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Structure change of beta-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study
Shao, Qiang; Yang, Lijiang; Gao, Yi Qin
2011-12-21
Source PublicationJOURNAL OF CHEMICAL PHYSICS
ISSN0021-9606
Volume135Issue:23
AbstractOur previous study showed that for the tested polypeptides which have similar beta-hairpin structures but different sequences, their folding free energy pathways are dominantly determined by the turn conformational propensity. In this study, we study how the turn conformational propensity affects the structure of hairpins. The folding of two mutants of GB1p peptide (GB1m2 and GB1m3), which have the optimized turn sequence ((6)DDATK(11)T -> (6)NPATG(11)K) with native structures unsolved, were simulated using integrated tempering sampling molecular dynamics simulations and the predicted stable structures were compared to wild-type GB1p. It was observed that the turn optimization of GB1p generates a more favored 5-residue type I' turn in addition to the 6-residue type I turn in wild-type GB1p. As a result two distinctly different hairpin structures are formed corresponding to the "misfolded" (M) and the "folded" (F) states. M state is a one-residue-shifted asymmetric beta-hairpin structure whereas F state has the similar symmetric hairpin structure as wild-type GB1p. The formation of the favored type I' turn has a small free energy barrier and leads to the shifted beta-hairpin structure, following the modified "zipping" model. The presence of disfavored type I turn structure makes the folding of a beta-hairpin consistent with the "hydrophobic-core-centric" model. On the other hand, the folding simulations on other two GB1p mutants (GB1r1 and GBr2), which have the position of the hydrophobic core cluster further away from the turn compared to wild-type GB1p, showed that moving the hydrophobic core cluster away from the turn region destabilizes but does not change the hairpin structure. Therefore, the present study showed that the turn conformational propensity is a key factor in affecting not only the folding pathways but also the stable structure of beta-hairpins, and the turn conformational change induced by the turn optimization leads to significant changes of beta-hairpin structure. (C) 2011 American Institute of Physics. [doi:10.1063/1.3668288]
DOI10.1063/1.3668288
Indexed BySCI
Language英语
WOS IDWOS:000298539900048
PublisherAMER INST PHYSICS
Citation statistics
Cited Times:19[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.iccas.ac.cn/handle/121111/71704
Collection中国科学院化学研究所
Corresponding AuthorGao, Yi Qin
AffiliationPeking Univ, Coll Chem & Mol Engn, Beijing Natl Lab Mol Sci, Beijing 100871, Peoples R China
Recommended Citation
GB/T 7714
Shao, Qiang,Yang, Lijiang,Gao, Yi Qin. Structure change of beta-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study[J]. JOURNAL OF CHEMICAL PHYSICS,2011,135(23).
APA Shao, Qiang,Yang, Lijiang,&Gao, Yi Qin.(2011).Structure change of beta-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study.JOURNAL OF CHEMICAL PHYSICS,135(23).
MLA Shao, Qiang,et al."Structure change of beta-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study".JOURNAL OF CHEMICAL PHYSICS 135.23(2011).
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