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Critical nucleation size in the folding of small apparently two‐state proteins
Author(s) -
Bai Yawen,
Zhou Hongyi,
Zhou Yaoqi
Publication year - 2004
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.03587604
Subject(s) - contact order , protein folding , native state , folding funnel , folding (dsp implementation) , lattice protein , topology (electrical circuits) , nucleation , downhill folding , limiting , state (computer science) , phi value analysis , chemistry , constraint (computer aided design) , chemical physics , crystallography , biophysics , biology , computer science , mathematics , biochemistry , combinatorics , geometry , algorithm , mechanical engineering , organic chemistry , electrical engineering , engineering
For apparently two‐state proteins, we found that the size (number of folded residues) of a transition state is mostly encoded by the topology, defined by total contact distance (TCD) of the native state, and correlates with its folding rate. This is demonstrated by using a simple procedure to reduce the native structures of the 41 two‐state proteins with native TCD as a constraint, and is further supported by analyzing the results of eight proteins from protein engineering studies. These results support the hypothesis that the major rate‐limiting process in the folding of small apparently two‐state proteins is the search for a critical number of residues with the topology close to that of the native state.