Dependence of internal friction on folding mechanism

Wenwei Zheng, David De Sancho, Travis Hoppe, Robert B. Best

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

An outstanding challenge in protein folding is understanding the origin of "internal friction" in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.

Original languageEnglish (US)
Pages (from-to)3283-3290
Number of pages8
JournalJournal of the American Chemical Society
Volume137
Issue number9
DOIs
StatePublished - Jan 1 2015
Externally publishedYes

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Friction
Internal friction
Proteins
Torsional stress
Viscosity
Protein folding
Energy barriers
Protein Folding
Peptides
Free energy
Reaction rates
Sampling
Atoms
Experiments

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Dependence of internal friction on folding mechanism. / Zheng, Wenwei; De Sancho, David; Hoppe, Travis; Best, Robert B.

In: Journal of the American Chemical Society, Vol. 137, No. 9, 01.01.2015, p. 3283-3290.

Research output: Contribution to journalArticle

Zheng, Wenwei ; De Sancho, David ; Hoppe, Travis ; Best, Robert B. / Dependence of internal friction on folding mechanism. In: Journal of the American Chemical Society. 2015 ; Vol. 137, No. 9. pp. 3283-3290.
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