Dynamics and cooperativity of Trp-cage folding

Arch Biochem Biophys. 2008 Jul 15;475(2):140-7. doi: 10.1016/j.abb.2008.04.024. Epub 2008 Apr 29.

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 3(10)-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 3(10)-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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computer Simulation
  • Hydrophobic and Hydrophilic Interactions
  • Models, Chemical
  • Peptides / chemistry*
  • Principal Component Analysis
  • Proline / chemistry
  • Protein Denaturation
  • Protein Folding*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Temperature
  • Time Factors
  • Tryptophan / chemistry*

Substances

  • Peptides
  • Trp-cage peptide
  • Tryptophan
  • Proline