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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.

Show MeSH
Bayesian inference tree derived from partial cyt b sequences of the lacertids. Numbers above branches are bootstrap support for MP (1000 replicates) / ML (10 replicates) analyses (>50 retained), and numbers below branches indicate Bayesian posterior probabilities (>90% retained). Based on the topological structure of phylogenetic trees, 15 species lacertids were defined approximated three major species groups (A, B and C).
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Figure 2: Bayesian inference tree derived from partial cyt b sequences of the lacertids. Numbers above branches are bootstrap support for MP (1000 replicates) / ML (10 replicates) analyses (>50 retained), and numbers below branches indicate Bayesian posterior probabilities (>90% retained). Based on the topological structure of phylogenetic trees, 15 species lacertids were defined approximated three major species groups (A, B and C).

Mentions: Based on the E.velox and L.vivipara as outgroups, molecular phylogenetic trees were reconstructed using MP method, which were virtually identical to the trees recovered in ML and BI analyses (Figure 2). The analyses found that the phylogenetic trees were consistent, and approximated three major species groups were defined for 15 species lacertids. Group A contained T.amurensis, T.tachydromoides, T.dorsalis, T.intermedius, and T.sylvaticus, Group B contained T.sauteri, T.smaragdinus, T.keuhnei, and T.sexlineatus. Group C contained the remaining species, including T.formosanus, T.wolteri, T.hsuehshanesis, T.toyamai, T.septentrionalis, and T.stejnegeri.


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)

Bayesian inference tree derived from partial cyt b sequences of the lacertids. Numbers above branches are bootstrap support for MP (1000 replicates) / ML (10 replicates) analyses (>50 retained), and numbers below branches indicate Bayesian posterior probabilities (>90% retained). Based on the topological structure of phylogenetic trees, 15 species lacertids were defined approximated three major species groups (A, B and C).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Bayesian inference tree derived from partial cyt b sequences of the lacertids. Numbers above branches are bootstrap support for MP (1000 replicates) / ML (10 replicates) analyses (>50 retained), and numbers below branches indicate Bayesian posterior probabilities (>90% retained). Based on the topological structure of phylogenetic trees, 15 species lacertids were defined approximated three major species groups (A, B and C).
Mentions: Based on the E.velox and L.vivipara as outgroups, molecular phylogenetic trees were reconstructed using MP method, which were virtually identical to the trees recovered in ML and BI analyses (Figure 2). The analyses found that the phylogenetic trees were consistent, and approximated three major species groups were defined for 15 species lacertids. Group A contained T.amurensis, T.tachydromoides, T.dorsalis, T.intermedius, and T.sylvaticus, Group B contained T.sauteri, T.smaragdinus, T.keuhnei, and T.sexlineatus. Group C contained the remaining species, including T.formosanus, T.wolteri, T.hsuehshanesis, T.toyamai, T.septentrionalis, and T.stejnegeri.

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