Sidechain Dynamics and Protein Folding

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dc.creatorKussell, E.
dc.creatorShimada, J.
dc.creatorShakhnovich, E. I.
dc.date2001-08-22
dc.date.accessioned2026-07-25T14:28:41Z
dc.descriptionThe processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein structure, with the fastest relaxing sidechains being involved in kinetically important positions. Traversal of the major folding transition state corresponds to the freezing of a small number of residues, while the rest of the chain proceeds towards equilibrium via backbone fluctuations around the native fold. The post-nucleation processes by which sidechains relax are characterized by very slow dynamics, and many barrier crossings, and thus resemble the behavior of a glass. At optimal temperature, however, the nucleated ensemble is energetically very close to equilibrium; slow relaxation is still observed. At lower temperatures, sidechain relaxation becomes a significant and very noticeable part of the folding reaction.
dc.identifierhttps://arxiv.org/abs/cond-mat/0108357
dc.identifierhttp://arxiv.org/abs/cond-mat/0108357
dc.identifier.urihttps://dspace.dare.co.zw/handle/123456789/25988
dc.subjectSoft Condensed Matter
dc.subjectBiological Physics
dc.subjectQuantitative Biology
dc.titleSidechain Dynamics and Protein Folding
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