Dataset Information

Molecular modeling of NK-CT1, from Indian monocellate cobra (Naja kaouthia) and its docking interaction with human DNA topoisomerase II alpha.

ABSTRACT: A 6.76 kDa molecular weight cardio and cytotoxic protein of 60 amino acids in length called NK-CT1, was purified from the venom of Indian monocellate cobra (Naja kaouthia) by ion-exchange chromatography and HPLC as described in our earlier report. Therefore it is of interest to utlize the sequence of NK-CT1 for further functional inference using molecular modeling and docking. Thus homology model of NK-CT1 is described in this report. The anti-proliferative activity of the protein, binding with human DNA topoisomerase-II alpha was demonstrated using docking data with AUTODOCK and AUTODOCK MGL tools. Data shows that M26, V27 and S28 of NK-CT1 is in close contact with the nucleotides of the oligonucleotide, bound with topoisomerase-II alpha complex.

SUBMITTER: Bandopadhyay P

PROVIDER: S-EPMC5267952 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Molecular modeling of NK-CT1, from Indian monocellate cobra (Naja kaouthia) and its docking interaction with human DNA topoisomerase II alpha.

Bandopadhyay Pathikrit P Halder Soma S Sarkar Mrinmoy M Kumar Bhunia Sujay S Dey Sananda S Gomes Antony A Giri Biplab B

Bioinformation 20160615 3

A 6.76 kDa molecular weight cardio and cytotoxic protein of 60 amino acids in length called NK-CT1, was purified from the venom of Indian monocellate cobra (Naja kaouthia) by ion-exchange chromatography and HPLC as described in our earlier report. Therefore it is of interest to utlize the sequence of NK-CT1 for further functional inference using molecular modeling and docking. Thus homology model of NK-CT1 is described in this report. The anti-proliferative activity of the protein, binding with ...[more]

PMID: 28149043

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Project description:ObjectivesThe objective of the present work was to examine the bacterial flora associated with the oral cavity of Indian cobra and to study their antibiogram.MethodsOral swabs, collected from six healthy (4 males and 2 females) adult cobra, were subjected to microbiological examination through differential media. A total of 74 isolates which demonstrated noticeable colony characters were studied with different biochemical tests. The strains that showed distinctive colonies, morphology and biochemical parameters were additionally subjected to phylogenetic characterization using 16S rRNA gene sequences. Further, the isolates were subjected to antimicrobial susceptibility testing using ICOSA-20-plus and ICOSA-20-minus.ResultsMicroscopic examination of the oral cavity of Indian cobra revealed the dominance of Gram-negative bacteria over Gram-positive. The oral microflora constituted of bacteria such as Salmonella sp. (S. typhi, S. paratyphi A); Pseudomonas sp. (P. aeruginosa, P. fluorescence); Proteus sp. (P. mirabilis, P. penneri, P. vulgaris); E. coli; Morganella sp.; Citrobacter sp. (C. diversus, C. freundii); Aeromonas sp. (A. hydrophila, A. salmonicida); Enterobacter sp. (E. aerogens); Acinetobacter sp. (A. baumannii); Neisseria sp.; Serratia sp.; Bacillus sp. (B. cereus, B. megatarium, B. atrophaeus and B. weihenstephanensis); Enterococcus sp. (E. faecalis, E. faecium); Staphylococcus sp. (S. aureus, S. epidermidis); Alcaligenes sp.; Chryseobacterium sp. and Micrococcus sp. Most of the isolates were resistant towards antibiotics such as Penicillin, Cefpodoxime, Amoxyclav, Co-Trimoxazole, Ticarcillin, Erythromycin and Nalidixic acid while sensitive towards Ciprofloxacin, Gentamicin, Ofloxacin, Sparfloxacin, Tobromycin, Ceftriaxone, Tetracycline, Novobiocin and Imipenem.ConclusionsThe secondary complications of the snake bite victims should be managed with appropriate antibiotics after proper examination of the bacterial flora from the wound sites.

Project description:BackgroundThe monocled cobra (Naja kaouthia) is a medically important venomous snake in Southeast Asia. Its venom has been shown to vary geographically in relation to venom composition and neurotoxic activity, indicating vast diversity of the toxin genes within the species. To investigate the polygenic trait of the venom and its locale-specific variation, we profiled and compared the venom gland transcriptomes of N. kaouthia from Malaysia (NK-M) and Thailand (NK-T) applying next-generation sequencing (NGS) technology.MethodsThe transcriptomes were sequenced on the Illumina HiSeq platform, assembled and followed by transcript clustering and annotations for gene expression and function. Pairwise or multiple sequence alignments were conducted on the toxin genes expressed. Substitution rates were studied for the major toxins co-expressed in NK-M and NK-T.Results and discussionThe toxin transcripts showed high redundancy (41-82% of the total mRNA expression) and comprised 23 gene families expressed in NK-M and NK-T, respectively (22 gene families were co-expressed). Among the venom genes, three-finger toxins (3FTxs) predominated in the expression, with multiple sequences noted. Comparative analysis and selection study revealed that 3FTxs are genetically conserved between the geographical specimens whilst demonstrating distinct differential expression patterns, implying gene up-regulation for selected principal toxins, or alternatively, enhanced transcript degradation or lack of transcription of certain traits. One of the striking features that elucidates the inter-geographical venom variation is the up-regulation of α-neurotoxins (constitutes ∼80.0% of toxin's fragments per kilobase of exon model per million mapped reads (FPKM)), particularly the long-chain α-elapitoxin-Nk2a (48.3%) in NK-T but only 1.7% was noted in NK-M. Instead, short neurotoxin isoforms were up-regulated in NK-M (46.4%). Another distinct transcriptional pattern observed is the exclusively and abundantly expressed cytotoxin CTX-3 in NK-T. The findings suggested correlation with the geographical variation in proteome and toxicity of the venom, and support the call for optimising antivenom production and use in the region. Besides, the current study uncovered full and partial sequences of numerous toxin genes from N. kaouthia which have not been reported hitherto; these include N. kaouthia-specific l-amino acid oxidase (LAAO), snake venom serine protease (SVSP), cystatin, acetylcholinesterase (AChE), hyaluronidase (HYA), waprin, phospholipase B (PLB), aminopeptidase (AP), neprilysin, etc. Taken together, the findings further enrich the snake toxin database and provide deeper insights into the genetic diversity of cobra venom toxins.

Dataset Information

Molecular modeling of NK-CT1, from Indian monocellate cobra (Naja kaouthia) and its docking interaction with human DNA topoisomerase II alpha.

Publications

Molecular modeling of NK-CT1, from Indian monocellate cobra (Naja kaouthia) and its docking interaction with human DNA topoisomerase II alpha.

Similar Datasets

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