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.
Highlights
One 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
MD Simulations are performed on H.pylori S-Ribosylhomocysteine lyase (LuxS) (LuxS_apo) and its four ligand bound (S-ribosylhomocysteine in both the active (KRI) and inactive (SRH) forms bound to one or both the subunits) forms (LuxS+S-Ribosylhomocysteine with intact ribose ring (SRH) - LuxS +2KRI) (10ns each) to obtain equilibrated structures which are analyzed as described in the subsequent sections
Interactions at the Active Site Dynamically stable hydrogen bonds made by the ligand (both inactive (SRH) and active (KRI) ligand) with LuxS residues are listed in Additional file 2: Supplemental Table SB1(a-b) for LuxS +ketone intermediate (KRI) and LuxS+2KRI and Additional file 2: Supplemental Table SB2(a-b) for LuxS+SRH and LuxS+2SRH respectively
Summary
One 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 its function. 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]. Our recent studies have shown that the conformational changes described by the network of side-chain interactions and redistribution of conformational populations can be accurately mapped onto free energy changes [23]
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