期刊
BIOPOLYMERS
卷 89, 期 9, 页码 747-760出版社
WILEY
DOI: 10.1002/bip.21004
关键词
alpha helix; protein folding; peptides models; simulation; NMR
资金
- NIGMS NIH HHS [R01 GM059658, R01 GM061678-08, GM 61678, R01 GM061678] Funding Source: Medline
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM061678, R01GM059658] Funding Source: NIH RePORTER
The temperature dependence of helical propensities for the peptides Ac-ZGG- (KAAAA)(3)X-NH2 (Z = Y or G, X A, K, and D-Arg) were studied both experimentally and by MD simulations. Good agreement is observed in both the absolute helical propensities as well as relative helical content along the sequence; the global minimum on the calculated free energy landscape corresponds to a single alpha-helical conformation running from K4 to A18 with some terminal fraying, particularly at the C-terminus. Energy component analysis shows that the single helix state has favorable intramolecular electrostatic energy due to hydrogen bonds, and that less-favorable two-helix globular states have favorable salvation energy. The central lysine residues do not appear to increase helicity; however, both experimental and simulation studies show increasing helicity in the series X = Ala -> Lys -> D-Arg. This C-capping preference was also experimentally confirmed in Ac-(KAAAA)(3)X-GY-NH2 and (KAAAA)(3)X-GY-NH2 sequences. The roles of the C-capping groups, and of lysines throughout the sequence, in the MD-derived ensembles are analyzed in detail. (C) 2008 Wiley Periodicals, Inc.
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