%0 Journal Article
%T Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis
%A Moitrayee Bhattacharyya
%A Saraswathi Vishveshwara
%J BMC Structural Biology
%D 2010
%I BioMed Central
%R 10.1186/1472-6807-10-27
%X In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione) for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites.In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure.Enzymes perform their function by responding precisely to their cognate ligands, yet retaining their overall shape and structure. This phenomenon was beautifully formulated in classical models such as the "MWC" model of Monod [1] and the "KNF" model of Koshland [2]. Such a phenomenological model, known as allostery, has played a major role in biochemistry in explaining the functioning
%U http://www.biomedcentral.com/1472-6807/10/27