Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Abstract

BackgroundOne of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function.ResultsIn 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.ConclusionsIn 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.

Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality

“…The optimal interaction cutoff, that can produce adequate graph representations for a wide range of protein structures, was determined as the transition point for the largest connected cluster 77 . According to this definition, the min I value often lies in the range 2-4% for a diverse spectrum of protein systems and molecular complexes [77][78][79][80][81][82] . A similar analysis was conducted in our study.…”

“…Graph-based protein networks that incorporated topology-based residue connectivity and 11 contact maps of residues cross-correlations obtained from MD simulations 77,78 have provided important insights into structural mechanisms underlying allosteric interactions and communication pathways in various protein systems [79][80][81][82][83][84][85] . By using connectivity networks of interacting residues, computational approaches have characterized rigid and flexible regions in protein structures, explaining thermal stability and activity of various proteins [86][87][88] .…”

Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study

“…A combination of molecular dynamics (MD) simulations and the protein structure network (PSN) analysis using graph-based approaches [93]–[100] can often identify functionally important structural changes in conformational populations of states. Mapping of the dynamical profiles obtained from GNM and NMA approaches with the protein network parameters) [95]–[98] can provide the distribution and reorganization of structurally stable residue networks upon ligand or protein binding. Computational studies have employed these dynamic approaches to model molecular mechanisms of allosteric signaling in the molecular chaperones [101]–[109].…”

S-Ribosylhomocysteine analogues modified at the ribosyl C-4 position

“…[21] These analogues were thought to be able to bind to one monomer of LuxS protein while blocking the correct association of the second monomer, possibly interfering with dimerization interfaces. [21–23] In theory, for example, the longer the alkyl chain incorporated at C4 position in analogs 18 , the more potent inhibition of dimerization of LuxS might be observed since inhibitor can reach both homodimer parts of the protein. The inhibitor might also block one monomer leading to the alteration of the activity and as a consequence conformational changes of the second monomer.…”