• HIROYUKI AZAKAMI

      Articles written in Journal of Biosciences

    • Computational prediction of active sites and ligands in different AHL quorum quenching lactonases and acylases

      ZULKAR NAIN UTPAL KUMAR ADHIKARI FARUQ ABDULLA NAHID HOSSAIN NIRMAL CHANDRA BARMAN FARIHA JASIN MANSUR HIROYUKI AZAKAMI MOHAMMAD MINNATUL KARIM

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      With the emergence of multidrug-resistant ‘superbug’, conventional treatments become obsolete. Quorumquenching (QQ), enzyme-dependent alteration of quorum sensing (QS), is now considered as a promisingantimicrobial therapy because of its potentiality to impede virulence gene expression without resulting ingrowth inhibition and antibiotic resistance. In our study, we intended to compare between two major QQenzyme groups (i.e., AHL lactonases and AHL acylases) in terms of their structural and functional aspects.The amino acid composition-based principal component analysis (PCA) suggested that probably there is nostructural and functional overlapping between the two groups of enzymes as well as within the lactonaseenzymes but the acylases may functionally be affected by one another. In subcellular localization analysis,we also found that most lactonases are cytoplasmic while acylases are periplasmic. Investigation on thesecondary structural features showed random coil dominates over a-helix and b-sheet in all evaluatedenzymes. For structural comparison, the tertiary structures of the selected proteins were modelled andsubmitted to the PMDB database (Accession ID: PM0081007 to PM0081018). Interestingly, sequencealignment revealed the presence of several conserved domains important for functions in both proteingroups. In addition, three amino acid residues, namely aspartic acid, histidine, and isoleucine, were commonin the active sites of all protein models while most frequent ligands were found to be 3C7, FEO, and PAC.Importantly, binding interactions of predicted ligands were similar to that of native QS signal molecules.Furthermore, hydrogen bonds analysis suggested six proteins are more stable than others. We believe thatthe knowledge of this comparative study could be useful for further research in the development of QSbaseduniversal antibacterial strategies.

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