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Prediction of folding rates and transition‐state placement from native‐state geometry
Author(s) -
Micheletti Cristian
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10342
Subject(s) - folding (dsp implementation) , state (computer science) , protein folding , topology (electrical circuits) , statistical physics , locality , contact order , native state , cluster analysis , measure (data warehouse) , order (exchange) , downhill folding , mathematics , computer science , geometry , algorithm , physics , phi value analysis , combinatorics , data mining , crystallography , artificial intelligence , chemistry , engineering , structural engineering , philosophy , linguistics , finance , nuclear magnetic resonance , economics
A variety of experimental and theoretical studies have established that the folding process of monomeric proteins is strongly influenced by the topology of the native state. In particular, folding times have been shown to correlate well with the contact order, a measure of contact locality. Our investigation focuses on identifying additional topologic properties that correlate with experimentally measurable quantities, such as folding rates and transition‐state placement, for both two‐ and three‐state folders. The validation against data from 40 experiments shows that a particular topological property that measures the interdependence of contacts, termed cliquishness or clustering coefficient, can account with statistically significant accuracy both for the transition state placement and especially for folding rates. The observed correlations can be further improved by optimally combining the distinct topological information captured by cliquishness and contact order. Proteins 2003;51:74–84. © 2003 Wiley‐Liss, Inc.