Molecular simulations of globins: Exploring the relationship between structure, dynamics and function

Podeu consultar el llibre complet a: http://hdl.handle.net/2445/32392The discovery in the last two decades of novel members of the globin superfamily has challenged the conventional view about the structure and function of globins. Thus, peculiar structural differences are expected to have direct influence on properties related to ligand migration, binding affinity and heme reactivity. Molecular simulations are a valuable tool to gain insigth into the molecular mechanisms that underlie those structural differences, and their relationship with the diversity of functional roles. In this work, the impact of molecular simulations in exploring the linkage between structure, dynamics and function is highlighted for three representative cases: the migration of ligands through the protein matrix of truncated hemoglobins, the modulation of binding affinity by heme distortion in protoglobin, and finally the functional implications due to the equilibrium between penta- and hexacoordination of the heme with distal histidine in neuroglobin

Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network

Computational identification of heme-binding residues is beneficial for predicting and designing novel heme proteins. Here we proposed a novel method for heme-binding residue prediction by exploiting topological properties of these residues in the residue interaction networks derived from three-dimensional structures. Comprehensive analysis showed that key residues located in heme-binding regions are generally associated with the nodes with higher degree, closeness and betweenness, but lower clustering coefficient in the network. HemeNet, a support vector machine (SVM) based predictor, was developed to identify heme-binding residues by combining topological features with existing sequence and structural features. The results showed that incorporation of network-based features significantly improved the prediction performance. We also compared the residue interaction networks of heme proteins before and after heme binding and found that the topological features can well characterize the heme-binding sites of apo structures as well as those of holo structures, which led to reliable performance improvement as we applied HemeNet to predicting the binding residues of proteins in the heme-free state. HemeNet web server is freely accessible at http://mleg.cse.sc.edu/hemeNet/

Ligation Tunes Protein Reactivity in an Ancient Haemoglobin: Kinetic Evidence for an Allosteric Mechanism in Methanosarcina acetivorans Protoglobin

Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics

H2S and NO cooperatively regulate vascular tone by activating a neuroendocrine HNO-TRPA1-CGRP signalling pathway

Nitroxyl (HNO) is a redox sibling of nitric oxide (NO) that targets distinct signalling pathways with pharmacological endpoints of high significance in the treatment of heart failure. Beneficial HNO effects depend, in part, on its ability to release calcitonin gene-related peptide (CGRP) through an unidentified mechanism. Here we propose that HNO is generated as a result of the reaction of the two gasotransmitters NO and H2S. We show that H2S and NO production colocalizes with transient receptor potential channel A1 (TRPA1), and that HNO activates the sensory chemoreceptor channel TRPA1 via formation of amino-terminal disulphide bonds, which results in sustained calcium influx. As a consequence, CGRP is released, which induces local and systemic vasodilation. H2S-evoked vasodilatatory effects largely depend on NO production and activation of HNO-TRPA1-CGRP pathway. We propose that this neuroendocrine HNO-TRPA1-CGRP signalling pathway constitutes an essential element for the control of vascular tone throughout the cardiovascular system

Molecular simulations of globins: Exploring the relationship between structure, dynamics and function

Podeu consultar el llibre complet a: http://hdl.handle.net/2445/32392The discovery in the last two decades of novel members of the globin superfamily has challenged the conventional view about the structure and function of globins. Thus, peculiar structural differences are expected to have direct influence on properties related to ligand migration, binding affinity and heme reactivity. Molecular simulations are a valuable tool to gain insigth into the molecular mechanisms that underlie those structural differences, and their relationship with the diversity of functional roles. In this work, the impact of molecular simulations in exploring the linkage between structure, dynamics and function is highlighted for three representative cases: the migration of ligands through the protein matrix of truncated hemoglobins, the modulation of binding affinity by heme distortion in protoglobin, and finally the functional implications due to the equilibrium between penta- and hexacoordination of the heme with distal histidine in neuroglobin

Docking to heme proteins.

In silico screening has become a valuable tool in drug design, but some drug targets represent real challenges for docking algorithms. This is especially true for metalloproteins, whose interactions with ligands are difficult to parametrize. Our docking algorithm, EADock, is based on the CHARMM force field, which assures a physically sound scoring function and a good transferability to a wide range of systems, but also exhibits difficulties in case of some metalloproteins. Here, we consider the therapeutically important case of heme proteins featuring an iron core at the active site. Using a standard docking protocol, where the iron-ligand interaction is underestimated, we obtained a success rate of 28% for a test set of 50 heme-containing complexes with iron-ligand contact. By introducing Morse-like metal binding potentials (MMBP), which are fitted to reproduce density functional theory calculations, we are able to increase the success rate to 62%. The remaining failures are mainly due to specific ligand-water interactions in the X-ray structures. Testing of the MMBP on a second data set of non iron binders (14 cases) demonstrates that they do not introduce a spurious bias towards metal binding, which suggests that they may reliably be used also for cross-docking studies