Helix Formation of the Villin Headpiece Protein Subdomain
Journal of the Korean Physical Society(2011)
摘要
By using successive 2001 time frames for the all-atom coordinates obtained from action-derived molecular dynamics simulations, we investigate the formation and stability of the three a.-helices (H1: residue 4-11, H2: residue 15-18, and H3: residue 23-30) for the 36-residue villin headpiece protein subdomain (HP-36) from the straightly-extended structure to the folded native structure. The distances of all twelve hydrogen bonds responsible for the formation of the three alpha-helices are directly measured as functions of the time-step index. According to our results, the third helix is strongly stable before the first and the second helices become stable. We find that the short second helix is never formed before the overall collapse, but that parts of the long first and third helices are formed before the collapse. Also, we find that all three alpha-helices are steadily formed after the overall collapse.
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关键词
Protein folding,Helix formation,Action-derived molecular dynamics
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