Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.
Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.
复制标题
森林动物细胞色素b全序列生物信息学分析及编码蛋白三级结构建模
DOI：
10.7150/ijbs.5.596
复制
发表时间：
2009-09-22
影响因子：
9.2
通讯作者：
Lu SQ
中科院分区：
文献类型：
--
作者：
Chen QL;Tang XS;Yao WJ;Lu SQ
对Takydromus sylvaticus细胞色素b（cyt b）基因全序列（1143bp）进行了测序。为了阐明Takydromus sylvaticus的系统发育位置，我们研究了15个Takydromus spp的系统发育。使用 cyt b 基因的 DNA 片段，通过最大简约 (MP)、贝叶斯推理 (BI) 和最大似然 (ML) 方法在东亚分布。结果支持鸭嘴兽合并为Takydromus，否定了鸭嘴兽的有效性。此外，对细胞色素b三级结构的预测显示，CD环区域包含两个形成发夹排列的短螺旋，即cd1和cd2。热稳定性分析表明CD环区域在热力学上不稳定，可能为位于血红素的氨基酸提供流动性，并可能为ISP（铁硫蛋白）顶部和Qo结合位点的空腔区域提供高灵活性。这表明细胞色素b的CD环区的两个短螺旋是ISP结合位点的主要部分。
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.