Optimized method for TAG protein homology modeling: In silico and experimental structural characterization.

TitleOptimized method for TAG protein homology modeling: In silico and experimental structural characterization.
Publication TypeJournal Article
Year of Publication2016
AuthorsTomar JSingh, Peddinti RKrishna
JournalInt J Biol Macromol
Date Published2016 Jul
KeywordsAcinetobacter baumannii, Adenine, Amino Acid Sequence, Bacterial Proteins, Cloning, Molecular, DNA Glycosylases, DNA, Bacterial, Enzyme Inhibitors, Escherichia coli, Gene Expression, Molecular Docking Simulation, Mutation, Protein Structure, Secondary, Protein Structure, Tertiary, Recombinant Proteins, Sequence Alignment, Structural Homology, Protein, Substrate Specificity, Thermodynamics, User-Computer Interface

The DNA glycosylases cleave CN glycosyl bond to release a free base and generate abasic sites concurrently. Function and structure of these enzymes in the pathogenic bacterium Acinetobacter baumannii and its closely related species are not well characterized. Inhibition of TAG enzyme is a promising drug design strategy against A. baumannii. Here optimized molecular modeling approaches were used to provide a structural scaffold of TAG. The recombinant TAG protein was expressed and purified to determine oligomeric state using size exclusion chromatography, which showed the existence of TAG protein as monomer (mwt ∼21kDa). Secondary structure and substrate binding were analyzed using CD are in good agreement with the in silico predictions. Near UV-CD spectrum shows the involvement of Tyr residues in substrate recognition. Molecular docking studies were performed to understand the molecular recognition interactions and this knowledge was used to identify the potent inhibitors using virtual screening. Residues crucial for DNA holding and enzyme catalysis are reconfirmed by the in silico mutational studies.

Alternate JournalInt. J. Biol. Macromol.
PubMed ID27017978