Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion

Wenwei Zheng, Robert B. Best

Research output: Contribution to journalArticle

21 Scopus citations

Abstract

Theoretical models have often modeled protein folding dynamics as diffusion on a low-dimensional free energy surface, a remarkable simplification. However, the accuracy of such an approximation and the number of dimensions required were not clear. For all-atom folding simulations of ten small proteins in explicit solvent we show that the folding dynamics can indeed be accurately described as diffusion on just a single coordinate, the fraction of native contacts (Q). The diffusion models reproduce both folding rates, and finer details such as transition-path durations and diffusive propagators. The Q-averaged diffusion coefficients decrease with chain length, as anticipated from energy landscape theory. Although the Q-diffusion model does not capture transition-path durations for the protein NuG2, we show that this can be accomplished by designing an improved coordinate Qopt. Overall, one-dimensional diffusion on a suitable coordinate turns out to be a remarkably faithful model for the dynamics of the proteins considered.

Original languageEnglish (US)
Pages (from-to)15247-15255
Number of pages9
JournalJournal of Physical Chemistry B
Volume119
Issue number49
DOIs
StatePublished - Dec 10 2015

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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