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Ashton AW. Preparing to strike: Acute events in signaling by the serpentine receptor for thromboxane A 2. Pharmacol Ther 2023:108478. [PMID: 37321373 DOI: 10.1016/j.pharmthera.2023.108478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
Over the last two decades, awareness of the (patho)physiological roles of thromboxane A2 signaling has been greatly extended. From humble beginnings as a short-lived stimulus that activates platelets and causes vasoconstriction to a dichotomous receptor system involving multiple endogenous ligands capable of modifying tissue homeostasis and disease generation in almost every tissue of the body. Thromboxane A2 receptor (TP) signal transduction is associated with the pathogenesis of cancer, atherosclerosis, heart disease, asthma, and host response to parasitic infection amongst others. The two receptors mediating these cellular responses (TPα and TPβ) are derived from a single gene (TBXA2R) through alternative splicing. Recently, knowledge about the mechanism(s) of signal propagation by the two receptors has undergone a revolution in understanding. Not only have the structural relationships associated with G-protein coupling been established but the modulation of that signaling by post-translational modification to the receptor has come sharply into focus. Moreover, the signaling of the receptor unrelated to G-protein coupling has become a burgeoning field of endeavor with over 70 interacting proteins currently identified. These data are reshaping the concept of TP signaling from a mere guanine nucleotide exchange factors for Gα activation to a nexus for the convergence of diverse and poorly characterized signaling pathways. This review summarizes the advances in understanding in TP signaling, and the potential for new growth in a field that after almost 50 years is finally coming of age.
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Affiliation(s)
- Anthony W Ashton
- Division of Cardiovascular Medicine, Lankenau Institute for Medical Research, Rm 128, 100 E Lancaster Ave, Wynnewood, PA 19096, USA; Division of Perinatal Research, Kolling Institute of Medical Research, Faculty of Medicine and Health, University of Sydney, St Leonards, NSW 2065, Australia.
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2
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Wiechmann AF, Martin TA, Horb ME. CRISPR/Cas9 mediated mutation of the mtnr1a melatonin receptor gene causes rod photoreceptor degeneration in developing Xenopus tropicalis. Sci Rep 2020; 10:13757. [PMID: 32792587 PMCID: PMC7426423 DOI: 10.1038/s41598-020-70735-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
Nighttime surges in melatonin levels activate melatonin receptors, which synchronize cellular activities with the natural light/dark cycle. Melatonin receptors are expressed in several cell types in the retina, including the photon-sensitive rods and cones. Previous studies suggest that long-term photoreceptor survival and retinal health is in part reliant on melatonin orchestration of circadian homeostatic activities. This scenario would accordingly envisage that disruption of melatonin receptor signaling is detrimental to photoreceptor health. Using in vivo CRISPR/Cas9 genomic editing, we discovered that a small deletion mutation of the Mel1a melatonin receptor (mtnr1a) gene causes a loss of rod photoreceptors in retinas of developing Xenopus tropicalis heterozygous, but not homozygous mutant tadpoles. Cones were relatively spared from degeneration, and the rod loss phenotype was not obvious after metamorphosis. Localization of Mel1a receptor protein appeared to be about the same in wild type and mutant retinas, suggesting that the mutant protein is expressed at some level in mutant retinal cells. The severe impact on early rod photoreceptor viability may signify a previously underestimated critical role in circadian influences on long-term retinal health and preservation of sight. These data offer evidence that disturbance of homeostatic, circadian signaling, conveyed through a mutated melatonin receptor, is incompatible with rod photoreceptor survival.
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Affiliation(s)
- Allan F Wiechmann
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Teryn A Martin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Marko E Horb
- Marine Biological laboratory, Woods Hole, MA, USA
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3
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 169:151-179. [PMID: 31952685 DOI: 10.1016/bs.pmbts.2019.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfamily of glycoprotein hormone receptors (GpHRs), di/oligomerization has been demonstrated to play a significant role in regulating its signaling activity at a cellular and physiological level and even pathophysiologically. Here we will describe and discuss the developments in our understanding of GPCR oligomerization, in both health and disease, from the study of this unique and complex subfamily of GPCRs with light on the luteinizing hormone receptor (LHR). Focus will be put on the results of an approach relying on the combination of atomistic modeling by protein-protein docking with super-resolution imaging. The latter could resolve single LHR molecules to ~8nm resolution in functional asymmetric dimers and oligomers, using dual-color photoactivatable dyes and localization microscopy (PD-PALM). Structural modeling of functionally asymmetric LHR trimers and tetramers strongly aligned with PD-PALM-imaged spatial arrangements, identifying multiple possible helix interfaces mediating inter-protomer associations. Diverse spatial and structural assemblies mediating GPCR oligomerization may acutely fine-tune the cellular signaling profile.
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4
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Durdagi S, Erol I, Salmas RE, Aksoydan B, Kantarcioglu I. Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors. Neurosci Lett 2018; 700:30-37. [PMID: 29684528 DOI: 10.1016/j.neulet.2018.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022]
Abstract
G Protein-Coupled Receptors (GPCRs) can form homo- and heterodimers or constitute higher oligomeric clusters with other heptahelical GPCRs. In this article, multiscale molecular modeling approaches as well as experimental techniques which are used to study oligomerization of GPCRs are reviewed. In particular, the effect of dimerization/oligomerization to the ligand binding affinity of individual protomers and also on the efficacy of the oligomer are discussed by including diverse examples from the literature. In addition, possible allosteric effects that may emerge upon interaction of GPCRs with membrane components, like cholesterol, is also discussed. Investigation of these above-mentioned interactions may greatly contribute to the candidate molecule screening studies and development of novel therapeutics with fewer adverse effects.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey
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5
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Nisar SP, Lordkipanidzé M, Jones ML, Dawood BB, Murden S, Cunningham MR, Mumford AD, Wilde JT, Watson SP, Lowe GC, Mundell SJ. A novel thromboxane A2 receptor N42S variant results in reduced surface expression and platelet dysfunction. Thromb Haemost 2017; 111:923-32. [DOI: 10.1160/th13-08-0672] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/19/2013] [Indexed: 11/05/2022]
Abstract
SummaryA small number of thromboxane receptor variants have been described in patients with a bleeding history that result in platelet dysfunction. We have identified a patient with a history of significant bleeding, who expresses a novel heterozygous thromboxane receptor variant that predicts an asparagine to serine substitution (N42S). This asparagine is conserved across all class A GPCRs, suggesting a vital role for receptor structure and function. We investigated the functional consequences of the TP receptor heterozygous N42S substitution by performing platelet function studies on platelet-rich plasma taken from the patient and healthy controls. We investigated the N42S mutation by expressing the wild-type (WT) and mutant receptor in human embryonic kidney (HEK) cells. Aggregation studies showed an ablation of arachidonic acid responses in the patient, whilst there was right-ward shift of the U46619 concentration response curve (CRC). Thromboxane generation was unaffected. Calcium mobilisation studies in cells lines showed a rightward shift of the U46619 CRC in N42S–expressing cells compared to WT. Radioligand binding studies revealed a reduction in BMax in platelets taken from the patient and in N42S–expressing cells, whilst cell studies confirmed poor surface expression. We have identified a novel thromboxane receptor variant, N42S, which results in platelet dysfunction due to reduced surface expression. It is associated with a significant bleeding history in the patient in whom it was identified. This is the first description of a naturally occurring variant that results in the substitution of this highly conserved residue and confirms the importance of this residue for correct GPCR function.
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6
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Methods used to study the oligomeric structure of G-protein-coupled receptors. Biosci Rep 2017; 37:BSR20160547. [PMID: 28062602 PMCID: PMC5398257 DOI: 10.1042/bsr20160547] [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] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 02/02/2023] Open
Abstract
G-protein-coupled receptors (GPCRs), which constitute the largest family of cell surface receptors, were originally thought to function as monomers, but are now recognized as being able to act in a wide range of oligomeric states and indeed, it is known that the oligomerization state of a GPCR can modulate its pharmacology and function. A number of experimental techniques have been devised to study GPCR oligomerization including those based upon traditional biochemistry such as blue-native PAGE (BN-PAGE), co-immunoprecipitation (Co-IP) and protein-fragment complementation assays (PCAs), those based upon resonance energy transfer, FRET, time-resolved FRET (TR-FRET), FRET spectrometry and bioluminescence resonance energy transfer (BRET). Those based upon microscopy such as FRAP, total internal reflection fluorescence microscopy (TIRFM), spatial intensity distribution analysis (SpIDA) and various single molecule imaging techniques. Finally with the solution of a growing number of crystal structures, X-ray crystallography must be acknowledged as an important source of discovery in this field. A different, but in many ways complementary approach to the use of more traditional experimental techniques, are those involving computational methods that possess obvious merit in the study of the dynamics of oligomer formation and function. Here, we summarize the latest developments that have been made in the methods used to study GPCR oligomerization and give an overview of their application.
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7
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Bartuzi D, Kaczor AA, Targowska-Duda KM, Matosiuk D. Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors. Molecules 2017; 22:molecules22020340. [PMID: 28241450 PMCID: PMC6155844 DOI: 10.3390/molecules22020340] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/27/2017] [Accepted: 02/15/2017] [Indexed: 12/16/2022] Open
Abstract
The growing number of studies on G protein-coupled receptors (GPCRs) family are a source of noticeable improvement in our understanding of the functioning of these proteins. GPCRs are responsible for a vast part of signaling in vertebrates and, as such, invariably remain in the spotlight of medicinal chemistry. A deeper insight into the underlying mechanisms of interesting phenomena observed in GPCRs, such as biased signaling or allosteric modulation, can be gained with experimental and computational studies. The latter play an important role in this process, since they allow for observations on scales inaccessible for most other methods. One of the key steps in such studies is proper computational reconstruction of actual ligand-receptor or protein-protein interactions, a process called molecular docking. A number of improvements and innovative applications of this method were documented recently. In this review, we focus particularly on innovations in docking to GPCRs.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | | | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
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8
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Capra V, Mauri M, Guzzi F, Busnelli M, Accomazzo MR, Gaussem P, Nisar SP, Mundell SJ, Parenti M, Rovati GE. Impaired thromboxane receptor dimerization reduces signaling efficiency: A potential mechanism for reduced platelet function in vivo. Biochem Pharmacol 2016; 124:43-56. [PMID: 27845050 DOI: 10.1016/j.bcp.2016.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/10/2016] [Indexed: 12/16/2022]
Abstract
Thromboxane A2 is a potent mediator of inflammation and platelet aggregation exerting its effects through the activation of a G protein-coupled receptor (GPCR), termed TP. Although the existence of dimers/oligomers in Class A GPCRs is widely accepted, their functional significance still remains controversial. Recently, we have shown that TPα and TPβ homo-/hetero-dimers interact through an interface of residues in transmembrane domain 1 (TM1) whose disruption impairs dimer formation. Here, biochemical and pharmacological characterization of this dimer deficient mutant (DDM) in living cells indicates a significant impairment in its response to agonists. Interestingly, two single loss-of-function TPα variants, namely W29C and N42S recently identified in two heterozygous patients affected by bleeding disorders, match some of the residues mutated in our DDM. These two naturally occurring variants display a reduced potency to TP agonists and are characterized by impaired dimer formation in transfected HEK-293T cells. These findings provide proofs that lack of homo-dimer formation is a crucial process for reduced TPα function in vivo, and might represent one molecular mechanism through which platelet TPα receptor dysfunction affects the patient(s) carrying these mutations.
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Key Words
- (Z)-7-[(1R,2R,3R,4S)-3-[[2-(phenylcarbamoyl)hydrazinyl]methyl]-7-oxabicyclo[2.2.1]heptan-2-yl]hept-5-enoic acid
- (Z)-7-[(1S,2S,3R,4R)-3-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxabicyclo[2.2.1]heptan-2-yl]hept-5-enoic acid
- (Z)-7-[(1S,2S,3S,4R)-3-[(E,3R)-3-hydroxy-4-(4-iodophenoxy)but-1-enyl]-7-oxabicyclo[2.2.1]heptan-2-yl]hept-5-enoic acid
- (Z)-7-[(1S,3R,4R,5S)-3-[(E,3R)-3-hydroxyoct-1-enyl]-6,6-dimethyl-4-bicyclo[3.1.1]heptanyl]hept-5-enoic acid
- 3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propanoic acid
- Eicosanoids
- G protein coupled receptors
- I-BOP (PubChem CID: 51015454)
- Pinane Thromboxane A2 (PTA2) (PubChem CID: 25834471)
- Platelets
- Ramatroban (PubChem CID: 123879)
- Receptor dimer
- SQ29,548 (PubChem CID: 6437074)
- Signal transduction
- Thromboxane A(2)
- U46619 (PubChem CID: 5311493)
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Affiliation(s)
- Valérie Capra
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy; Department of Health Science, University of Milan, Milano, Italy.
| | - Mario Mauri
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| | - Francesca Guzzi
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| | - Marta Busnelli
- CNR, Institute of Neuroscience, University of Milan, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy.
| | - Maria Rosa Accomazzo
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy.
| | - Pascale Gaussem
- Inserm UMR-S1140, Faculte' de Pharmacie, Université Paris Descartes, Sorbonne Paris Cité, Paris and AP-HP, Hopital Européen Georges Pompidou, Service d'Hématologie Biologique, Paris, France.
| | - Shaista P Nisar
- School of Physiology and Pharmacology, University of Bristol, Bristol BS8 1TD, UK.
| | - Stuart J Mundell
- School of Physiology and Pharmacology, University of Bristol, Bristol BS8 1TD, UK.
| | - Marco Parenti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| | - G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy.
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9
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Guaitoli G, Raimondi F, Gilsbach BK, Gómez-Llorente Y, Deyaert E, Renzi F, Li X, Schaffner A, Jagtap PKA, Boldt K, von Zweydorf F, Gotthardt K, Lorimer DD, Yue Z, Burgin A, Janjic N, Sattler M, Versées W, Ueffing M, Ubarretxena-Belandia I, Kortholt A, Gloeckner CJ. Structural model of the dimeric Parkinson's protein LRRK2 reveals a compact architecture involving distant interdomain contacts. Proc Natl Acad Sci U S A 2016; 113:E4357-66. [PMID: 27357661 PMCID: PMC4968714 DOI: 10.1073/pnas.1523708113] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large, multidomain protein containing two catalytic domains: a Ras of complex proteins (Roc) G-domain and a kinase domain. Mutations associated with familial and sporadic Parkinson's disease (PD) have been identified in both catalytic domains, as well as in several of its multiple putative regulatory domains. Several of these mutations have been linked to increased kinase activity. Despite the role of LRRK2 in the pathogenesis of PD, little is known about its overall architecture and how PD-linked mutations alter its function and enzymatic activities. Here, we have modeled the 3D structure of dimeric, full-length LRRK2 by combining domain-based homology models with multiple experimental constraints provided by chemical cross-linking combined with mass spectrometry, negative-stain EM, and small-angle X-ray scattering. Our model reveals dimeric LRRK2 has a compact overall architecture with a tight, multidomain organization. Close contacts between the N-terminal ankyrin and C-terminal WD40 domains, and their proximity-together with the LRR domain-to the kinase domain suggest an intramolecular mechanism for LRRK2 kinase activity regulation. Overall, our studies provide, to our knowledge, the first structural framework for understanding the role of the different domains of full-length LRRK2 in the pathogenesis of PD.
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Affiliation(s)
- Giambattista Guaitoli
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Francesco Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; Cell Networks, University of Heidelberg, 69120 Heidelberg, Germany
| | - Bernd K Gilsbach
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, The Netherlands; Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Yacob Gómez-Llorente
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Egon Deyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Vlaams Instituut voor Biotechnologie, Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Fabiana Renzi
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Xianting Li
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adam Schaffner
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029; Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Pravin Kumar Ankush Jagtap
- Center for Integrated Protein Science Munich at Department of Chemistry, Technische Universität München, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Karsten Boldt
- Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Felix von Zweydorf
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Katja Gotthardt
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | | | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | | | - Michael Sattler
- Center for Integrated Protein Science Munich at Department of Chemistry, Technische Universität München, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Vlaams Instituut voor Biotechnologie, Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany
| | - Iban Ubarretxena-Belandia
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, The Netherlands;
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany;
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10
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Hoxha M, Buccellati C, Capra V, Garella D, Cena C, Rolando B, Fruttero R, Carnevali S, Sala A, Rovati G, Bertinaria M. In vitro pharmacological evaluation of multitarget agents for thromboxane prostanoid receptor antagonism and COX-2 inhibition. Pharmacol Res 2016; 103:132-43. [DOI: 10.1016/j.phrs.2015.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 11/15/2015] [Indexed: 11/29/2022]
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11
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Hu G, Xiao F, Li Y, Li Y, Vongsangnak W. Protein-Protein Interface and Disease: Perspective from Biomolecular Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:57-74. [PMID: 27928579 DOI: 10.1007/10_2016_40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions are involved in many important biological processes and molecular mechanisms of disease association. Structural studies of interfacial residues in protein complexes provide information on protein-protein interactions. Characterizing protein-protein interfaces, including binding sites and allosteric changes, thus pose an imminent challenge. With special focus on protein complexes, approaches based on network theory are proposed to meet this challenge. In this review we pay attention to protein-protein interfaces from the perspective of biomolecular networks and their roles in disease. We first describe the different roles of protein complexes in disease through several structural aspects of interfaces. We then discuss some recent advances in predicting hot spots and communication pathway analysis in terms of amino acid networks. Finally, we highlight possible future aspects of this area with respect to both methodology development and applications for disease treatment.
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Affiliation(s)
- Guang Hu
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China.
| | - Fei Xiao
- School of Basic Medicine and Biological Sciences, Medical College of Soochow University, Suzhou, 215123, China
| | - Yuqian Li
- School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yuan Li
- Center for Systems Biology, School of Electronic and Information Engineering, Soochow University, Suzhou, 215006, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
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12
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Meng XY, Mezei M, Cui M. Computational approaches for modeling GPCR dimerization. Curr Pharm Biotechnol 2015; 15:996-1006. [PMID: 25307013 DOI: 10.2174/1389201015666141013102515] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/09/2014] [Accepted: 08/18/2014] [Indexed: 11/22/2022]
Abstract
Growing experimental evidences suggest that dimerization and oligomerization are important for G Protein- Coupled Receptors (GPCRs) function. The detailed structural information of dimeric/oligomeric GPCRs would be very important to understand their function. Although it is encouraging that recently several experimental GPCR structures in oligomeric forms have appeared, experimental determination of GPCR structures in oligomeric forms is still a big challenge, especially in mimicking the membrane environment. Therefore, development of computational approaches to predict dimerization of GPCRs will be highly valuable. In this review, we summarize computational approaches that have been developed and used for modeling of GPCR dimerization. In addition, we introduce a novel two-dimensional Brownian Dynamics based protein docking approach, which we have recently adapted, for GPCR dimer prediction.
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Affiliation(s)
| | | | - Meng Cui
- Institute of Quantitative Biology and Medicine, Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou 215123, China.
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13
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Kaczor AA, Guixà-González R, Carrió P, Poso A, Dove S, Pastor M, Selent J. Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors. Mol Inform 2015; 34:246-55. [PMID: 27490170 DOI: 10.1002/minf.201400088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 02/19/2015] [Indexed: 01/08/2023]
Abstract
In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, κ opioid receptor dimer, β1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data.
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Affiliation(s)
- Agnieszka A Kaczor
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland phone: +48815357365; fax: +48815357366. .,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Lab, Faculty of Pharmacy with Division for Medical Analytics, 4A Chodźki St., PL-20059 Lublin, Poland. .,Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain. .,Department of Pharmaceutical Chemistry II, Institute of Pharmacy, University of Regensburg, DE-93040 Regensburg, Germany.
| | - Ramon Guixà-González
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Pau Carrió
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland phone: +48815357365; fax: +48815357366
| | - Stefan Dove
- Department of Pharmaceutical Chemistry II, Institute of Pharmacy, University of Regensburg, DE-93040 Regensburg, Germany
| | - Manuel Pastor
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain
| | - Jana Selent
- Research Unit on Biomedical Informatics (GRIB), PRBB, Dr Aiguader 88, E-08003 Barcelona, Spain.
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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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15
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Kaczor AA, Selent J, Sanz F, Pastor M. Modeling Complexes of Transmembrane Proteins: Systematic Analysis of ProteinProtein Docking Tools. Mol Inform 2013; 32:717-33. [PMID: 27480064 DOI: 10.1002/minf.201200150] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/16/2013] [Indexed: 01/25/2023]
Abstract
Proteinprotein docking methodology is frequently used to model complexes of transmembrane proteins, in particular oligomers of G protein-coupled receptors (GPCRs), even if its applicability for these systems has never been fully validated. The aim of this work is to perform a systematic study on the suitability of some widely-used proteinprotein docking software for modeling complexes of transmembrane proteins. In this study we tested the programs ZDOCK, ClusPro, HEX, GRAMM-X, PatchDock, SymmDock, and HADDOCK, using a set of membrane protein oligomers for which the 3D structure has been obtained experimentally, including opsin dimer, the recently published chemokine CXCR4 and kappa opioid receptor dimers. The results show that the docking success depends on the applied docking algorithm and scoring functions, but also on inherent structural features of the transmembrane proteins. Thus, proteins with large interface surfaces, rich in surface cavities, high-order symmetry, and small conformational change upon complex formation are well predicted more often than proteins without these features. The results of this systematic analysis provide guidelines that can be used for obtaining reliable models of transmembrane proteins, including GPCRs. Therefore they can be useful for the application of structure-based methods in drug discovery projects involving these targets.
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Affiliation(s)
- Agnieszka A Kaczor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550. .,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Faculty of Pharmacy with Division for Medical Analytics, Medical University of Lublin 4A Chodźki St., PL-20059 Lublin, Poland.
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550.
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute). Dr. Aiguader 88, Barcelona, Spain phone: +48 815357365, fax: +48 815357355; phone: +34 933160515, fax: +34 93 316 0550
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16
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Full and partial agonists of thromboxane prostanoid receptor unveil fine tuning of receptor superactive conformation and G protein activation. PLoS One 2013; 8:e60475. [PMID: 23555978 PMCID: PMC3610872 DOI: 10.1371/journal.pone.0060475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 02/26/2013] [Indexed: 01/14/2023] Open
Abstract
The intrahelical salt bridge between E/D3.49 and R3.50 within the E/DRY motif on helix 3 (H3) and the interhelical hydrogen bonding between the E/DRY and residues on H6 are thought to be critical in stabilizing the class A G protein-coupled receptors in their inactive state. Removal of these interactions is expected to generate constitutively active receptors. This study examines how neutralization of E3.49/6.30 in the thromboxane prostanoid (TP) receptor alters ligand binding, basal, and agonist-induced activity and investigates the molecular mechanisms of G protein activation. We demonstrate here that a panel of full and partial agonists showed an increase in affinity and potency for E129V and E240V mutants. Yet, even augmenting the sensitivity to detect constitutive activity (CA) with overexpression of the receptor or the G protein revealed resistance to an increase in basal activity, while retaining fully the ability to cause agonist-induced signaling. However, direct G protein activation measured through bioluminescence resonance energy transfer (BRET) indicates that these mutants more efficiently communicate and/or activate their cognate G proteins. These results suggest the existence of additional constrains governing the shift of TP receptor to its active state, together with an increase propensity of these mutants to agonist-induced signaling, corroborating their definition as superactive mutants. The particular nature of the TP receptor as somehow “resistant” to CA should be examined in the context of its pathophysiological role in the cardiovascular system. Evolutionary forces may have favored regulation mechanisms leading to low basal activity and selected against more highly active phenotypes.
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17
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Analysis of GPCR Dimerization Using Acceptor Photobleaching Resonance Energy Transfer Techniques. Methods Enzymol 2013; 521:311-27. [DOI: 10.1016/b978-0-12-391862-8.00017-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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18
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Quaternary Structure Predictions and Structural Communication Features of GPCR Dimers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:105-42. [DOI: 10.1016/b978-0-12-386931-9.00005-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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19
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Gracia E, Farré D, Cortés A, Ferrer-Costa C, Orozco M, Mallol J, Lluís C, Canela EI, McCormick PJ, Franco R, Fanelli F, Casadó V. The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors. FASEB J 2012. [PMID: 23193172 DOI: 10.1096/fj.12-212621] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The enzyme adenosine deaminase (ADA) is a multifunctional protein that can both degrade adenosine and bind extracellularly to adenosine receptors, acting as an allosteric modulator regulating the hormonal effects of adenosine. The molecular regions of ADA responsible for the latter are unknown. In this work, alanine scanning mutagenesis of various ADA amino acid stretches, selected through in silico docking experiments, allowed us to identify regions of the enzyme responsible for modulating both its catalytic activity and its ability to modulate agonist binding to A and A adenosine receptors (AR and AR). The combination of computational and in vitro experiments show that the structural gate to the catalytic site; i.e., the α-1 helix containing residues L58-I72 and the loop containing residues A184-I188 of ADA, were important to maintain both the catalytic efficiency of the enzyme and its action as an allosteric modulator of the adenosine receptors. These data are consistent with a predicted supramolecular assembly, in which ADA bridges AR and CD26 and are in line with the notion that the interaction of ADA with adenosine receptors has an important role in the immunosynapse. We propose that it is the ADA open form, but not the closed one, that is responsible for the functional interaction with A₁R and A₂AR.
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Affiliation(s)
- Eduard Gracia
- Laboratory of Molecular Neurobiology, Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
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20
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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