alexa Abstract | In silico structure analysis of potassium channel Bgk toxin and its docking prediction with human voltage gated potassium (Kv) channel

Journal of Chemical and Pharmaceutical Research
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Abstract

Kappa actitoxin Bg1a or Potassium channel Bgk toxin is voltage-gated potassium (Kv) channel blocker toxin extracted from sea anemone Bunodosoma granulifera. The present study represents a detailed in silico analysis of the Bgk toxin. Primary structure and transmembrane helix analysis were done through Pepstat tool and TMHMM server respectively. Secondary structure, signal peptide and cysteine disulfide prediction was made though PsiPred workbench, Signal P server and DiANNA 1.1 web server respectively. Protein disorderliness and immunogenicity prediction were carried on through PrDos and POPI 2.0 server respectively. Docking simulation was performed through the application of ClusPro server. The phylogenetic tree was constructed by COBALT multiple alignment tools and the tree were redrawn through Phifi server. Motif, protein family and hydrophobicity were also predicted through Interproscan, Pfam and Protscale. The paper aimed towards the characterization of kappa Bgk toxin through bioinformatics tools. The input from such bioinformatic analyses will be a novel and important approach for paving a way in searching new products of pharmacological interest and may later be helpful in designing vaccine against this toxin. The primary structure prediction showed that kappa Bgk toxin is a stable and basic protein. The secondary structure prediction revealed that the presence of alpha helices and coils as its secondary structural elements. The hydrophobicity prediction showed that this toxin is of hydrophilic nature. Whereas transmembrane prediction reflected that this toxin is a soluble protein with no transmembrane domains. Further the toxin has no signal sequence. Three cysteine disulfide bonds were predicted in the toxin. It has only a ShK motif and belongs to Pfam-A family. This toxin showed disorderness and the predicted immunogenecity of CTL response was moderate. The toxin illustrates a distinct phylogenetic relationship with related toxins of other sea anemone species. There are distinct disordered regions on the toxin. Molecular docking of the Bgk toxin with voltage gated potassium channel illustrated a definite binding which may be related to protein disorderness and presence of cysteine disulfide bonds.

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Author(s): Sriparna Ray and Jayanta Sinha

Keywords

in silico analysis, Kappa actitoxin Bg1a, human voltage gated potassium channel, protein docking., docking

 
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