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Int J Biol Sci 2009; 5(6):596-602. doi:10.7150/ijbs.5.596

Research Paper

Bioinformatics Analysis the Complete Sequences of Cytochrome b of Takydromus sylvaticus and Modeling the Tertiary Structure of Encoded Protein

Qi-Long CHEN1,2, Xin-Sheng TANG1, Wen-Juan YAO2, Shun-Qing LU1, ✉

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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How to cite this article:
CHEN QL, TANG XS, YAO WJ, LU SQ. Bioinformatics Analysis the Complete Sequences of Cytochrome b of Takydromus sylvaticus and Modeling the Tertiary Structure of Encoded Protein. Int J Biol Sci 2009; 5(6):596-602. doi:10.7150/ijbs.5.596. Available from http://www.ijbs.com/v05p0596.htm