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The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation
Shao, Qiang; Gao, Yi Qin
2011-10-07
Source PublicationJOURNAL OF CHEMICAL PHYSICS
ISSN0021-9606
Volume135Issue:13
AbstractMolecular dynamics simulations using the integrated tempering sampling method were performed for the folding of wild-type B domain of protein A (BdpA). Starting from random and stretched structures, these simulations allow us to fold this protein into the native-like structure frequently, achieving very small backbone (1.7 angstrom) and all heavy-atom root-mean-square deviation (2.6 angstrom). Therefore, the method used here increases the efficiency of configuration sampling and thermodynamics characterization by molecular dynamics simulation. Although inconsistency exists between the calculation and experiments for the absolute stabilities, as a limitation of the force field parameters, the calculated order of helix stability (H3 > H2 > H1) is consistent with that determined by experiments for individual separate helices. The lowest free energy folding pathway of BdpA was found to start with a barrierless and non-cooperative structural collapse from the entirely extended (E) state, which leads to a physiologically unfolded (P) state consisting of multiple stable structures with few native inter-helical hydrophobic interactions formed. In the P state, only H3 is fully structured. The final formation of H1 (and to a lesser extent, H2) in the folded (F) state requires the packing of the inter-helical hydrophobic contacts. In addition, it was found that stabilities of backbone hydrogen bonds are significantly affected by their positions relative to the inter-helical hydrophobic core. As temperature increases, the stability of the hydrogen bonds exposed to the solvent tends to increase while that of the hydrogen bonds buried within the hydrophobic core decreases. Finally, we discuss implications of this study on the general folding mechanism of proteins. (C) 2011 American Institute of Physics. [doi:10.1063/1.3630127]
DOI10.1063/1.3630127
Indexed BySCI
Language英语
WOS IDWOS:000295625400069
PublisherAMER INST PHYSICS
Citation statistics
Cited Times:20[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.iccas.ac.cn/handle/121111/73898
Collection中国科学院化学研究所
Corresponding AuthorGao, Yi Qin
AffiliationPeking Univ, Beijing Natl Lab Mol Sci, Coll Chem & Mol Engn, Beijing 100871, Peoples R China
Recommended Citation
GB/T 7714
Shao, Qiang,Gao, Yi Qin. The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation[J]. JOURNAL OF CHEMICAL PHYSICS,2011,135(13).
APA Shao, Qiang,&Gao, Yi Qin.(2011).The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation.JOURNAL OF CHEMICAL PHYSICS,135(13).
MLA Shao, Qiang,et al."The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation".JOURNAL OF CHEMICAL PHYSICS 135.13(2011).
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