Complex network analysis of free-energy landscapes.

Details

Serval ID
serval:BIB_F498BCD12D3C
Type
Article: article from journal or magazin.
Collection
Publications
Title
Complex network analysis of free-energy landscapes.
Journal
Proceedings of the National Academy of Sciences of the United States of America
Author(s)
Gfeller D., De Los Rios P., Caflisch A., Rao F.
ISSN
0027-8424 (Print)
ISSN-L
0027-8424
Publication state
Published
Issued date
2007
Peer-reviewed
Oui
Volume
104
Number
6
Pages
1817-1822
Language
english
Abstract
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.

Keywords
Alanine/analogs & derivatives, Models, Chemical, Protein Folding, Thermodynamics
Pubmed
Web of science
Open Access
Yes
Create date
15/12/2014 13:24
Last modification date
20/08/2019 16:21
Usage data