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Sarasola LI, del Torrent CL, Pérez-Arévalo A, Argerich J, Casajuana-Martín N, Chevigné A, Fernández-Dueñas V, Ferré S, Pardo L, Ciruela F. The ADORA1 mutation linked to early-onset Parkinson’s disease alters adenosine A1-A2A receptor heteromer formation and function. Biomed Pharmacother 2022; 156:113896. [DOI: 10.1016/j.biopha.2022.113896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 01/14/2023] Open
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2
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Uzonwanne VO, Navabi A, Obayemi JD, Hu J, Salifu AA, Ghahremani S, Ndahiro N, Rahbar N, Soboyejo W. Triptorelin-functionalized PEG-coated biosynthesized gold nanoparticles: Effects of receptor-ligand interactions on adhesion to triple negative breast cancer cells. BIOMATERIALS ADVANCES 2022; 136:212801. [PMID: 35929297 DOI: 10.1016/j.bioadv.2022.212801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/26/2022] [Accepted: 04/09/2022] [Indexed: 11/29/2022]
Abstract
This paper presents the results of an experimental and computational study of the adhesion of triptorelin-conjugated PEG-coated biosynthesized gold nanoparticles (GNP-PEG-TRP) to triple-negative breast cancer (TNBC) cells. The adhesion is studied at the nanoscale using a combination of atomic force microscopy (AFM) experiments and molecular dynamics (MD) simulations. The AFM measurements showed that the triptorelin-functionalized gold nanoparticles (GNP-TRP and GNP-PEG-TRP) have higher adhesion to triple-negative breast cancer cells (TNBC) than non-tumorigenic breast cells. The increased adhesion of GNP-TRP and GNP-PEG-TRP to TNBC is also attributed to the overexpression of LHRH receptors on the surfaces of both TNBC. Finally, the molecular dynamics model reveals insights into the effects of receptor density, molecular configuration, and receptor-ligand docking characteristics on the interactions of triptorelin-functionalized PEG-coated gold nanoparticles with TNBC. A three to nine-fold increase in the adhesion is predicted between triptorelin-functionalized PEG-coated gold nanoparticles and TNBC cells. The implications of the results are then discussed for the specific targeting of TNBC.
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Affiliation(s)
- Vanessa O Uzonwanne
- Department of Materials Science and Engineering, Worcester Polytechnic Institute (WPI), 100 Institute Road, Worcester, MA 01609, USA
| | - Arvand Navabi
- Department of Civil Engineering, Worcester Polytechnic Institute (WPI), Kaven Hall, 100 Institute Road, Worcester, MA 01609, USA
| | - John D Obayemi
- Department of Mechanical Engineering, Worcester Polytechnic Institute (WPI), 100 Institute Road, Worcester, MA 01609, USA; Department of Biomedical Engineering, Worcester Polytechnic Institute (WPI), Gateway Park, Life Sciences and Bioengineering Center, 60 Prescott Street, Worcester, MA 01605, USA
| | - Jingjie Hu
- Division of Vascular and Interventional Radiology, Mayo Clinic, 13400 East Shea Blvd., Scottsdale, AZ 85259, USA
| | - Ali A Salifu
- Department of Mechanical Engineering, Worcester Polytechnic Institute (WPI), 100 Institute Road, Worcester, MA 01609, USA; Department of Biomedical Engineering, Worcester Polytechnic Institute (WPI), Gateway Park, Life Sciences and Bioengineering Center, 60 Prescott Street, Worcester, MA 01605, USA
| | - Shahnaz Ghahremani
- Department of Biomedical Engineering, Worcester Polytechnic Institute (WPI), Gateway Park, Life Sciences and Bioengineering Center, 60 Prescott Street, Worcester, MA 01605, USA
| | - Nelson Ndahiro
- Department of Chemical Engineering, Worcester Polytechnic Institute (WPI), 100 Institute Road, Worcester, MA 01609, USA
| | - Nima Rahbar
- Department of Civil Engineering, Worcester Polytechnic Institute (WPI), Kaven Hall, 100 Institute Road, Worcester, MA 01609, USA
| | - Winston Soboyejo
- Department of Materials Science and Engineering, Worcester Polytechnic Institute (WPI), 100 Institute Road, Worcester, MA 01609, USA; Department of Mechanical Engineering, Worcester Polytechnic Institute (WPI), 100 Institute Road, Worcester, MA 01609, USA; Department of Biomedical Engineering, Worcester Polytechnic Institute (WPI), Gateway Park, Life Sciences and Bioengineering Center, 60 Prescott Street, Worcester, MA 01605, USA.
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3
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Tzoupis H, Nteli A, Androutsou ME, Tselios T. Gonadotropin-Releasing Hormone and GnRH Receptor: Structure, Function and Drug Development. Curr Med Chem 2021; 27:6136-6158. [PMID: 31309882 DOI: 10.2174/0929867326666190712165444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND Gonadotropin-Releasing Hormone (GnRH) is a key element in sexual maturation and regulation of the reproductive cycle in the human organism. GnRH interacts with the pituitary cells through the activation of the Gonadotropin Releasing Hormone Receptors (GnRHR). Any impairments/dysfunctions of the GnRH-GnRHR complex lead to the development of various cancer types and disorders. Furthermore, the identification of GnRHR as a potential drug target has led to the development of agonist and antagonist molecules implemented in various treatment protocols. The development of these drugs was based on the information derived from the functional studies of GnRH and GnRHR. OBJECTIVE This review aims at shedding light on the versatile function of GnRH and GnRH receptor and offers an apprehensive summary regarding the development of different agonists, antagonists and non-peptide GnRH analogues. CONCLUSION The information derived from these studies can enhance our understanding of the GnRH-GnRHR versatile nature and offer valuable insight into the design of new more potent molecules.
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Affiliation(s)
| | - Agathi Nteli
- Department of Chemistry, University of Patras, Rion GR-26504, Greece
| | - Maria-Eleni Androutsou
- Vianex S.A., Tatoiou Str., 18th km Athens-Lamia National Road, Nea Erythrea 14671, Greece
| | - Theodore Tselios
- Department of Chemistry, University of Patras, Rion GR-26504, Greece
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4
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Navarro G, Gonzalez A, Campanacci S, Rivas-Santisteban R, Reyes-Resina I, Casajuana-Martin N, Cordomí A, Pardo L, Franco R. Experimental and computational analysis of biased agonism on full-length and a C-terminally truncated adenosine A 2A receptor. Comput Struct Biotechnol J 2020; 18:2723-2732. [PMID: 33101610 PMCID: PMC7550916 DOI: 10.1016/j.csbj.2020.09.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022] Open
Abstract
Biased agonism, the ability of agonists to differentially activate downstream signaling pathways by stabilizing specific receptor conformations, is a key issue for G protein-coupled receptor (GPCR) signaling. The C-terminal domain might influence this functional selectivity of GPCRs as it engages G proteins, GPCR kinases, β-arrestins, and several other proteins. Thus, the aim of this paper is to compare the agonist-dependent selectivity for intracellular pathways in a heterologous system expressing the full-length (A2AR) and a C-tail truncated (A2AΔ40R lacking the last 40 amino acids) adenosine A2A receptor, a GPCR that is already targeted in Parkinson’s disease using a first-in-class drug. Experimental data such as ligand binding, cAMP production, β-arrestin recruitment, ERK1/2 phosphorylation and dynamic mass redistribution assays, which correspond to different aspects of signal transduction, were measured upon the action of structurally diverse compounds (the agonists adenosine, NECA, CGS-21680, PSB-0777 and LUF-5834 and the SCH-58261 antagonist) in cells expressing A2AR and A2AΔ40R. The results show that taking cAMP levels and the endogenous adenosine agonist as references, the main difference in bias was obtained with PSB-0777 and LUF-5834. The C-terminus is dispensable for both G-protein and β-arrestin recruitment and also for MAPK activation. Unrestrained molecular dynamics simulations, at the μs timescale, were used to understand the structural arrangements of the binding cavity, triggered by these chemically different agonists, facilitating G protein binding with different efficacy.
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Affiliation(s)
- Gemma Navarro
- Dept. Biochemistry and Physiology, Faculty of Pharmacy and Food Science. Universitat de Barcelona. Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas. Instituto de Salud Carlos III, Madrid, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Stefano Campanacci
- Dept. Biochemistry and Molecular Biomedicine. School of Biology. Universitat de Barcelona. Barcelona. Spain
| | - Rafael Rivas-Santisteban
- Dept. Biochemistry and Physiology, Faculty of Pharmacy and Food Science. Universitat de Barcelona. Barcelona, Spain
- Dept. Biochemistry and Molecular Biomedicine. School of Biology. Universitat de Barcelona. Barcelona. Spain
| | - Irene Reyes-Resina
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas. Instituto de Salud Carlos III, Madrid, Spain
- Dept. Biochemistry and Molecular Biomedicine. School of Biology. Universitat de Barcelona. Barcelona. Spain
| | - Nil Casajuana-Martin
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain d Faculty of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Rafael Franco
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas. Instituto de Salud Carlos III, Madrid, Spain
- School of Chemistry. Universitat de Barcelona. Barcelona. Spain
- Corresponding author at: School of Chemistry, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain.
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5
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Mayol E, García-Recio A, Tiemann JKS, Hildebrand PW, Guixà-González R, Olivella M, Cordomí A. HomolWat: a web server tool to incorporate 'homologous' water molecules into GPCR structures. Nucleic Acids Res 2020; 48:W54-W59. [PMID: 32484557 PMCID: PMC7319549 DOI: 10.1093/nar/gkaa440] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/29/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022] Open
Abstract
Internal water molecules play an essential role in the structure and function of membrane proteins including G protein-coupled receptors (GPCRs). However, technical limitations severely influence the number and certainty of observed water molecules in 3D structures. This may compromise the accuracy of further structural studies such as docking calculations or molecular dynamics simulations. Here we present HomolWat, a web application for incorporating water molecules into GPCR structures by using template-based modelling of homologous water molecules obtained from high-resolution structures. While there are various tools available to predict the positions of internal waters using energy-based methods, the approach of borrowing lacking water molecules from homologous GPCR structures makes HomolWat unique. The tool can incorporate water molecules into a protein structure in about a minute with around 85% of water recovery. The web server is freely available at http://lmc.uab.es/homolwat.
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Affiliation(s)
- Eduardo Mayol
- Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Adrián García-Recio
- Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, Medical University Leipzig, Leipzig, Sachsen 04107, Germany
- Institute of Medical Physics and Biophysics, Charité Universitätsmedizin Berlin, Berlin 101179, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Medical University Leipzig, Leipzig, Sachsen 04107, Germany
- Institute of Medical Physics and Biophysics, Charité Universitätsmedizin Berlin, Berlin 101179, Germany
- Berlin Insitute of Health (BIH), 10178 Berlin, Germany
| | - Ramon Guixà-González
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
- Condensed Matter Theory Group, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland
| | - Mireia Olivella
- Bioinformatics and Medical Statistics Group, University of Vic-Central University of Catalonia, Barcelona 08500, Spain
| | - Arnau Cordomí
- Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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Teng D, Chen J, Li D, Wu Z, Li W, Tang Y, Liu G. Computational Insights into Molecular Activation and Positive Cooperative Mechanisms of FFAR1 Modulators. J Chem Inf Model 2020; 60:3214-3230. [DOI: 10.1021/acs.jcim.0c00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Dan Teng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jianhui Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Dongping Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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7
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Pérez-Benito L, Llinas del Torrent C, Pardo L, Tresadern G. The computational modeling of allosteric modulation of metabotropic glutamate receptors. FROM STRUCTURE TO CLINICAL DEVELOPMENT: ALLOSTERIC MODULATION OF G PROTEIN-COUPLED RECEPTORS 2020; 88:1-33. [DOI: 10.1016/bs.apha.2020.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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QTY code designed thermostable and water-soluble chimeric chemokine receptors with tunable ligand affinity. Proc Natl Acad Sci U S A 2019; 116:25668-25676. [PMID: 31776256 DOI: 10.1073/pnas.1909026116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chemokine receptors are of great interest as they play a critical role in many immunological and pathological processes. The ability to study chemokine receptors in aqueous solution without detergent would be significant because natural receptors require detergents to become soluble. We previously reported using the QTY code to design detergent-free chemokine receptors. We here report the design of 2 detergent-free chimeric chemokine receptors that were experimentally unattainable in detergent solution. We designed chimeric receptors by switching the N terminus and 3 extracellular (EC) loops between different receptors. Specifically, we replaced the N terminus and 3 EC loops of CCR5QTY with the N terminus and 3 EC loops of CXCR4. The ligand for CXCR4; namely CXCL12, binds to the chimeric receptor CCR5QTY (7TM)-CXCR4 (N terminus+3 EC loops), but with lower affinity compared to CXCR4; the CCL5 ligand of CCR5 binds the chimeric receptor with ∼20× lower affinity. The chimeric design helps to elucidate the mechanism of native receptor-ligand interaction. We also show that all detergent-free QTY-designed chemokine receptors, expressed in Escherichia coli, bind to their respective chemokines with affinities in the nanomolar (nM) range, similar to the affinities of native receptors and SF9-produced QTY variants. These QTY-designed receptors exhibit remarkable thermostability in the presence of arginine and retain ligand-binding activity after heat treatment at 60 °C for 4 h and 24 h, and at 100 °C for 10 min. Our design approach enables affordable scale-up production of detergent-free QTY variant chemokine receptors with tunable functionality for various uses.
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9
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Lesca E, Panneels V, Schertler GFX. The role of water molecules in phototransduction of retinal proteins and G protein-coupled receptors. Faraday Discuss 2019; 207:27-37. [PMID: 29410984 DOI: 10.1039/c7fd00207f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
G protein coupled receptors (GPCRs) are a key family of membrane proteins in all eukaryotes and also very important drug targets for medical intervention. The extensively studied visual pigment rhodopsin is a prime example of a family A GPCR. Its chromophore ligand retinal is covalently linked to a lysine in helix seven forming a protonated Schiff base. Interestingly, this is the same situation in other-non-GPCR-retinal proteins, like the prototype light-driven microbial proton pump bacteriorhodopsin, albeit there is no (or only a very remote) phylogenetical link. Close to the retinal ligand, several water molecules help to organise a functionally important hydrogen bond network that undergoes significant changes during photo-activation. Such water-mediated networks are also critical for ligand binding of other GPCRs and they are becoming increasingly important in drug discovery. GPCRs also contain a partially conserved water mediated hydrogen bond network that stabilises the ground state of the receptor, and rearrangement of this network leads to the stabilization of the active state. Some water molecules have a specific role in this process to appropriately orient specific residues relative to the Schiff base, and to modulate the fine structure of the transmembrane bundle, particularly near the intracellular G protein binding site. While the atomic details of these mechanisms are still missing, the recent developments in free electron lasers (FELs) are enabling us to begin to observe the changes in waters and relevant side chains shortly after photo activation at an unprecedented level of spatial and temporal resolution.
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Affiliation(s)
- Elena Lesca
- Division of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
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10
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Alfonso-Prieto M, Navarini L, Carloni P. Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations. Front Mol Biosci 2019; 6:29. [PMID: 31131282 PMCID: PMC6510167 DOI: 10.3389/fmolb.2019.00029] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022] Open
Abstract
Human G-protein coupled receptors (GPCRs) convey a wide variety of extracellular signals inside the cell and they are one of the main targets for pharmaceutical intervention. Rational drug design requires structural information on these receptors; however, the number of experimental structures is scarce. This gap can be filled by computational models, based on homology modeling and docking techniques. Nonetheless, the low sequence identity across GPCRs and the chemical diversity of their ligands may limit the quality of these models and hence refinement using molecular dynamics simulations is recommended. This is the case for olfactory and bitter taste receptors, which constitute the first and third largest GPCR groups and show sequence identities with the available GPCR templates below 20%. We have developed a molecular dynamics approach, based on the combination of molecular mechanics and coarse grained (MM/CG), tailored to study ligand binding in GPCRs. This approach has been applied so far to bitter taste receptor complexes, showing significant predictive power. The protein/ligand interactions observed in the simulations were consistent with extensive mutagenesis and functional data. Moreover, the simulations predicted several binding residues not previously tested, which were subsequently verified by carrying out additional experiments. Comparison of the simulations of two bitter taste receptors with different ligand selectivity also provided some insights into the binding determinants of bitter taste receptors. Although the MM/CG approach has been applied so far to a limited number of GPCR/ligand complexes, the excellent agreement of the computational models with the mutagenesis and functional data supports the applicability of this method to other GPCRs for which experimental structures are missing. This is particularly important for the challenging case of GPCRs with low sequence identity with available templates, for which molecular docking shows limited predictive power.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.,Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Paolo Carloni
- Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.,Institute for Neuroscience and Medicine INM-11, Forschungszentrum Jülich, Jülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Vietnam
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11
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Heyden M. Heterogeneity of water structure and dynamics at the protein-water interface. J Chem Phys 2019; 150:094701. [PMID: 30849897 DOI: 10.1063/1.5081739] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this molecular dynamics simulation study, we analyze the local structural and dynamic properties of water hydrating the protein ubiquitin on a spatial grid with 1 Å resolution. This allows for insights into the spatial distribution of water number densities, molecular orientations, translations, and rotations as a function of distance from the protein surface. Water molecule orientations follow a heterogeneous distribution with preferred local orientations of water dipoles and O-H bond vectors up to 10-15 Å distances from the protein, while local variations of the water number density converge to homogeneous bulk-like values within less than 8 Å. Interestingly, we find that the long-ranged orientational structure of water does not impact either the translational or rotational dynamics of water. Instead, heterogeneous distributions of local dynamical parameters and averaged dynamical retardation factors are only found close to the protein surface and follow a distance dependence comparable to heterogeneities in the local water number density. This study shows that the formation of nanodomains of preferred water orientations far from the protein does not significantly impact dynamical processes probed as a non-local average in most experiments.
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Affiliation(s)
- Matthias Heyden
- School of Molecular Sciences and Center for Biological Physics, Arizona State University, Tempe, Arizona 85287-1604, USA
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12
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Llinas Del Torrent C, Casajuana-Martin N, Pardo L, Tresadern G, Pérez-Benito L. Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5. J Chem Inf Model 2019; 59:2456-2466. [PMID: 30811196 DOI: 10.1021/acs.jcim.8b00924] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The metabotropic glutamate 5 (mGlu5) receptor is a class C G protein-coupled receptor (GPCR) that is implicated in several CNS disorders making it a popular drug discovery target. Years of research have revealed allosteric mGlu5 ligands showing an unexpected complete switch in functional activity despite only small changes in their chemical structure, resulting in positive allosteric modulators (PAM) or negative allosteric modulators (NAM) for the same scaffold. Up to now, the origins of this effect are not understood, causing difficulties in a drug discovery context. In this work, experimental data was gathered and analyzed alongside docking and Molecular Dynamics (MD) calculations for three sets of PAM and NAM pairs. The results consistently show the role of specific interactions formed between ligand substituents and amino acid side chains that block or promote local movements associated with receptor activation. The work provides an explanation for how such small structural changes lead to remarkable differences in functional activity. While this work can greatly help drug discovery programs avoid these switches, it also provides valuable insight into the mechanisms of class C GPCR allosteric activation. Furthermore, the approach shows the value of applying MD to understand functional activity in drug design programs, even for such close structural analogues.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Nil Casajuana-Martin
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain.,Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
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13
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Abstract
G protein-coupled receptors (GPCRs) represent both the largest class of drug targets and the largest family of human membrane proteins. Recent three-dimensional structures have revealed the presence of many water molecules buried inside GPCRs, but the functional role of these water molecules has been unclear. Using extensive atomic-level computer simulations, we find that, although most of these waters are highly mobile, a few are stable. These stable water molecules mediate state-dependent and state-independent polar networks that are conserved across diverse GPCRs. These findings promise to help guide the rational design of GPCR-targeted drugs. G protein-coupled receptors (GPCRs) have evolved to recognize incredibly diverse extracellular ligands while sharing a common architecture and structurally conserved intracellular signaling partners. It remains unclear how binding of diverse ligands brings about GPCR activation, the common structural change that enables intracellular signaling. Here, we identify highly conserved networks of water-mediated interactions that play a central role in activation. Using atomic-level simulations of diverse GPCRs, we show that most of the water molecules in GPCR crystal structures are highly mobile. Several water molecules near the G protein-coupling interface, however, are stable. These water molecules form two kinds of polar networks that are conserved across diverse GPCRs: (i) a network that is maintained across the inactive and the active states and (ii) a network that rearranges upon activation. Comparative analysis of GPCR crystal structures independently confirms the striking conservation of water-mediated interaction networks. These conserved water-mediated interactions near the G protein-coupling region, along with diverse water-mediated interactions with extracellular ligands, have direct implications for structure-based drug design and GPCR engineering.
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14
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White KL, Eddy MT, Gao ZG, Han GW, Lian T, Deary A, Patel N, Jacobson KA, Katritch V, Stevens RC. Structural Connection between Activation Microswitch and Allosteric Sodium Site in GPCR Signaling. Structure 2018; 26:259-269.e5. [PMID: 29395784 DOI: 10.1016/j.str.2017.12.013] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/21/2017] [Accepted: 12/27/2017] [Indexed: 12/18/2022]
Abstract
Sodium ions are endogenous allosteric modulators of many G-protein-coupled receptors (GPCRs). Mutation of key residues in the sodium binding motif causes a striking effect on G-protein signaling. We report the crystal structures of agonist complexes for two variants in the first sodium coordination shell of the human A2A adenosine receptor, D522.50N and S913.39A. Both structures present an overall active-like conformation; however, the variants show key changes in the activation motif NPxxY. Changes in the hydrogen bonding network in this microswitch suggest a possible mechanism for modified G-protein signaling and enhanced thermal stability. These structures, signaling data, and thermal stability analysis with a panel of pharmacological ligands provide a basis for understanding the role of the sodium-coordinating residues on stability and G-protein signaling. Utilizing the D2.50N variant is a promising method for stabilizing class A GPCRs to accelerate structural efforts and drug discovery.
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Affiliation(s)
- Kate L White
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Matthew T Eddy
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Tiffany Lian
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Alexander Deary
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Nilkanth Patel
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vsevolod Katritch
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Raymond C Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA.
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15
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Vickery ON, Carvalheda CA, Zaidi SA, Pisliakov AV, Katritch V, Zachariae U. Intracellular Transfer of Na + in an Active-State G-Protein-Coupled Receptor. Structure 2018; 26:171-180.e2. [PMID: 29249607 PMCID: PMC5805466 DOI: 10.1016/j.str.2017.11.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/13/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]
Abstract
Playing a central role in cell signaling, G-protein-coupled receptors (GPCRs) are the largest superfamily of membrane proteins and form the majority of drug targets in humans. How extracellular agonist binding triggers the activation of GPCRs and associated intracellular effector proteins remains, however, poorly understood. Structural studies have revealed that inactive class A GPCRs harbor a conserved binding site for Na+ ions in the center of their transmembrane domain, accessible from the extracellular space. Here, we show that the opening of a conserved hydrated channel in the activated state receptors allows the Na+ ion to egress from its binding site into the cytosol. Coupled with protonation changes, this ion movement occurs without significant energy barriers, and can be driven by physiological transmembrane ion and voltage gradients. We propose that Na+ ion exchange with the cytosol is a key step in GPCR activation. Further, we hypothesize that this transition locks receptors in long-lived active-state conformations.
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Affiliation(s)
- Owen N Vickery
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Catarina A Carvalheda
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Saheem A Zaidi
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrei V Pisliakov
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Vsevolod Katritch
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Ulrich Zachariae
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK.
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16
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Evolutionary action and structural basis of the allosteric switch controlling β 2AR functional selectivity. Nat Commun 2017; 8:2169. [PMID: 29255305 PMCID: PMC5735088 DOI: 10.1038/s41467-017-02257-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 11/15/2017] [Indexed: 12/18/2022] Open
Abstract
Functional selectivity of G-protein-coupled receptors is believed to originate from ligand-specific conformations that activate only subsets of signaling effectors. In this study, to identify molecular motifs playing important roles in transducing ligand binding into distinct signaling responses, we combined in silico evolutionary lineage analysis and structure-guided site-directed mutagenesis with large-scale functional signaling characterization and non-negative matrix factorization clustering of signaling profiles. Clustering based on the signaling profiles of 28 variants of the β2-adrenergic receptor reveals three clearly distinct phenotypical clusters, showing selective impairments of either the Gi or βarrestin/endocytosis pathways with no effect on Gs activation. Robustness of the results is confirmed using simulation-based error propagation. The structural changes resulting from functionally biasing mutations centered around the DRY, NPxxY, and PIF motifs, selectively linking these micro-switches to unique signaling profiles. Our data identify different receptor regions that are important for the stabilization of distinct conformations underlying functional selectivity. Ligand-induced biased signaling is thought to result in part from ligand-specific receptor conformations that cause the engagement of distinct effectors. Here the authors trace and evaluate the impact of mutations of the β2–adrenergic receptor on multiple signaling outputs to provide structural-level insight into the determinants of GPCR functional selectivity.
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17
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Fierro F, Suku E, Alfonso-Prieto M, Giorgetti A, Cichon S, Carloni P. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis. Front Mol Biosci 2017; 4:63. [PMID: 28932739 PMCID: PMC5592726 DOI: 10.3389/fmolb.2017.00063] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.
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Affiliation(s)
- Fabrizio Fierro
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany
| | - Eda Suku
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorf, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Biotechnology, University of VeronaVerona, Italy
| | - Sven Cichon
- Institute of Neuroscience and Medicine INM-1, Forschungszentrum JülichJülich, Germany.,Institute for Human Genetics, Department of Genomics, Life&Brain Center, University of BonnBonn, Germany.,Division of Medical Genetics, Department of Biomedicine, University of BaselBasel, Switzerland
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule AachenAachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National UniversityHanoi, Vietnam
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18
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Kim J, Liu M, Hilty C. Modeling of Polarization Transfer Kinetics in Protein Hydration Using Hyperpolarized Water. J Phys Chem B 2017; 121:6492-6498. [PMID: 28613875 DOI: 10.1021/acs.jpcb.7b03052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Water-protein interactions play a central role in protein structure, dynamics, and function. These interactions, traditionally, have been studied using nuclear magnetic resonance (NMR) by measuring chemical exchange and nuclear Overhauser effect (NOE). Polarization transferred from hyperpolarized water can result in substantial transient signal enhancements of protein resonances due to these processes. Here, we use dissolution dynamic nuclear polarization and flow-NMR for measuring the pH dependence of transferred signals to the protein trypsin. A maximum enhancement of 20 is visible in the amide proton region of the spectrum at pH 6.0, and of 47 at pH 7.5. The aliphatic region is enhanced up to 2.3 times at pH 6.0 and up to 2.5 times at pH 7.5. The time dependence of these observed signals can be modeled quantitatively using rate equations incorporating chemical exchange to amide sites and, optionally, intramolecular NOE to aliphatic protons. On the basis of these two- and three-site models, average exchange (kex) and cross-relaxation rates (σ) obtained were kex = 12 s-1, σ = -0.33 s-1 for pH 7.5 and kex = 1.8 s-1, σ = -0.72 s-1 for pH 6.0 at a temperature of 304 K. These values were validated using conventional EXSY and NOESY measurements. In general, a rapid measurement of exchange and cross-relaxation rates may be of interest for the study of structural changes of the protein occurring on the same time scale. Besides protein-water interactions, interactions with cosolvent or solutes can further be investigated using the same methods.
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Affiliation(s)
- Jihyun Kim
- Chemistry Department, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Mengxiao Liu
- Chemistry Department, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Christian Hilty
- Chemistry Department, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
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19
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Abstract
High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.
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20
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Tomobe K, Yamamoto E, Kholmurodov K, Yasuoka K. Water permeation through the internal water pathway in activated GPCR rhodopsin. PLoS One 2017; 12:e0176876. [PMID: 28493967 PMCID: PMC5426653 DOI: 10.1371/journal.pone.0176876] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/18/2017] [Indexed: 12/13/2022] Open
Abstract
Rhodopsin is a light-driven G-protein-coupled receptor that mediates signal transduction in eyes. Internal water molecules mediate activation of the receptor in a rhodopsin cascade reaction and contribute to conformational stability of the receptor. However, it remains unclear how internal water molecules exchange between the bulk and protein inside, in particular through a putative solvent pore on the cytoplasmic. Using all-atom molecular dynamics simulations, we identified the solvent pore on cytoplasmic side in both the Meta II state and the Opsin. On the other hand, the solvent pore does not exist in the dark-adapted rhodopsin. We revealed two characteristic narrow regions located within the solvent pore in the Meta II state. The narrow regions distinguish bulk and the internal hydration sites, one of which is adjacent to the conserved structural motif "NPxxY". Water molecules in the solvent pore diffuse by pushing or sometimes jumping a preceding water molecule due to the geometry of the solvent pore. These findings revealed a total water flux between the bulk and the protein inside in the Meta II state, and suggested that these pathways provide water molecules to the crucial sites of the activated rhodopsin.
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Affiliation(s)
- Katsufumi Tomobe
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Eiji Yamamoto
- Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kholmirzo Kholmurodov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, 141980, Russia
- Dubna State University, Dubna, 141980, Russia
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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21
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Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
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22
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Flanagan CA, Manilall A. Gonadotropin-Releasing Hormone (GnRH) Receptor Structure and GnRH Binding. Front Endocrinol (Lausanne) 2017; 8:274. [PMID: 29123501 PMCID: PMC5662886 DOI: 10.3389/fendo.2017.00274] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
Gonadotropin-releasing hormone (GnRH) regulates reproduction. The human GnRH receptor lacks a cytoplasmic carboxy-terminal tail but has amino acid sequence motifs characteristic of rhodopsin-like, class A, G protein-coupled receptors (GPCRs). This review will consider how recent descriptions of X-ray crystallographic structures of GPCRs in inactive and active conformations may contribute to understanding GnRH receptor structure, mechanism of activation and ligand binding. The structures confirmed that ligands bind to variable extracellular surfaces, whereas the seven membrane-spanning α-helices convey the activation signal to the cytoplasmic receptor surface, which binds and activates heterotrimeric G proteins. Forty non-covalent interactions that bridge topologically equivalent residues in different transmembrane (TM) helices are conserved in class A GPCR structures, regardless of activation state. Conformation-independent interhelical contacts account for a conserved receptor protein structure and their importance in the GnRH receptor structure is supported by decreased expression of receptors with mutations of residues in the network. Many of the GnRH receptor mutations associated with congenital hypogonadotropic hypogonadism, including the Glu2.53(90) Lys mutation, involve amino acids that constitute the conserved network. Half of the ~250 intramolecular interactions in GPCRs differ between inactive and active structures. Conformation-specific interhelical contacts depend on amino acids changing partners during activation. Conserved inactive conformation-specific contacts prevent receptor activation by stabilizing proximity of TM helices 3 and 6 and a closed G protein-binding site. Mutations of GnRH receptor residues involved in these interactions, such as Arg3.50(139) of the DRY/S motif or Tyr7.53(323) of the N/DPxxY motif, increase or decrease receptor expression and efficiency of receptor coupling to G protein signaling, consistent with the native residues stabilizing the inactive GnRH receptor structure. Active conformation-specific interhelical contacts stabilize an open G protein-binding site. Progress in defining the GnRH-binding site has recently slowed, with evidence that Tyr6.58(290) contacts Tyr5 of GnRH, whereas other residues affect recognition of Trp3 and Gly10NH2. The surprisingly consistent observations that GnRH receptor mutations that disrupt GnRH binding have less effect on "conformationally constrained" GnRH peptides may now be explained by crystal structures of agonist-bound peptide receptors. Analysis of GPCR structures provides insight into GnRH receptor function.
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Affiliation(s)
- Colleen A. Flanagan
- Faculty of Health Sciences, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- *Correspondence: Colleen A. Flanagan,
| | - Ashmeetha Manilall
- Faculty of Health Sciences, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
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23
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Vickery ON, Machtens JP, Zachariae U. Membrane potentials regulating GPCRs: insights from experiments and molecular dynamics simulations. Curr Opin Pharmacol 2016; 30:44-50. [PMID: 27474871 PMCID: PMC5080454 DOI: 10.1016/j.coph.2016.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/27/2023]
Abstract
G-protein coupled receptors (GPCRs) form the largest class of membrane proteins in humans and the targets of most present drugs. Membrane potential is one of the defining characteristics of living cells. Recent work has shown that the membrane voltage, and changes thereof, modulates signal transduction and ligand binding in GPCRs. As it may allow differential signalling patterns depending on tissue, cell type, and the excitation status of excitable cells, GPCR voltage sensitivity could have important implications for their pharmacology. This review summarises recent experimental insights on GPCR voltage regulation and the role of molecular dynamics simulations in identifying the structural basis of GPCR voltage-sensing. We discuss the potential significance for drug design on GPCR targets from excitable and non-excitable cells.
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Affiliation(s)
- Owen N Vickery
- Physics, School of Science and Engineering, University of Dundee, Nethergate Dundee DD1 4NH, UK; Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jan-Philipp Machtens
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Ulrich Zachariae
- Physics, School of Science and Engineering, University of Dundee, Nethergate Dundee DD1 4NH, UK; Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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24
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Vickery ON, Machtens JP, Tamburrino G, Seeliger D, Zachariae U. Structural Mechanisms of Voltage Sensing in G Protein-Coupled Receptors. Structure 2016; 24:997-1007. [PMID: 27210286 PMCID: PMC4906246 DOI: 10.1016/j.str.2016.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/01/2022]
Abstract
G-protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins and one-third of all drug targets in humans. A number of recent studies have reported evidence for substantial voltage regulation of GPCRs. However, the structural basis of GPCR voltage sensing has remained enigmatic. Here, we present atomistic simulations on the δ-opioid and M2 muscarinic receptors, which suggest a structural and mechanistic explanation for the observed voltage-induced functional effects. The simulations reveal that the position of an internal Na(+) ion, recently detected to bind to a highly conserved aqueous pocket in receptor crystal structures, strongly responds to voltage changes. The movements give rise to gating charges in excellent agreement with previous experimental recordings. Furthermore, free energy calculations show that these rearrangements of Na(+) can be induced by physiological membrane voltages. Due to its role in receptor function and signal bias, the repositioning of Na(+) has important general implications for signal transduction in GPCRs.
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MESH Headings
- Animals
- Crystallography, X-Ray
- Humans
- Ion Channel Gating
- Models, Molecular
- Molecular Dynamics Simulation
- Protein Binding
- Protein Structure, Secondary
- Receptor, Muscarinic M2/chemistry
- Receptor, Muscarinic M2/metabolism
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/metabolism
- Sodium/metabolism
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Affiliation(s)
- Owen N Vickery
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Jan-Philipp Machtens
- Forschungszentrum Jülich GmbH, Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Leo-Brandt-Strasse, 52428 Jülich, Germany
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Daniel Seeliger
- Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach an der Riss, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK.
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25
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Bitter taste receptors: Novel insights into the biochemistry and pharmacology. Int J Biochem Cell Biol 2016; 77:184-96. [PMID: 26995065 DOI: 10.1016/j.biocel.2016.03.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 01/14/2023]
Abstract
Bitter taste receptors (T2Rs) belong to the super family of G protein-coupled receptors (GPCRs). There are 25 T2Rs expressed in humans, and these interact with a large and diverse group of bitter ligands. T2Rs are expressed in many extra-oral tissues and can perform diverse physiological roles. Structure-function studies led to the identification of similarities and dissimilarities between T2Rs and Class A GPCRs including amino acid conservation and novel motifs. However, the efficacy of most of the T2R ligands is not yet elucidated and the biochemical pharmacology of T2Rs is poorly understood. Recent studies on T2Rs characterized novel ligands including blockers for these receptors that include inverse agonist and antagonists. In this review we discuss the techniques used for elucidating bitter blockers, concept of ligand bias, generic amino acid numbering, the role of cholesterol, and conserved water molecules in the biochemistry and pharmacology of T2Rs.
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26
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Characterization of a novel water pocket inside the human Cx26 hemichannel structure. Biophys J 2015; 107:599-612. [PMID: 25099799 DOI: 10.1016/j.bpj.2014.05.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023] Open
Abstract
Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket-termed the IC pocket-located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability.
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27
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Functional elements of the gastric inhibitory polypeptide receptor: Comparison between secretin- and rhodopsin-like G protein-coupled receptors. Biochem Pharmacol 2015; 96:237-46. [PMID: 26043830 DOI: 10.1016/j.bcp.2015.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/28/2015] [Indexed: 12/25/2022]
Abstract
Innovative crystallographic techniques have resulted in an exponential growth in the number of solved G-protein coupled receptor (GPCR) structures and a better understanding of the mechanisms of class A receptor activation and G protein binding. The recent release of the type 1 receptor for the corticotropin-releasing factor and the glucagon receptor structures, two members of the secretin-like family, gives the opportunity to understand these mechanisms of activation in this family of GPCRs. Here, we addressed the comparison of the functional elements of class A and secretin-like GPCRs, using the glucose-dependent insulinotropic polypeptide receptor (GIPR) as a model receptor. Inactive and active models of GIPR permitted to select, by structural homology with class A GPCRs, several residues that may form key interactions presumably involved in receptor activation and Gs coupling, for pharmacological evaluation. Mutants on these amino acids were expressed in HEKT 293 cells and characterized in terms of GIP-induced cAMP production. We identified various functional domains spanning from the peptide-binding to the G protein pockets: including: a network linking the extracellular part of transmembrane (TM) 6 with TMs 2 and 7; a polar lock that resembles the ionic-lock in class A GPCRs; an interaction between TMs 3 and 7 that favors activation; and two clusters of polar/charged and of hydrophobic residues that interact with the C-terminus of the Gα. The results show that despite the low degree of sequence similarity between rhodopsin- and secretin-like GPCRs, the two families share conserved elements in their mechanisms of activation and G protein binding.
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28
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Lee S, Bhattacharya S, Tate CG, Grisshammer R, Vaidehi N. Structural dynamics and thermostabilization of neurotensin receptor 1. J Phys Chem B 2015; 119:4917-28. [PMID: 25807267 PMCID: PMC4564841 DOI: 10.1021/jp510735f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The neurotensin receptor NTSR1 binds the peptide agonist neurotensin (NTS) and signals preferentially via the Gq protein. Recently, Grisshammer and co-workers reported the crystal structure of a thermostable mutant NTSR1-GW5 with NTS bound. Understanding how the mutations thermostabilize the structure would allow efficient design of thermostable mutant GPCRs for protein purification, and subsequent biophysical studies. Using microsecond scale molecular dynamics simulations (4 μs) of the thermostable mutant NTSR1-GW5 and wild type NTSR1, we have elucidated the structural and energetic factors that affect the thermostability and dynamics of NTSR1. The thermostable mutant NTSR1-GW5 is found to be less flexible and less dynamic than the wild type NTSR1. The point mutations confer thermostability by improving the interhelical hydrogen bonds, hydrophobic packing, and receptor interactions with the lipid bilayer, especially in the intracellular regions. During MD, NTSR1-GW5 becomes more hydrated compared to wild type NTSR1, with tight hydrogen bonded water clusters within the transmembrane core of the receptor, thus providing evidence that water plays an important role in improving helical packing in the thermostable mutant. Our studies provide valuable insights into the stability and functioning of NTSR1 that will be useful in future design of thermostable mutants of other peptide GPCRs.
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Affiliation(s)
- Sangbae Lee
- †Division of Immunology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Supriyo Bhattacharya
- †Division of Immunology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
| | - Christopher G Tate
- ‡MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Reinhard Grisshammer
- §Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - Nagarajan Vaidehi
- †Division of Immunology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010, United States
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29
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Li Q, Kim SK, Goddard WA, Chen G, Tan H. Predicted structures for kappa opioid G-protein coupled receptor bound to selective agonists. J Chem Inf Model 2015; 55:614-27. [PMID: 25642595 DOI: 10.1021/ci500523z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human kappa opioid receptor (κ-OR), a G protein-coupled receptor (GPCR), has been identified as a drug target for treatment of such human disorders as pain perception, neuroendocrine physiology, affective behavior, and cognition. In order to find more selective and active agonists, one would like to do structure based drug design. Indeed, there is an X-ray structure for an antagonist bound to κ-OR, but structures for activated GPCRs are quite different from those for the inactive GPCRs. Here we predict the ensemble of 24 low-energy structures of human kappa opioid receptor (κ-OR), obtained by application of the GEnSeMBLE (GPCR Ensemble of Structures in Membrane Bilayer Environment) complete sampling method, which evaluates 13 trillion combinations of tilt and rotation angles for κ-OR to select the best 24. To validate these structures, we used the DarwinDock complete sampling method to predict the binding sites for five known agonists (ethylketocyclazocine, bremazocine, pentazocine, nalorphine, and morphine) bound to all 24 κ-OR conformations. We find that some agonists bind selectively to receptor conformations that lack the salt bridge between transmembrane domains 3 and 6 as expected for active conformations. These 3D structures for κ-OR provide a structural basis for understanding ligand binding and activation of κ-OR, which should be useful for guiding subtype specific drug design.
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Affiliation(s)
- Quanjie Li
- †Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125, United States.,‡College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Soo-Kyung Kim
- †Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - William A Goddard
- †Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Guangju Chen
- ‡College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Hongwei Tan
- ‡College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
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30
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McCorvy JD, Roth BL. Structure and function of serotonin G protein-coupled receptors. Pharmacol Ther 2015; 150:129-42. [PMID: 25601315 DOI: 10.1016/j.pharmthera.2015.01.009] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 12/12/2014] [Indexed: 12/18/2022]
Abstract
Serotonin receptors are prevalent throughout the nervous system and the periphery, and remain one of the most lucrative and promising drug discovery targets for disorders ranging from migraine headaches to neuropsychiatric disorders such as schizophrenia and depression. There are 14 distinct serotonin receptors, of which 13 are G protein-coupled receptors (GPCRs), which are targets for approximately 40% of the approved medicines. Recent crystallographic and biochemical evidence has provided a converging understanding of the basic structure and functional mechanics of GPCR activation. Currently, two GPCR crystal structures exist for the serotonin family, the 5-HT1B and 5-HT2B receptor, with the antimigraine and valvulopathic drug ergotamine bound. The first serotonin crystal structures not only provide the first evidence of serotonin receptor topography but also provide mechanistic explanations into functional selectivity or biased agonism. This review will detail the findings of these crystal structures from a molecular and mutagenesis perspective for driving rational drug design for novel therapeutics incorporating biased signaling.
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MESH Headings
- Allosteric Site
- Animals
- Ergotamine/pharmacology
- Ergotamine/therapeutic use
- GTP-Binding Proteins/physiology
- Heart Valve Diseases/drug therapy
- Heart Valve Diseases/metabolism
- Humans
- Migraine Disorders/drug therapy
- Migraine Disorders/metabolism
- Models, Molecular
- Protein Conformation
- Receptor, Serotonin, 5-HT1B/chemistry
- Receptor, Serotonin, 5-HT1B/metabolism
- Receptor, Serotonin, 5-HT2B/chemistry
- Receptor, Serotonin, 5-HT2B/metabolism
- Receptors, Serotonin/chemistry
- Receptors, Serotonin/metabolism
- Serotonin Receptor Agonists/pharmacology
- Serotonin Receptor Agonists/therapeutic use
- Signal Transduction
- Vasoconstrictor Agents/pharmacology
- Vasoconstrictor Agents/therapeutic use
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Affiliation(s)
- John D McCorvy
- Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA
| | - Bryan L Roth
- Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA
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31
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Nisar SP, Jones ML, Cunningham MR, Mumford AD, Mundell SJ. Rare platelet GPCR variants: what can we learn? Br J Pharmacol 2014; 172:3242-53. [PMID: 25231155 DOI: 10.1111/bph.12941] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 12/31/2022] Open
Abstract
Platelet-expressed GPCRs are critical regulators of platelet function. Pharmacological blockade of these receptors forms a powerful therapeutic tool in the treatment and prevention of arterial thrombosis associated with coronary atherosclerosis and ischaemic stroke. However, anti-thrombotic drug therapy is associated with high inter-patient variability in therapeutic response and adverse bleeding side effects. In order to optimize the use of existing anti-platelet drugs and to develop new therapies, more detailed knowledge is required relating to the molecular mechanisms that regulate GPCR and therefore platelet function. One approach has been to identify rare, function-disrupting mutations within key platelet proteins in patients with bleeding disorders. In this review, we describe how an integrated functional genomics strategy has contributed important structure-function information about platelet GPCRs with specific emphasis upon purinergic and thromboxane A2 receptors. We also discuss the potential implications these findings have for pharmacotherapy and for understanding the molecular basis of mild bleeding disorders.
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Affiliation(s)
- S P Nisar
- School of Physiology and Pharmacology, University of Bristol, Bristol, UK
| | - M L Jones
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - M R Cunningham
- School of Physiology and Pharmacology, University of Bristol, Bristol, UK
| | - A D Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - S J Mundell
- School of Physiology and Pharmacology, University of Bristol, Bristol, UK
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Ranganathan A, Dror RO, Carlsson J. Insights into the Role of Asp792.50 in β2 Adrenergic Receptor Activation from Molecular Dynamics Simulations. Biochemistry 2014; 53:7283-96. [DOI: 10.1021/bi5008723] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anirudh Ranganathan
- Science for Life Laboratory, Box 1031, SE-171 21 Solna, Sweden
- Department
of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ron O. Dror
- Department
of Computer Science, Department of Molecular and Cellular Physiology,
and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Jens Carlsson
- Science for Life Laboratory, Box 1031, SE-171 21 Solna, Sweden
- Department
of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
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33
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Ramon E, Cordomí A, Aguilà M, Srinivasan S, Dong X, Moore AT, Webster AR, Cheetham ME, Garriga P. Differential light-induced responses in sectorial inherited retinal degeneration. J Biol Chem 2014; 289:35918-28. [PMID: 25359768 DOI: 10.1074/jbc.m114.609958] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Retinitis pigmentosa (RP) is a group of genetically and clinically heterogeneous inherited degenerative retinopathies caused by abnormalities of photoreceptors or retinal pigment epithelium in the retina leading to progressive sight loss. Rhodopsin is the prototypical G-protein-coupled receptor located in the vertebrate retina and is responsible for dim light vision. Here, novel M39R and N55K variants were identified as causing an intriguing sector phenotype of RP in affected patients, with selective degeneration in the inferior retina. To gain insights into the molecular aspects associated with this sector RP phenotype, whose molecular mechanism remains elusive, the mutations were constructed by site-directed mutagenesis, expressed in heterologous systems, and studied by biochemical, spectroscopic, and functional assays. M39R and N55K opsins had variable degrees of chromophore regeneration when compared with WT opsin but showed no gross structural misfolding or altered trafficking. M39R showed a faster rate for transducin activation than WT rhodopsin with a faster metarhodopsinII decay, whereas N55K presented a reduced activation rate and an altered photobleaching pattern. N55K also showed an altered retinal release from the opsin binding pocket upon light exposure, affecting its optimal functional response. Our data suggest that these sector RP mutations cause different protein phenotypes that may be related to their different clinical progression. Overall, these findings illuminate the molecular mechanisms of sector RP associated with rhodopsin mutations.
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Affiliation(s)
- Eva Ramon
- From the Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain
| | - Arnau Cordomí
- the Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Mònica Aguilà
- the University College London Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, United Kingdom, and
| | - Sundaramoorthy Srinivasan
- From the Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain
| | - Xiaoyun Dong
- From the Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain
| | - Anthony T Moore
- the University College London Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, United Kingdom, and the Moorfields Eye Hospital, London EC1V 2PD, United Kingdom
| | - Andrew R Webster
- the University College London Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, United Kingdom, and the Moorfields Eye Hospital, London EC1V 2PD, United Kingdom
| | - Michael E Cheetham
- the University College London Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, United Kingdom, and
| | - Pere Garriga
- From the Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain,
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34
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Sabbadin D, Ciancetta A, Moro S. Perturbation of fluid dynamics properties of water molecules during G protein-coupled receptor-ligand recognition: the human A2A adenosine receptor as a key study. J Chem Inf Model 2014; 54:2846-55. [PMID: 25245783 DOI: 10.1021/ci500397y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recent advances in structural biology revealed that water molecules play a crucial structural role in the protein architecture and ligand binding of G protein-coupled receptors. In this work, we present an alternative approach to monitor the time-dependent organization of water molecules during the final stage of the ligand-receptor recognition process by means of membrane molecular dynamics simulations. We inspect the variation of fluid dynamics properties of water molecules upon ligand binding with the aim to correlate the results with the binding affinities. The outcomes of this analysis are transferred into a bidimensional graph called water fluid dynamics maps, that allow a fast graphical identification of protein "hot-spots" characterized by peculiar shape and electrostatic properties that can play a critical role in ligand binding. We hopefully believe that the proposed approach might represent a valuable tool for structure-based drug discovery that can be extended to cases where crystal structures are not yet available, or have not been solved at high resolution.
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Affiliation(s)
- Davide Sabbadin
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
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35
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Sun X, Ågren H, Tu Y. Functional Water Molecules in Rhodopsin Activation. J Phys Chem B 2014; 118:10863-73. [DOI: 10.1021/jp505180t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Xianqiang Sun
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
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36
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Tehan BG, Bortolato A, Blaney FE, Weir MP, Mason JS. Unifying family A GPCR theories of activation. Pharmacol Ther 2014; 143:51-60. [PMID: 24561131 DOI: 10.1016/j.pharmthera.2014.02.004] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 10/25/2022]
Abstract
Several new pairs of active and inactive GPCR structures have recently been solved enabling detailed structural insight into the activation process, not only of rhodopsin but now also of the β2 adrenergic, M2 muscarinic and adenosine A2A receptors. Combined with structural analyses they have enabled us to examine the different recent theories proposed for GPCR activation and show that they are all indeed parts of the same process, and are intrinsically related through their effect on the central hydrophobic core of GPCRs. This new unifying general process of activation is consistent with the identification of known constitutively active mutants and an in-depth conservational analysis of significant residues implicated in the process.
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Affiliation(s)
- Benjamin G Tehan
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom.
| | - Andrea Bortolato
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Frank E Blaney
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Malcolm P Weir
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Jonathan S Mason
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
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37
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Szulczyk D, Bielenica A, Dobrowolski MA, Dobrzycki L, Krawiecka M, Kuran B, Struga M. Synthesis and structure evaluation of new complex butylarylpiperazin-1-yl derivatives. Med Chem Res 2014; 23:1519-1536. [PMID: 24489455 PMCID: PMC3905170 DOI: 10.1007/s00044-013-0740-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 08/17/2013] [Indexed: 11/30/2022]
Abstract
A series of arylpiperazine derivatives of 1,16-diphenyl-19-azahexacyclo-[14.5.1.02,15.03,8.09,14.017,21]docosa-2,3,5,7,8,9,11,13,14-nonaene-18,20,22-trione and 4,10-diphenyl-1H,2H,3H,5H-indeno[1,2-f]isoindole-1,3,5-trione was synthesized. The pharmacological profile of compound 4 at the 5-HT1A receptor was measured by binding assay. The title compounds were tested in cell-based assay against the human immunodeficiency virus type-1. The X-ray crystallographic studies of derivatives 2, 6, 7, 11, 19, and 20 were presented.
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Affiliation(s)
- Daniel Szulczyk
- Department of Medical Chemistry, Faculty of Medicine, Medical University of Warsaw, Oczki 3 Street, 02-007 Warsaw, Poland
| | - Anna Bielenica
- Department of Medical Chemistry, Faculty of Medicine, Medical University of Warsaw, Oczki 3 Street, 02-007 Warsaw, Poland
| | - Michał A Dobrowolski
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
| | - Lukasz Dobrzycki
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Street, 02-093 Warsaw, Poland
| | - Mariola Krawiecka
- Department of Medical Chemistry, Faculty of Medicine, Medical University of Warsaw, Oczki 3 Street, 02-007 Warsaw, Poland
| | - Bożena Kuran
- Department of Medical Chemistry, Faculty of Medicine, Medical University of Warsaw, Oczki 3 Street, 02-007 Warsaw, Poland
| | - Marta Struga
- Department of Medical Chemistry, Faculty of Medicine, Medical University of Warsaw, Oczki 3 Street, 02-007 Warsaw, Poland
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38
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Sabbadin D, Ciancetta A, Moro S. Bridging molecular docking to membrane molecular dynamics to investigate GPCR-ligand recognition: the human A₂A adenosine receptor as a key study. J Chem Inf Model 2014; 54:169-83. [PMID: 24359090 DOI: 10.1021/ci400532b] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of cell-surface receptors and about one-third of the actual targets of clinically used drugs. Following the progress made in the field of GPCRs structural determination, docking-based screening for novel potent and selective ligands is becoming an increasingly adopted strategy in the drug discovery process. However, this methodology is not yet able to anticipate the "bioactive" binding mode and discern it among other conformations. In the present work, we present a novel approach consisting in the integration of molecular docking and membrane MD simulations with the aim to merge the rapid sampling of ligand poses into in the binding site, typical of docking algorithms, with the thermodynamic accuracy of MD simulations in describing, at the molecular level, the stability a GPCR-ligand complex embedded into explicit lipid-water environment. To validate our approach, we have chosen as a key study the human A(2A) adenosine receptor (hA(2A) AR) and selected four receptor-antagonist complexes and one receptor-agonist complex that have been recently crystallized. In light of the obtained results, we believe that our novel strategy can be extended to other GPCRs and might represent a valuable tool to anticipate the "bioactive" conformation of high-affinity ligands.
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Affiliation(s)
- Davide Sabbadin
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
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39
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Gonzalez A, Cordomí A, Matsoukas M, Zachmann J, Pardo L. Modeling of G Protein-Coupled Receptors Using Crystal Structures: From Monomers to Signaling Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:15-33. [DOI: 10.1007/978-94-007-7423-0_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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40
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Park PSH. Constitutively active rhodopsin and retinal disease. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2014; 70:1-36. [PMID: 24931191 DOI: 10.1016/b978-0-12-417197-8.00001-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells of the retina that initiates scotopic vision. In the dark, rhodopsin is bound to the chromophore 11-cis retinal, which locks the receptor in an inactive state. The maintenance of an inactive rhodopsin in the dark is critical for rod photoreceptor cells to remain highly sensitive. Perturbations by mutation or the absence of 11-cis retinal can cause rhodopsin to become constitutively active, which leads to the desensitization of photoreceptor cells and, in some instances, retinal degeneration. Constitutive activity can arise in rhodopsin by various mechanisms and can cause a variety of inherited retinal diseases including Leber congenital amaurosis, congenital night blindness, and retinitis pigmentosa. In this review, the molecular and structural properties of different constitutively active forms of rhodopsin are overviewed, and the possibility that constitutive activity can arise from different active-state conformations is discussed.
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Affiliation(s)
- Paul Shin-Hyun Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio, USA.
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41
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Gutiérrez-de-Terán H, Massink A, Rodríguez D, Liu W, Han GW, Joseph JS, Katritch I, Heitman LH, Xia L, Ijzerman AP, Cherezov V, Katritch V, Stevens RC. The role of a sodium ion binding site in the allosteric modulation of the A(2A) adenosine G protein-coupled receptor. Structure 2013; 21:2175-85. [PMID: 24210756 DOI: 10.1016/j.str.2013.09.020] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/25/2013] [Accepted: 09/27/2013] [Indexed: 12/14/2022]
Abstract
The function of G protein-coupled receptors (GPCRs) can be modulated by a number of endogenous allosteric molecules. In this study, we used molecular dynamics, radioligand binding, and thermostability experiments to elucidate the role of the recently discovered sodium ion binding site in the allosteric modulation of the human A(2A) adenosine receptor, conserved among class A GPCRs. While the binding of antagonists and sodium ions to the receptor was noncompetitive in nature, the binding of agonists and sodium ions appears to require mutually exclusive conformational states of the receptor. Amiloride analogs can also bind to the sodium binding pocket, showing distinct patterns of agonist and antagonist modulation. These findings suggest that physiological concentrations of sodium ions affect functionally relevant conformational states of GPCRs and can help to design novel synthetic allosteric modulators or bitopic ligands exploiting the sodium ion binding pocket.
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Affiliation(s)
- Hugo Gutiérrez-de-Terán
- Fundación Pública Galega de Medicina Xenómica, Hospital Clínico Universitario de Santiago, E-15706 Santiago de Compostela, Spain; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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42
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Rose A, Theune D, Goede A, Hildebrand PW. MP:PD--a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins. Nucleic Acids Res 2013; 42:D347-51. [PMID: 24194596 PMCID: PMC3965053 DOI: 10.1093/nar/gkt1062] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The membrane protein packing database (MP:PD) (http://proteinformatics.charite.de/mppd) is a database of helical membrane proteins featuring internal atomic packing densities, cavities and waters. Membrane proteins are not tightly packed but contain a considerable number of internal cavities that differ in volume, polarity and solvent accessibility as well as in their filling with internal water. Internal cavities are supposed to be regions of high physical compressibility. By serving as mobile hydrogen bonding donors or acceptors, internal waters likely facilitate transition between different functional states. Despite these distinct functional roles, internal cavities of helical membrane proteins are not well characterized, mainly because most internal waters are not resolved by crystal structure analysis. Here we combined various computational biophysical techniques to characterize internal cavities, reassign positions of internal waters and calculate internal packing densities of all available helical membrane protein structures and stored them in MP:PD. The database can be searched using keywords and entries can be downloaded. Each entry can be visualized in Provi, a Jmol-based protein viewer that provides an integrated display of low energy waters alongside membrane planes, internal packing density, hydrophobic cavities and hydrogen bonds.
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Affiliation(s)
- Alexander Rose
- Charité University Medicine Berlin, Institute of Medical Physics and Biophysics, ProteinFormatics Group, Charitéplatz 1, 10117 Berlin and Charité University Medicine Berlin, Institute for Physiology, Structural Bioinformatics Group, Lindenberger Weg 80, 13125 Berlin
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43
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Karamitri A, Renault N, Clement N, Guillaume JL, Jockers R. Minireview: Toward the establishment of a link between melatonin and glucose homeostasis: association of melatonin MT2 receptor variants with type 2 diabetes. Mol Endocrinol 2013; 27:1217-33. [PMID: 23798576 DOI: 10.1210/me.2013-1101] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The existence of interindividual variations in G protein-coupled receptor sequences has been recognized early on. Recent advances in large-scale exon sequencing techniques are expected to dramatically increase the number of variants identified in G protein-coupled receptors, giving rise to new challenges regarding their functional characterization. The current minireview will illustrate these challenges based on the MTNR1B gene, which encodes the melatonin MT2 receptor, for which exon sequencing revealed 40 rare nonsynonymous variants in the general population and in type 2 diabetes (T2D) cohorts. Functional characterization of these MT2 mutants revealed 14 mutants with loss of Gi protein activation that associate with increased risk of T2D development. This repertoire of disease-associated mutants is a rich source for structure-activity studies and will help to define the still poorly understood role of melatonin in glucose homeostasis and T2D development in humans. Defining the functional defects in carriers of rare MT2 mutations will help to provide personalized therapies to these patients in the future.
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Affiliation(s)
- Angeliki Karamitri
- Institut National de la Santé et de la Recherche Médicale, U1016, Institut Cochin, Paris, France
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Ahn KH, Scott CE, Abrol R, Goddard WA, Kendall DA. Computationally-predicted CB1 cannabinoid receptor mutants show distinct patterns of salt-bridges that correlate with their level of constitutive activity reflected in G protein coupling levels, thermal stability, and ligand binding. Proteins 2013; 81:1304-17. [PMID: 23408552 DOI: 10.1002/prot.24264] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/21/2013] [Accepted: 01/21/2013] [Indexed: 11/09/2022]
Abstract
The cannabinoid receptor 1 (CB1), a member of the class A G-protein-coupled receptor (GPCR) family, possesses an observable level of constitutive activity. Its activation mechanism, however, has yet to be elucidated. Previously we discovered dramatic changes in CB1 activity due to single mutations; T3.46A, which made the receptor inactive, and T3.46I and L3.43A, which made it essentially fully constitutively active. Our subsequent prediction of the structures of these mutant receptors indicated that these changes in activity are explained in terms of the pattern of salt-bridges in the receptor region involving transmembrane domains 2, 3, 5, and 6. Here we identified key salt-bridges, R2.37 + D6.30 and D2.63 + K3.28, critical for CB1 inactive and active states, respectively, and generated new mutant receptors that we predicted would change CB1 activity by either precluding or promoting these interactions. We find that breaking the R2.37 + D6.30 salt-bridge resulted in substantial increase in G-protein coupling activity and reduced thermal stability relative to the wild-type reflecting the changes in constitutive activity from inactive to active. In contrast, breaking the D2.63 + K3.28 salt-bridge produced the opposite profile suggesting this interaction is critical for the receptor activation. Thus, we demonstrate an excellent correlation with the predicted pattern of key salt-bridges and experimental levels of activity and conformational flexibility. These results are also consistent with the extended ternary complex model with respect to shifts in agonist and inverse agonist affinity and provide a powerful framework for understanding the molecular basis for the multiple stages of CB1 activation and that of other GPCRs in general.
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Affiliation(s)
- Kwang H Ahn
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092, USA
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Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS. Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. J Chem Inf Model 2013; 53:1700-13. [DOI: 10.1021/ci4001458] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Ben G. Tehan
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Michael S. Bodnarchuk
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan W. Essex
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
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Palczewski K, Orban T. From atomic structures to neuronal functions of g protein-coupled receptors. Annu Rev Neurosci 2013; 36:139-64. [PMID: 23682660 DOI: 10.1146/annurev-neuro-062012-170313] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
G protein-coupled receptors (GPCRs) are essential mediators of signal transduction, neurotransmission, ion channel regulation, and other cellular events. GPCRs are activated by diverse stimuli, including light, enzymatic processing of their N-termini, and binding of proteins, peptides, or small molecules such as neurotransmitters. GPCR dysfunction caused by receptor mutations and environmental challenges contributes to many neurological diseases. Moreover, modern genetic technology has helped identify a rich array of mono- and multigenic defects in humans and animal models that connect such receptor dysfunction with disease affecting neuronal function. The visual system is especially suited to investigate GPCR structure and function because advanced imaging techniques permit structural studies of photoreceptor neurons at both macro and molecular levels that, together with biochemical and physiological assessment in animal models, provide a more complete understanding of GPCR signaling.
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Affiliation(s)
- Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA.
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Nygaard R, Zou Y, Dror RO, Mildorf TJ, Arlow DH, Manglik A, Pan AC, Liu CW, Fung JJ, Bokoch MP, Thian FS, Kobilka TS, Shaw DE, Mueller L, Prosser RS, Kobilka BK. The dynamic process of β(2)-adrenergic receptor activation. Cell 2013; 152:532-42. [PMID: 23374348 DOI: 10.1016/j.cell.2013.01.008] [Citation(s) in RCA: 621] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 12/03/2012] [Accepted: 01/07/2013] [Indexed: 01/14/2023]
Abstract
G-protein-coupled receptors (GPCRs) can modulate diverse signaling pathways, often in a ligand-specific manner. The full range of functionally relevant GPCR conformations is poorly understood. Here, we use NMR spectroscopy to characterize the conformational dynamics of the transmembrane core of the β(2)-adrenergic receptor (β(2)AR), a prototypical GPCR. We labeled β(2)AR with (13)CH(3)ε-methionine and obtained HSQC spectra of unliganded receptor as well as receptor bound to an inverse agonist, an agonist, and a G-protein-mimetic nanobody. These studies provide evidence for conformational states not observed in crystal structures, as well as substantial conformational heterogeneity in agonist- and inverse-agonist-bound preparations. They also show that for β(2)AR, unlike rhodopsin, an agonist alone does not stabilize a fully active conformation, suggesting that the conformational link between the agonist-binding pocket and the G-protein-coupling surface is not rigid. The observed heterogeneity may be important for β(2)AR's ability to engage multiple signaling and regulatory proteins.
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Affiliation(s)
- Rie Nygaard
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Mumford AD, Nisar S, Darnige L, Jones ML, Bachelot-Loza C, Gandrille S, Zinzindohoue F, Fischer AM, Mundell SJ, Gaussem P. Platelet dysfunction associated with the novel Trp29Cys thromboxane A₂ receptor variant. J Thromb Haemost 2013; 11:547-54. [PMID: 23279270 DOI: 10.1111/jth.12117] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 12/23/2012] [Indexed: 11/30/2022]
Abstract
BACKGROUND Genetic variations that affect the structure of the thromboxane A2 receptor (TP receptor) provide insights into the function of this key platelet and vascular receptor, but are very rare in unselected populations. OBJECTIVES To determine the functional consequences of the TP receptor Trp29Cys (W29C) substitution. PATIENTS/METHODS We performed a detailed phenotypic analysis of an index case (P1) with reduced platelet aggregation and secretion responses to TP receptor pathway activators, and a heterozygous TP receptor W29C substitution. An analysis of the variant W29C TP receptor expressed in heterologous cells was performed. RESULTS Total TP receptor expression in platelets from P1 was similar to that of controls, but there was reduced maximum binding and reduced affinity of binding to the TP receptor antagonist [(3) H]SQ29548. HEK293 cells transfected with W29C TP receptor cDNA showed similar total TP receptor expression to wild-type (WT) controls. However, the TP receptor agonist U46619 was less potent at inducing rises in cytosolic free Ca(2+) in HEK293 cells expressing the W29C TP receptor than in WT controls, indicating reduced receptor function. Immunofluorescence microscopy and cell surface ELISA showed intracellular retention and reduced cell surface expression of the W29C TP receptor in HEK293 cells. Consistent with the platelet phenotype, both maximum binding and the affinity of binding of [(3) H]SQ29548 to the W29C TP receptor were reduced compared to WT controls. CONCLUSION These findings extend the phenotypic description of the very rare disorder TP receptor deficiency, and show that the W29C substitution reduces TP receptor function by reducing surface receptor expression and by disrupting ligand binding.
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MESH Headings
- 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid/pharmacology
- Blood Coagulation Disorders/blood
- Blood Coagulation Disorders/genetics
- Blood Platelets/drug effects
- Blood Platelets/metabolism
- Bridged Bicyclo Compounds, Heterocyclic
- Calcium/blood
- Enzyme-Linked Immunosorbent Assay
- Fatty Acids, Unsaturated
- Genetic Predisposition to Disease
- Genetic Variation
- HEK293 Cells
- Humans
- Hydrazines/metabolism
- Ligands
- Male
- Microscopy, Fluorescence
- Middle Aged
- Phenotype
- Platelet Aggregation/drug effects
- Platelet Aggregation/genetics
- Radioligand Assay
- Receptors, Thromboxane A2, Prostaglandin H2/agonists
- Receptors, Thromboxane A2, Prostaglandin H2/blood
- Receptors, Thromboxane A2, Prostaglandin H2/deficiency
- Receptors, Thromboxane A2, Prostaglandin H2/genetics
- Transfection
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Affiliation(s)
- A D Mumford
- Bristol Heart Institute, University of Bristol, Bristol, UK.
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49
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Characterization of the dynamic events of GPCRs by automated computational simulations. Biochem Soc Trans 2013; 41:205-12. [DOI: 10.1042/bst20120287] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The recent advances in membrane protein crystallography have provided extremely valuable structural information of the superfamily of GPCRs (G-protein-coupled receptors). This has been particularly true for a few receptors whose structure was solved several times under different biochemical conditions. It follows that the mechanisms of receptor conformational equilibrium and related dynamic events can be explored by computational simulations. In the present article, we summarize our recent understanding of several dynamic features of GPCRs, accomplished through the use of MD (molecular dynamics) simulations. Our pipeline for the MD simulations of GPCRs, implemented in the web service http://gpcr.usc.es, is updated in the present paper and illustrated by recent applications. Special emphasis is put on the A2A adenosine receptor, one of the selected cases where crystal structures in several conformations and conditions exist, and on the dimerization process of the CXCR4 (CXC chemokine receptor 4).
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Deupi X. Quantification of structural distortions in the transmembrane helices of GPCRs. Methods Mol Biol 2013; 914:219-35. [PMID: 22976031 DOI: 10.1007/978-1-62703-023-6_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
A substantial part of the structural and much of the functional information about G protein-coupled receptors (GPCRs) comes from studies on rhodopsin. Thus, analysis tools for detailed structure comparison are key to see to what extent this information can be extended to other GPCRs. Among the methods to evaluate protein structures and, in particular, helix distortions, HELANAL has the advantage that it provides data (local bend and twist angles) that can be easily translated to structural effects, as a local opening/tightening of the helix.In this work I show how HELANAL can be used to extract detailed structural information of the transmembrane bundle of GPCRs, and I provide some examples on how these data can be interpreted to study basic principles of protein structure, to compare homologous proteins and to study mechanisms of receptor activation. Also, I show how in combination with the sequence analysis tools provided by the program GMoS, distortions in individual receptors can be put in the context of the whole Class A GPCR family. Specifically, quantification of the strong proline-induced distortions in the transmembrane bundle of rhodopsin shows that they are not standard proline kinks. Moreover, the helix distortions in transmembrane helix (TMH) 5 and TMH 6 of rhodopsin are also present in the rest of GPCR crystal structures obtained so far, and thus, rhodopsin-based homology models have modeled correctly these strongly distorted helices. While in some cases the inherent "rhodopsin bias" of many of the GPCR models to date has not been a disadvantage, the availability of more templates will clearly result in better homology models. This type of analysis can be, of course, applied to any protein, and it may be particularly useful for the structural analysis of other membrane proteins. A detailed knowledge of the local structural changes related to ligand binding and how they are translated into larger-scale movements of transmembrane domains is key to understand receptor activation.
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Affiliation(s)
- Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland.
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