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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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Front (a) and back (b) views shows the thermostability of CD loop region of cyt b. Light blue to red colors show stable to unstable regions, respectively. Tertiary structures are shown in the space-fill mode.
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Figure 5: Front (a) and back (b) views shows the thermostability of CD loop region of cyt b. Light blue to red colors show stable to unstable regions, respectively. Tertiary structures are shown in the space-fill mode.

Mentions: Furthermore, we noticed that the CD loop contains two short helices, including cd1 and cd2. Thermostability analysis shows that the structure of CD-loop region is unstable thermodynamically and may provide mobility to amino acids located at the heme (Figure 5), and might provide high flexibility to the top of ISP (iron-sulfur protein) and the cavity region of Qo binding site. Esser et al. analyzed eight structures of mitochondrial bc1 with bound on Qo site inhibitors, and indicated that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cyt b, and especially, as the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP 27. Zhu et al. also determined the presteady-state kinetics of ISP and cytochrome bL reduction by ubiquinol, and postulated that the iron-sulfur protein accepts the first electron from ubiquinol to generate ubisemiquinone anion to reduce heme bL 28. On the basis of this mentioned, we speculated the CD loop region is a dominating portion for ISP binding site, and the existence of instability in the CD loop could affect the function of these two short helices. This hypothesis will be investigated by further experiments.


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)

Front (a) and back (b) views shows the thermostability of CD loop region of cyt b. Light blue to red colors show stable to unstable regions, respectively. Tertiary structures are shown in the space-fill mode.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Front (a) and back (b) views shows the thermostability of CD loop region of cyt b. Light blue to red colors show stable to unstable regions, respectively. Tertiary structures are shown in the space-fill mode.
Mentions: Furthermore, we noticed that the CD loop contains two short helices, including cd1 and cd2. Thermostability analysis shows that the structure of CD-loop region is unstable thermodynamically and may provide mobility to amino acids located at the heme (Figure 5), and might provide high flexibility to the top of ISP (iron-sulfur protein) and the cavity region of Qo binding site. Esser et al. analyzed eight structures of mitochondrial bc1 with bound on Qo site inhibitors, and indicated that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cyt b, and especially, as the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP 27. Zhu et al. also determined the presteady-state kinetics of ISP and cytochrome bL reduction by ubiquinol, and postulated that the iron-sulfur protein accepts the first electron from ubiquinol to generate ubisemiquinone anion to reduce heme bL 28. On the basis of this mentioned, we speculated the CD loop region is a dominating portion for ISP binding site, and the existence of instability in the CD loop could affect the function of these two short helices. This hypothesis will be investigated by further experiments.

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