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Entropy capacity determines protein folding
Author(s) -
Galzitskaya Oxana V.,
Garbuzynskiy Sergiy O.
Publication year - 2006
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.20851
Subject(s) - protein folding , contact order , entropy (arrow of time) , conformational entropy , lattice protein , chemistry , protein structure , folding (dsp implementation) , downhill folding , thermodynamics , phi value analysis , crystallography , statistical physics , physics , biochemistry , molecule , organic chemistry , electrical engineering , engineering
Search and study of the general principles that govern kinetics and thermodynamics of protein folding generate a new insight into the factors controlling this process. Here, based on the known experimental data and using theoretical modeling of protein folding, we demonstrate that there exists an optimal relationship between the average conformational entropy and the average energy of contacts per residue—that is, an entropy capacity—for fast protein folding. Statistical analysis of conformational entropy and number of contacts per residue for 5829 protein structures from four general structural classes (all‐α, all‐β, α/β, α+β) demonstrates that each class of proteins has its own class‐specific average number of contacts (class α/β has the largest number of contacts) and average conformational entropy per residue (class all‐α has the largest number of rotatable angles ϕ, ψ, and χ per residue). These class‐specific features determine the folding rates: α proteins are the fastest folding proteins, then follow β and α+β proteins, and finally α/β proteins are the slowest ones. Our result is in agreement with the experimental folding rates for 60 proteins. This suggests that structural and sequence properties are important determinants of protein folding rates. Proteins 2006. © 2006 Wiley‐Liss, Inc.