1,721,175 research outputs found
Dimerization of the lutropin receptor: Insights from computational modeling
No full textA computational approach based upon rigid-body docking, ad hoc filtering, and cluster analysis has been carried out to predict likely interfaces in LHR homodimers. Quaternary structure predictions emphasize the role of helices 4, 5 and 6, with prominence to helix 4, in mediating inter-monomer interactions. Intermolecular interactions essentially involve the transmembrane domains rather than the hydrophilic loops and do not implicate disulfide bridges.Collectively, molecular dynamics simulations on the isolated receptor and computational modeling of LHR homodimerization suggest that mutation-induced LHR activation favors H4-H4 contacts involving the highly conserved W491 from both the receptors monomers
Theoretical study on mutation-induced activation of the luteinizing hormone receptor
No full textHere, three-dimensional model building and molecular dynamics simulations of the luteinizing hormone receptor have been employed to generate hypotheses about the molecular mechanisms underlying the activation of the receptor induced by naturally occurring activating mutations. The comparative analysis of the wild-type receptor and of 16 constitutively active or inactive mutants has been instrumental in inferring the structural/dynamic features which could characterize the inactive and the active forms of the receptor. These features have been also employed for predicting the functional behavior of new receptor mutants. The results of this study might provide a structural framework to interpret the pathological effects induced by mutations of the luteinizing hormone receptor. In addition, the proposed theoretical model could be useful for engineering new mutations or ligands able to modulate receptor function
Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants
No full textDisease-causing missense mutations in membrane proteins, such as rhodopsin mutations associated with the autosomal dominant form of retinitis pigmentosa (ADRP), are often linked to defects in folding and/or trafficking. The mechanical unfolding of wild-type rhodopsin was compared with that of 20 selected ADRP-linked mutants more or less defective in folding and retinal binding. Rhodopsin fold is characterized by networks of amino acids in the retinal and G-protein binding sites likely to play a role in the stability and function of the protein. The distribution of highly connected nodes in the network reflects the existence of a diffuse intramolecular communication inside and between the 2 poles of the helix bundle, which makes pathogenic mutations share similar phenotypes irrespective of topological and physicochemical differences between them. Because of this communication, the ADRP-linked rhodopsin mutations share a more or less marked ability to impair selected hubs in the protein structure network. The extent of this structural effect relates to the severity of the biochemical defect caused by mutation. The investigative strategy employed in this study is likely to apply to all structurally known membrane proteins particularly susceptible to misassembly-causing mutations
Molecular basis of ligand binding and receptor activation in the oxytocin and vasopressin receptor family
No full textAlthough it is now widely accepted that G-protein-coupled receptors exist in at least two allosteric states, inactive and active, and that the spontaneous equilibrium between the two is regulated by various events including the binding of specific agonists and antagonists, the molecular counterparts of these functionally different states are still poorly understood. In this paper, we review our current knowledge concerning the structure-function relationships of the oxytocin and vasopressin receptors, focusing in particular on the process of receptor activation. Using a combined approach of site-directed mutagenesis and molecular modelling, we investigated the molecular events leading to agonist-dependent and -independent receptor activation in the human oxytocin receptor. Our analysis allows us to propose that the active conformations of this receptor are characterised by similar rearrangements of its cytosolic regions that ultimately lead to the opening of a putative docking site for the G-protein. Furthermore, the dynamics of these motions are similar to that observed in the alpha1B-adrenergic receptor, thus suggesting that, although activated by different ligands, the process of receptor isomerization in these two receptors is regulated by the same cluster of highly conserved residues and that common molecular events are responsible for receptor activation in different G-protein-coupled receptors
Prediction of MEF2A-DNA interface by rigid body docking: A tool for fast estimation of protein mutational effects on DNA binding
No full textThe protein-protein docking algorithm ZDOCK has been challenged for the first time to predict protein-DNA contacts. The computational approach defined in this study has proven effectiveness in fast in silico estimations of mutational effects of the MEF2A transcription factor on DNA binding
Structural Aspects of the Luteinizing Hormone Receptor: Information from Molecular Modeling and Mutagenesis
No full textThe luteinizing hormone receptor (LHR) is a member of the superfamily of G protein-coupled receptors and, in humans, binds two closely related ligands, members of the heterodimeric glycoprotein hormone family. This receptor is an essential component of the reproductive axis in males and females, and a number of naturally occurring pathophysiologic activating and inactivating mutations have been described. This review deals with the current state of knowledge of the structure of LHR based on molecular modeling and the supporting experimental data from engineered and naturally occurring mutations
Modeling the structural communication in supramolecular complexes involving GPCRs
No full textThis article describes a computational strategy aimed at studying the structural communication in G-Protein Coupled Receptors (GPCRs) and G proteins. The strategy relies on comparative Molecular Dynamics (MD) simulations and analyses of wild-type (i.e., reference state) vs. mutated (i.e., perturbed state), or free (i.e., reference state) vs. bound (i.e., perturbed state) forms of a GPCR or a G protein. Bound forms of a GPCR include complexes with small ligands and/or receptor dimers/oligomers, whereas bound forms of heterotrimeric GDP-bound G proteins concern the complex with a GPCR. The computational strategy includes structure prediction of a receptor monomer (in the absence of high-resolution structure), a receptor dimer/oligomer, and a receptor-G protein complex, which constitute the inputs of MD simulations. Finally, the analyses of the MD trajectories are instrumental in inferring the structural/dynamics differences between reference and perturbed states of a GPCR or a G protein. In this respect, focus will be put on the analysis of protein structure networks and communication paths
Understanding the mutation-induced activation of the lutropin receptor from computer simulation
No full textThe luteinizing hormone receptor (LHR) is a member of the superfamily of G protein-coupled receptors and, in humans, binds two closely related ligands, members of the heterodimer glycoprotein hormone family. This receptor is an essential component of the reproductive axis in males and females and is particularly prone to spontaneous pathogenic activating and inactivating mutations.3D-model building and computer simulations have been employed to study the mutation-induced activation mechanism of the LHR.The results of molecular simulations on different LHR models converge into the hypothesis that the arginine of E/DRY/W sequence is an important switch of the LHR activation. They also suggest that a structural modification at the interface between the cytosolic extensions of helix 3 and helix 6 is important in the mutation-induced LHR activation and/or G protein recognition. The theoretical models provide insights into the structural features of the LHR sites susceptible to spontaneous activating mutations, constituting also useful tools for "in silico" prediction of the functional behaviour of LHR mutants
Constitutively active G protein-coupled receptor mutants: implications on receptor function and drug action
No full textMutations of GPCRs can increase their constitutive (agonist-independent) activity. Some of these mutations have been artificially introduced by site-directed mutagenesis; others occur spontaneously in human diseases. The analysis of constitutively active GPCR mutants has attracted a large interest in the past decade, providing an important contribution to our understanding of the molecular mechanisms underlying receptor function and drug action
Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling
No full textHerein we make an overview of the results of our computational experiments aimed at gaining insight into the molecular mechanisms of GPCR functioning either in their normal conditions or when hit by gain-of-function or loss-of-function mutations. Molecular simulations of a number of GPCRs in their wild type and mutated as well as free and ligand-bound forms were instrumental in inferring the structural features, which differentiate the mutation- and ligand-induced active from the inactive states. These features essentially reside in the interaction pattern of the E/DRY arginine and in the degree of solvent exposure of selected cytosolic domains. Indeed, the active states differ from the inactive ones in the weakening of the interactions made by the highly conserved arginine and in the increase in solvent accessibility of the cytosolic interface between helices 3 and 6. Where possible, the structural hallmarks of the active and inactive receptor states are translated into molecular descriptors useful for in silico functional screening of novel receptor mutants or ligands. Computational modeling of the supramolecular organization of GPCRs and their intracellular partners is the current challenge toward a deep understanding of their functioning mechanisms
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