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Side‐chain dynamics and protein folding
Author(s) -
Kussell Edo,
Shimada Jun,
Shakhnovich Eugene I.
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.10426
Subject(s) - side chain , folding funnel , protein folding , folding (dsp implementation) , chemical physics , lattice protein , contact order , molecular dynamics , chemistry , downhill folding , crystallography , native state , phi value analysis , computational chemistry , polymer , biochemistry , organic chemistry , electrical engineering , engineering
Abstract The processes by which protein side chains reach equilibrium during a folding reaction are investigated using both lattice and all‐atom simulations. We find that rates of side‐chain relaxation exhibit a distribution over the protein structure, with the fastest relaxing side chains located in positions kinetically important for folding. Traversal of the major folding transition state corresponds to the freezing of a small number of side chains, belonging to the folding nucleus, whereas the rest of the protein proceeds toward equilibrium via backbone fluctuations around the native fold. The postnucleation processes by which side chains relax are characterized by very slow dynamics and many barrier crossings, and thus resemble the behavior of a glass. Proteins 2003;52:303–321. © 2003 Wiley‐Liss, Inc.