Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase

Abstract

Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to fully harness their potential in drug discovery. In this study, molecular dynamics simulations and nuclear magnetic resonance spectroscopy are used to investigate how increases in temperature affect allostery in imidazole glycerol phosphate synthase. Results demonstrate that temperature increase triggers a cascade of local amino acid-to-amino acid dynamics that remarkably resembles the allosteric activation that takes place upon effector binding. The differences in the allosteric response elicited by temperature increase as opposed to effector binding are conditional to the alterations of collective motions induced by either mode of activation. This work provides an atomistic picture of temperature-dependent allostery, which could be harnessed to more precisely control enzyme function.

Connected Component Analysis of Dynamical Perturbation Contact Networks

“…After showing that the CCA approach can effectively detect the propagation of the atomic contact perturbations associated with the allosteric pathways of bacterial IGPS, in the following, we discuss the application of this approach to other proteins and conditions. In particular, in our previous investigations, we demonstrated the peculiar effects that temperature has on the allosteric pathways of bacterial IGPS . The temperature increase significantly alters the collective motions associated with the IGPS allostery but, unexpectedly, it also triggers a cascade of local contact perturbations (probed with our DPCN approach) that remarkably resembles the allosteric activation induced by the effector binding, i.e., the allosteric pathways along side R of the IGPS complex.…”

“…From this quite intricate picture, one can still extract some clues about the overall contact changes in the IGPS complex due to effector binding. In fact, a significant amount of contact changes, represented by (colored) edges is clearly visible at the HisF/HisH interface, as a consequence of changes in the relative motion between the two subunits (namely, the breathing motion), which has been shown to be an allosteric effect associated with the effector binding. ,− ,, However, the pattern associated with the most important contribution to the allosteric pathways, which is running along one side of IGPS (namely, side R), is difficult to detect in the complete DPCN graph since the visual inspection of a large number of edges represents a quite tedious work.…”

“…By constructing a protein graph weighted by differences in atomic contacts between two systems, such as the apo- and effector-bound IGPS enzymes, the DPCN can capture allosteric pathways previously described in the literature. , Moreover, the DPCN is a powerful tool not only for studying allostery but, in general, can be potentially used for comparisons of MD simulations. This highly transferable method has been demonstrated to be quite useful for studies of various protein dynamics, including the allostery of bacterial IGPS at high temperatures, yeast IGPS, and adenosine monophosphate-activated protein kinase (AMPK), making it a valuable tool. ,− In this work, we investigated the capabilities of the connected component (CC) analysis (CCA) tool − in providing a fast, robust, and unbiased analysis of DPCNs. The CCA approach can partition the contact network by grouping connected nodes, similar to what has been successfully done for energy-weighted protein graphs, with the advantage of providing information on the local propagation of the perturbations.…”

“…The impressive functionality of IGPS lies in the ability of its active site to detect the allosteric effector over a distance of approximately 25 Å through an allosteric signal that is initiated in the HisF protein and is transferred to the HisH subunit. In a series of computational studies of IGPS allostery, ,,− we have predicted that the allosteric propagation mechanism involves a collection of both short- and long-range displacements, i.e., a set of local (hydrophobic, salt-bridges, and H-bond) interactions that increase the correlations of inter-residue motions on one side of the protein (“side R”, opposite to “side L” indicating right and left sides in the representation depicted in Figure A, respectively) and a slow collective motion that alters the HisF/HisH interface, namely, the breathing motion. , Our earlier theoretical predictions have been successfully used to design allosteric drugs and IGPS mutants that alter the IGPS allosteric pathways, resulting in inactive enzymes. Very recently, both short- and long-range predicted effects have been demonstrated experimentally by X-ray structural characterization of active IGPS ternary complexes and light-switching activation, respectively.…”

“…Compared to more commonly used weighted protein networks, such as those involving weights based on correlated motions obtained from MD simulations, ,,− using dynamical contact networks provides complementary information to acquire a deep knowledge of allosteric signal propagation. This is particularly valid when the allosteric pathways involve the propagation of local contact perturbations from the effector to the active site, as has been demonstrated in IGPS. ,,− In fact, using correlated motions features the limitation of compressing the atomistic details of the signal propagation in a single numerical coefficient for each interacting amino acid pair. Thus, recovering the atomistic information from a protein graph based on correlation coefficients requires the re-analysis of the MD simulations, while the DPCN graph can be easily decomposed in subgraphs for specific types of interactions (e.g., considering only hydrophobic residues or ionic ones, or just backbone atoms to focus on partial folding/unfolding events, etc.…”