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.
journal_name
Proc Natl Acad Sci U S Aauthors
Gfeller D,De Los Rios P,Caflisch A,Rao Fdoi
10.1073/pnas.0608099104subject
Has Abstractpub_date
2007-02-06 00:00:00pages
1817-22issue
6eissn
0027-8424issn
1091-6490pii
0608099104journal_volume
104pub_type
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