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 language | English (US) |
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Pages (from-to) | 140-147 |
Number of pages | 8 |
Journal | Archives of Biochemistry and Biophysics |
Volume | 475 |
Issue number | 2 |
DOIs | |
State | Published - Jul 15 2008 |
Externally published | Yes |
Keywords
- Correlated motions
- Implicit solvent model
- Molecular dynamics
- Protein folding
- Trp-cage
ASJC Scopus subject areas
- Biophysics
- Biochemistry
- Molecular Biology