oui
Volume
104
Numéro
6
Pages
1817-1822
Langue
anglais
Résumé
The kinetics of biomolecular isomerization processes, such as protein folding, is governed by a free-energy surface of high dimensionality and complexity. As an alternative to projections into one or two dimensions, the free-energy surface can be mapped into a weighted network where nodes and links are configurations and direct transitions among them, respectively. In this work, the free-energy basins and barriers of the alanine dipeptide are determined quantitatively using an algorithm to partition the network into clusters (i.e., states) according to the equilibrium transitions sampled by molecular dynamics. The network-based approach allows for the analysis of the thermodynamics and kinetics of biomolecule isomerization without reliance on arbitrarily chosen order parameters. Moreover, it is shown on low-dimensional models, which can be treated analytically, as well as for the alanine dipeptide, that the broad-tailed weight distribution observed in their networks originates from free-energy basins with mainly enthalpic character.

Mots-clé
Alanine/analogs & derivatives, Models, Chemical, Protein Folding, Thermodynamics
Pubmed
Web of science
Open Access
Oui
Création de la notice
15/12/2014 13:24
Dernière modification de la notice
20/08/2019 16:21
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