Structural characterization of γ-repressor folding from all-atom molecular dynamics simulations

Yanxin Liu, Johan Strümpfer, Peter L. Freddolino, Martin Gruebele, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

The five-helix bundle γ-repressor fragment is a fast-folding protein. A length of 80 amino acid residues puts it on the large end among all known microsecond folders, and its size poses a computational challenge for molecular dynamics (MD) studies. We simulated the folding of a novel γ-repressor fast-folding mutant (γ-HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observed reversible folding and unfolding of γ-repressor in a 10 μs trajectory. The folding kinetics was also investigated through a set of MD simulations run at different temperatures that together covered more than 125 μs. The protein was seen to fold into a native-like topology at intermediate temperature, and a slow-folding pathway was identified. The simulations suggest new experimental observables for better monitoring of the folding process, and a novel mutation is expected to accelerate γ-repressor folding.

Original languageEnglish (US)
Pages (from-to)1117-1123
Number of pages7
JournalJournal of Physical Chemistry Letters
Volume3
Issue number9
DOIs
StatePublished - May 3 2012

ASJC Scopus subject areas

  • Materials Science(all)
  • Physical and Theoretical Chemistry

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