Topological Quantities Determining the Folding/Unfolding Rate of Two-state Folding Proteins

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We investigate various topological and energy parameters from the protein native structure and find combinations of some parameters that are well correlated with the rate of folding/unfolding. For folding, the topological quantity that combines the clustering coefficient and the long-range order (or total contact distance/contact order) has a high correlation with the folding rate, expressed as ln k (F) , obtained from standard experimental conditions. For unfolding, a combination of the impact of edge removal, obtained from the protein structure, and the stability of the native protein structure, as expressed by the free energy change Delta G, gives a good correlation with unfolding rate, ln k (U) .
Publisher
SPRINGER/PLENUM PUBLISHERS
Issue Date
2010-07
Language
English
Article Type
Article
Keywords

TRANSITION-STATE PLACEMENT; SINGLE-DOMAIN PROTEINS; AQUEOUS-SOLUTIONS; CONTACT ORDER; AMINO-ACIDS; SH3 DOMAIN; ENTHALPIC INTERACTION; COMPLEX NETWORKS; RATE PREDICTION; 4-HELIX BUNDLE

Citation

JOURNAL OF SOLUTION CHEMISTRY, v.39, pp.943 - 958

ISSN
0095-9782
DOI
10.1007/s10953-010-9556-3
URI
http://hdl.handle.net/10203/93933
Appears in Collection
CH-Journal Papers(저널논문)
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