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.
Highlights
Snake venom consists of a large number of biologically active peptides, proteins, non-proteins, macromolecules as well as several metallic elements
Uniprot Blast was performed with the primary amino acid sequence of NK-CT1 as query, using BLOSUM62 matrix, having threshold value of 10 and allowing gap and filtering the low complexity region to find out the family of NK-CT1
Conserved Domain Analysis by CDD Sequence of NK-CT1 was analysed in CDD database (Conserved Domain Database) of NCBI to find out the span and composition of conserved protein sequence region present in it.CDD database is a resource for the annotation of protein sequences with the location of footprints of conserved domain, and functional sites which are inferred from these footprints
Summary
Snake venom consists of a large number of biologically active peptides, proteins, non-proteins, macromolecules as well as several metallic elements. Methodology: Template Selection The primary amino acid sequence (60 amino acids) of NK-CT1, as already reported in our earlier study [6], was used for protein blast search (BLASTP 2.2.29) [10] as query against PDB database using BLOSUM80 matrix having gap costs as existence = 10 and extension=1 and using compositional score matrix alignment [11] to scale all substitution scores by an analytically determined constant, while leaving the gap scores fixed. This procedure was adopted to get more accurate E-value rather than standard un-scaled score. PROMOTIF [25] analysis was performed (a tool nested under ProFunc database) for the identification of biochemical functions of NK-CT1 from its three dimensional structure using both sequence and structure based methods for prediction of motifs present in NK-CT1, which includes supersecondary structures i.e. beta turns, 310 helices, beta hairpins
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