Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

Corey Hardin, Zaida Luthey-Schulten, Peter G. Wolynes

Research output: Contribution to journalArticlepeer-review

Abstract

We discuss the construction of a simple, off-lattice model protein with a comparatively detailed representation of the protein backbone, and use it to address some general aspects of the folding kinetics of a small helical protein and two peptide fragments. The model makes use of an associative memory hamiltonian to smoothly interpolate between the limits of a native contact only, or Gō, potential and a statistical pair potential derived from a database of known structures. We have observed qualitatively different behavior in these two limits. In the Gō limit, we see apparently barrier- less folding. As we increase the roughness of the model energy landscape, we can observe the emergence of the characteristic activated temperature dependence previously seen in lattice studies and analytical theories. We are also able to study the dependence of the folding kinetics on local interactions such as hydrogen bonds, and we discuss the implications of these results for the formation of secondary structure at intermediate stages of the folding reaction.

Original languageEnglish (US)
Pages (from-to)281-294
Number of pages14
JournalProteins: Structure, Function and Genetics
Volume34
Issue number3
DOIs
StatePublished - Feb 15 1999

Keywords

  • Energy landscape
  • Gō model
  • Kinetics
  • Molecular dynamics
  • Protein folding

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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