Journal
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
Volume 475, Issue 2, Pages 140-147Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.abb.2008.04.024
Keywords
molecular dynamics; Trp-cage; protein folding; correlated motions; implicit solvent model
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Funding
- NCRR NIH HHS [P41 RR-01081] Funding Source: Medline
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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. (C) 2008 Elsevier Inc. All rights reserved.
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