Dynamics and cooperativity of Trp-cage folding.
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.
Hu
Zehan
Z
Institute of Materia Medica/Department of Chemistry, School of Science, Beijing University of Chemical Technology, P.O. Box 99, BeiSuanHuan East Road 15, Beijing 100029, PR China.
Tang
Yanhui
Y
Wang
Houfang
H
Zhang
Xu
X
Lei
Ming
M
D000595:Amino Acid Sequence; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D025341:Principal Component Analysis; D011392:Proline / Q000737:chemistry; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013696:Temperature; D013997:Time Factors; D014364:Tryptophan / Q000737:chemistry*
D010455:Peptides; C508725:Trp-cage peptide; D014364:Tryptophan; D011392:Proline