ISSN: 1449-2288International Journal of Biological Sciences
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Int J Biol Sci 2009; 5(6):596-602. doi:10.7150/ijbs.5.596 This issue Cite
Research Paper
Bioinformatics Analysis the Complete Sequences of Cytochrome b of Takydromus sylvaticus and Modeling the Tertiary Structure of Encoded Protein
1. College of Life and Environment Science, Huangshan University, Huangshan, Anhui, 245021, China
2. Bio-electronic Centre of Shanghai University, Shanghai, 200072, China
Abstract
Cytochrome b (cyt b) gene complete sequences (1143bp) of Takydromus sylvaticus were sequenced. In order to clarify the phylogenetic position of the Takydromus sylvaticus, we investigated the phylogeny of 15 Takydromus spp. distributed in East-Asia by Maximum Parsimony (MP), Bayesian Inference (BI), and Maximum Likelihood (ML) methods using DNA fragments of cyt b genes. The results supported that the Platyplacopus merged into Takydromus and negated the validity of Platyplacopus. Furthermore, the prediction of tertiary structures of cyt b exhibited the CD loop region contain two short helices forming a hairpin arrangement, namely cd1 and cd2. Thermostability analysis shows that the CD-loop region is unstable thermodynamically and may provide mobility to amino acids located at the heme, and might provide high flexibility to the top of ISP (iron-sulfur protein) and the cavity region of Qo binding site. It suggested that the two short helices of CD loop region of cyt b was a dominating portion for ISP binding site.
Keywords: Takydromus sylvaticus, Cytochrome b (cyt b), Phylogeny, homology modeling, tertiary structure
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