Computational protocol: Overexpressed HDAC8 in cervical cancer cells shows functional redundancy of tubulin deacetylation with HDAC6

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[…] The amino acid sequences of tubulins were retrieved from NCBI database (Accession numbers: AAH33064.1, AAH20946.1, and AAF34188.1 for alpha, beta and gamma tubulin respectively). They were further subjected to multiple sequence alignment using Clustal omega [] to infer sequence conservation among the tubulin proteins. The sequences were analysed for functional conserved regions using Pfam database []. The crystal structures for beta-tubulin (PDB ID: 2XRP_A) and gamma-tubulin (PDB ID: 3CB2_A) were available in the database. However, Alpha-tubulin c did not have any structure in PDB and therefore its structure was built using homology modelling. Protein BLAST in eukaryotic genomes was carried out to analyse the sequence homology and identity. Homology modelling of Alpha tubulin was carried out by I-TASSER, an online webserver for protein structure prediction and structure-based function annotation []. The tertiary structure prediction was performed by I-TASSER server by using the best align template. Out of the generated models of the target sequence, the best template (PDB ID: 4I4T_A) was selected based on the significant sequence identity, C-Score, TM score and RMSD values of template structure. […]

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