Side-chain dynamics and protein folding

Edo Kussell, Jun Shimada, Eugene I. Shakhnovich

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)303-321
Number of pages19
JournalProteins: Structure, Function and Genetics
Volume52
Issue number2
DOIs
StatePublished - Aug 1 2003

Keywords

  • Glass transition
  • Nucleation mechanism
  • Protein folding
  • Side-chain dynamics
  • Side-chain packing

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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