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Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.

Chen QL, Tang XS, Yao WJ, Lu SQ - Int. J. Biol. Sci. (2009)

Bottom Line: The results supported that the Platyplacopus merged into Takydromus and negated the validity of Platyplacopus.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.

View Article: PubMed Central - PubMed

Affiliation: College of Life and Environment Science, Huangshan University, Huangshan, Anhui, 245021, 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.

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MP tree based on 12S rRNA gene sequences data. Numbers at node are bootstrap values (1000 replicates) from MP method 10
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Figure 4: MP tree based on 12S rRNA gene sequences data. Numbers at node are bootstrap values (1000 replicates) from MP method 10

Mentions: In the trees, the T.dorsalis was closed to the sister groups of T. sylvaticus and T.intermedius with strongly support values (figure 2), and shows the relationships of these species are much closer. However, in our previous study, we found that the T. sylvaticus and T.dorsalis formed sister groups, and then closed to T.intermedius, which based on 12S rRNA gene for phylogenetic analyses 10 (figure 4). It shows the more relationships of these three lacertids are unclarity, although the T.sylvaticus, T.dorsalis, and T.intermedius always clustering in a branch. This phenomenon will be investigated by further experiments and data.


Bioinformatics analysis of the complete sequences of cytochrome b of Takydromus sylvaticus and modeling the tertiary structure of encoded protein.

Chen QL, Tang XS, Yao WJ, Lu SQ - Int. J. Biol. Sci. (2009)

MP tree based on 12S rRNA gene sequences data. Numbers at node are bootstrap values (1000 replicates) from MP method 10
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2748471&req=5

Figure 4: MP tree based on 12S rRNA gene sequences data. Numbers at node are bootstrap values (1000 replicates) from MP method 10
Mentions: In the trees, the T.dorsalis was closed to the sister groups of T. sylvaticus and T.intermedius with strongly support values (figure 2), and shows the relationships of these species are much closer. However, in our previous study, we found that the T. sylvaticus and T.dorsalis formed sister groups, and then closed to T.intermedius, which based on 12S rRNA gene for phylogenetic analyses 10 (figure 4). It shows the more relationships of these three lacertids are unclarity, although the T.sylvaticus, T.dorsalis, and T.intermedius always clustering in a branch. This phenomenon will be investigated by further experiments and data.

Bottom Line: The results supported that the Platyplacopus merged into Takydromus and negated the validity of Platyplacopus.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.

View Article: PubMed Central - PubMed

Affiliation: College of Life and Environment Science, Huangshan University, Huangshan, Anhui, 245021, 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.

Show MeSH