Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks

The protein structure networks (PSN) are constructed and graph theoretical analysis is performed on the structures obtained from X-ray crystallography and on the modelled ones. The interfaces, which are known to contain the active site, are characterized from the PSNs of these homodimeric proteins. The key features presented by the protein interfaces are investigated for the classification of the proteins in relation to their function. From our analysis, structural interface motifs are identified for each class in our dataset, which showed distinctly different pattern at the interface of LuxS for the probiotics and some extremophiles. Our analysis also reveals potential sites of mutation and geometric patterns at the interface that was not evident from conventional sequence alignment studies.The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials.Quorum sensing is a widespread mechanism of intercellular communication among bacteria controlling its gene expression as a function of cell density. Two major quorum sensing pathways, with characteristic signalling molecules, AI-1 and AI-2, have been identified[1]. LuxS is one of the principal components in the biosynthetic pathway of AI-2, the universal signal for bacterial inter-species communication. In some organisms, quorum sensing by LuxS has been shown to have a profound effect on pathogenicity by affecting toxin production or flagellar morphogenesis and hence motility and colonization. However, in some other species it has no dir