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Amplification, In-silico classification, characterization and molecular modeling of Histone H2B gene from Setaria cervi
Sudhanshu Shekhar Yadav1, Vinay Kumar Singh2, Eva Liebau3, Sushma Rathaur1*
1Department of Biochemistry, 2Centre for Bioinformatics, Faculty of Science, Banaras Hindu University, Varanasi 221005, U.P., India 3Westfalische Wilhelms-Uinversitat, Institute of Animal Physiology, Department of Molecular Physiology, Hindenburgplatz-55, Muenster, Germany.
Yadav SS, SinghVK, Liebau E, Rathaur S., Amplification, In-silico classification, characterization and molecular modeling of Histone H2B gene from Setaria cervi, Online J Bioinform, 13(2):232-245, 2012. Setaria cervi was screened for antifilarial agents by gene identification, behavior and genome organization. H2B gene was identified using primers generated from closely related species Brugia malayi. A 0.75kb amplified product from cDNA of S. cervi was used as template; gene sequences (JQ622388; AFI23673) were 83.3% of Brugia malayi and Loa loa. Functional domain analysis with Interproscan server revealed an amplified putative protein similar to Histone H2B (IPR000558), Histone core (IPR007125) and Histone fold (IPR009072) patterns. Model structure (PM0078101) and classification lineage (126.96.36.199) suggested that the existing protein was a histone subunit consisting of an alpha fold with orthogonal bundle architecture. H2B-DNA interactions stabilize the nucleosome and H2B could modulate chromatin structure during DNA repair, replication, transcription and chromatin compaction. DNA-Histone protein interaction showed that residues 61Asn, 62Lys, 63Arg, 67Ser, 69Arg, 67Arg, 89Ser, 93Lys, 97Lys, 99Asn and 102Lys of H2B protein binded with wrapped DNA in genome of S. cervi. H2B histone protein could be a potential drug target for filariasis since inhibition of histone protein (H2B) synthesis blocks the cell division at S-phase of cell cycle which could prevent its transmission.
Keywords: Amplification, Homology modeling, Histone H2B, Setaria cervi, Filariasis, Drug target.