Dynamics and cooperativity of Trp-cage folding

Zehan Hu, Yanhui Tang, Houfang Wang, Xu Zhang, Ming Lei

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

In this study, multiple independent molecular dynamics (MD) simulations on Trp-cage folding were performed at 300, 325 and 375 K using generalized Born (GB) implicit solvent model. The orientational movement of the side-chain of Trp6 to form a hydrophobic core with 310-helix was observed. The breaking/formation of a salt bridge between Asp9 and Arg16 was proposed to be the prerequisite for Trp-cage folding/refolding. Our results demonstrate that the cooperation between the salt bridge and the Trp6 orientation leads to a stable tertiary structure of Trp-cage. Analyses on backbone concerted motions at different temperatures indicate that interactions between Trp6 and 310-helix & Pro18 and between Pro12 and Pro17 & Pro18 are weakened at 375 K but strengthened at lower temperatures, suggesting that they could be the potential driving force of hydrophobic collapse.

Original languageEnglish (US)
Pages (from-to)140-147
Number of pages8
JournalArchives of Biochemistry and Biophysics
Volume475
Issue number2
DOIs
StatePublished - Jul 15 2008
Externally publishedYes

Keywords

  • Correlated motions
  • Implicit solvent model
  • Molecular dynamics
  • Protein folding
  • Trp-cage

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology

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