1
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Chau KD, Hauser FE, Van Nynatten A, Daane JM, Harris MP, Chang BSW, Lovejoy NR. Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes. J Mol Evol 2024; 92:93-103. [PMID: 38416218 DOI: 10.1007/s00239-024-10156-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 01/12/2024] [Indexed: 02/29/2024]
Abstract
Ecological and evolutionary transitions offer an excellent opportunity to examine the molecular basis of adaptation. Fishes of the order Beloniformes include needlefishes, flyingfishes, halfbeaks, and allies, and comprise over 200 species occupying a wide array of habitats-from the marine epipelagic zone to tropical rainforest rivers. These fishes also exhibit a diversity of diets, including piscivory, herbivory, and zooplanktivory. We investigated how diet and habitat affected the molecular evolution of cone opsins, which play a key role in bright light and colour vision and are tightly linked to ecology and life history. We analyzed a targeted-capture dataset to reconstruct the evolutionary history of beloniforms and assemble cone opsin sequences. We implemented codon-based clade models of evolution to examine how molecular evolution was affected by habitat and diet. We found high levels of positive selection in medium- and long-wavelength beloniform opsins, with piscivores showing increased positive selection in medium-wavelength opsins and zooplanktivores showing increased positive selection in long-wavelength opsins. In contrast, short-wavelength opsins showed purifying selection. While marine/freshwater habitat transitions have an effect on opsin molecular evolution, we found that diet plays a more important role. Our study suggests that evolutionary transitions along ecological axes produce complex adaptive interactions that affect patterns of selection on genes that underlie vision.
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Affiliation(s)
- Katherine D Chau
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Biology, York University, Toronto, ON, Canada
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Alexander Van Nynatten
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Biology, University of Victoria, Victoria, Canada
| | - Jacob M Daane
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | | | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nathan R Lovejoy
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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2
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Bueschbell B, Magalhães PR, Barreto CA, Melo R, Schiedel AC, Machuqueiro M, Moreira IS. The World of GPCR dimers - Mapping dopamine receptor D 2 homodimers in different activation states and configuration arrangements. Comput Struct Biotechnol J 2023; 21:4336-4353. [PMID: 37711187 PMCID: PMC10497915 DOI: 10.1016/j.csbj.2023.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are known to dimerize, but the molecular and structural basis of GPCR dimers is not well understood. In this study, we developed a computational framework to generate models of symmetric and asymmetric GPCR dimers using different monomer activation states and identified their most likely interfaces with molecular details. We chose the dopamine receptor D2 (D2R) homodimer as a case study because of its biological relevance and the availability of structural information. Our results showed that transmembrane domains 4 and 5 (TM4 and TM5) are mostly found at the dimer interface of the D2R dimer and that these interfaces have a subset of key residues that are mostly nonpolar from TM4 and TM5, which was in line with experimental studies. In addition, TM2 and TM3 appear to be relevant for D2R dimers. In some cases, the inactive configuration is unaffected by the partnered protomer, whereas in others, the active protomer adopts the properties of an inactive receptor. Additionally, the β-arrestin configuration displayed the properties of an active receptor in the absence of an agonist, suggesting that a switch to another meta-state during dimerization occurred. Our findings are consistent with the experimental data, and this method can be adapted to study heterodimers and potentially extended to include additional proteins such as G proteins or β-arrestins. In summary, this approach provides insight into the impact of the conformational status of partnered protomers on the overall quaternary GPCR macromolecular structure and dynamics.
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Affiliation(s)
- Beatriz Bueschbell
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-456 Coimbra, Portugal
- IIIs-Institute for Interdisciplinary Research, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Pedro R. Magalhães
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande C8 bdg, 1749-016 Lisboa, Portugal
| | - Carlos A.V. Barreto
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-456 Coimbra, Portugal
- IIIs-Institute for Interdisciplinary Research, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Rita Melo
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3000-456 Coimbra, Portugal
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, University of Coimbra, Coimbra, Portugal
| | - Anke C. Schiedel
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany
| | - Miguel Machuqueiro
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande C8 bdg, 1749-016 Lisboa, Portugal
| | - Irina S. Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-535 Coimbra, Portugal
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3
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The transmembrane domains of GPCR dimers as targets for drug development. Drug Discov Today 2023; 28:103419. [PMID: 36309194 DOI: 10.1016/j.drudis.2022.103419] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/06/2022] [Accepted: 10/20/2022] [Indexed: 02/02/2023]
Abstract
G-protein-coupled receptors (GPCRs) can form homodimers or heterodimers that modulate specific signal transduction pathways to regulate a wide range of physiological and pathological functions. As such, GPCR dimers are novel drug targets for disorders including depression, hypertension, diabetes, and vascular dementia. The interaction between two receptors in a GPCR dimer involves a conformational change in the transmembrane domain (TMD). It has been demonstrated that the TMD has an important role in GPCR dimer formation and stability in vitro and in vivo. Moreover, increasing evidence shows that the TMD of GPCRs affects the function of dimers. Therefore, the TMD of GPCRs is an emerging target for the development of drugs to treat diseases that involve GPCR dimerization.
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4
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Juza R, Musilek K, Mezeiova E, Soukup O, Korabecny J. Recent advances in dopamine D 2 receptor ligands in the treatment of neuropsychiatric disorders. Med Res Rev 2023; 43:55-211. [PMID: 36111795 DOI: 10.1002/med.21923] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023]
Abstract
Dopamine is a biologically active amine synthesized in the central and peripheral nervous system. This biogenic monoamine acts by activating five types of dopamine receptors (D1-5 Rs), which belong to the G protein-coupled receptor family. Antagonists and partial agonists of D2 Rs are used to treat schizophrenia, Parkinson's disease, depression, and anxiety. The typical pharmacophore with high D2 R affinity comprises four main areas, namely aromatic moiety, cyclic amine, central linker and aromatic/heteroaromatic lipophilic fragment. From the literature reviewed herein, we can conclude that 4-(2,3-dichlorophenyl), 4-(2-methoxyphenyl)-, 4-(benzo[b]thiophen-4-yl)-1-substituted piperazine, and 4-(6-fluorobenzo[d]isoxazol-3-yl)piperidine moieties are critical for high D2 R affinity. Four to six atoms chains are optimal for D2 R affinity with 4-butoxyl as the most pronounced one. The bicyclic aromatic/heteroaromatic systems are most frequently occurring as lipophilic appendages to retain high D2 R affinity. In this review, we provide a thorough overview of the therapeutic potential of D2 R modulators in the treatment of the aforementioned disorders. In addition, this review summarizes current knowledge about these diseases, with a focus on the dopaminergic pathway underlying these pathologies. Major attention is paid to the structure, function, and pharmacology of novel D2 R ligands, which have been developed in the last decade (2010-2021), and belong to the 1,4-disubstituted aromatic cyclic amine group. Due to the abundance of data, allosteric D2 R ligands and D2 R modulators from patents are not discussed in this review.
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Affiliation(s)
- Radomir Juza
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Eva Mezeiova
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Korabecny
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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5
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Chen X, Yuan Y, Chen Y, Yu J, Wang J, Chen J, Guo Y, Pu X. Biased Activation Mechanism Induced by GPCR Heterodimerization: Observations from μOR/δOR Dimers. J Chem Inf Model 2022; 62:5581-5600. [PMID: 36377848 DOI: 10.1021/acs.jcim.2c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
GPCRs regulate multiple intracellular signaling cascades. Biasedly activating one signaling pathway over the others provides additional clinical utility to optimize GPCR-based therapies. GPCR heterodimers possess different functions from their monomeric states, including their selectivity to different transducers. However, the biased signaling mechanism induced by the heterodimerization remains unclear. Motivated by the issue, we select an important GPCR heterodimer (μOR/δOR heterodimer) as a case and use microsecond Gaussian accelerated molecular dynamics simulation coupled with potential of mean force and protein structure network (PSN) to probe mechanisms regarding the heterodimerization-induced constitutive β-arrestin activity and efficacy change of the agonist DAMGO. The results show that only the lowest energy state of the μOR/δOR heterodimer, which adopts a slightly outward shift of TM6 and an ICL2 conformation close to the receptor core, can selectively accommodate β-arrestins. PSN further reveals important roles of H8, ICL1, and ICL2 in regulating the constitutive β-arrestin-biased activity for the apo μOR/δOR heterodimer. In addition, the heterodimerization can allosterically alter the binding mode of DAMGO mainly by means of W7.35. Consequently, DAMGO transmits the structural signal mainly through TM6 and TM7 in the dimer, rather than TM3 similar to the μOR monomer, thus changing the efficacy of DAMGO from a balanced agonist to the β-arrestin-biased one. On the other side, the binding of DAMGO to the heterodimer can stabilize μOR/δOR heterodimers through a stronger interaction of TM1/TM1 and H8/H8, accordingly enhancing the interaction of μOR with δOR and the binding affinity of the dimer to the β-arrestin. The agonist DAMGO does not change main compositions of the regulation network from the dimer interface to the transducer binding pocket of the μOR protomer, but induces an increase in the structural communication of the network, which should contribute to the enhanced β-arrestin coupling. Our observations, for the first time, reveal the molecular mechanism of the biased signaling induced by the heterodimerization for GPCRs, which should be beneficial to more comprehensively understand the GPCR bias signaling.
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Affiliation(s)
- Xin Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu610041, China
| | - Yichi Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jin Yu
- Department of Physics and Astronomy, University of California, Irvine, California92697, United States
| | - Jingzhou Wang
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu610064, China
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6
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Paradis JS, Feng X, Murat B, Jefferson RE, Sokrat B, Szpakowska M, Hogue M, Bergkamp ND, Heydenreich FM, Smit MJ, Chevigné A, Bouvier M, Barth P. Computationally designed GPCR quaternary structures bias signaling pathway activation. Nat Commun 2022; 13:6826. [PMID: 36369272 PMCID: PMC9652377 DOI: 10.1038/s41467-022-34382-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
Communication across membranes controls critical cellular processes and is achieved by receptors translating extracellular signals into selective cytoplasmic responses. While receptor tertiary structures can be readily characterized, receptor associations into quaternary structures are challenging to study and their implications in signal transduction remain poorly understood. Here, we report a computational approach for predicting receptor self-associations, and designing receptor oligomers with various quaternary structures and signaling properties. Using this approach, we designed chemokine receptor CXCR4 dimers with reprogrammed binding interactions, conformations, and abilities to activate distinct intracellular signaling proteins. In agreement with our predictions, the designed CXCR4s dimerized through distinct conformations and displayed different quaternary structural changes upon activation. Consistent with the active state models, all engineered CXCR4 oligomers activated the G protein Gi, but only specific dimer structures also recruited β-arrestins. Overall, we demonstrate that quaternary structures represent an important unforeseen mechanism of receptor biased signaling and reveal the existence of a bias switch at the dimer interface of several G protein-coupled receptors including CXCR4, mu-Opioid and type-2 Vasopressin receptors that selectively control the activation of G proteins vs β-arrestin-mediated pathways. The approach should prove useful for predicting and designing receptor associations to uncover and reprogram selective cellular signaling functions.
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Affiliation(s)
- Justine S Paradis
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Xiang Feng
- Interfaculty Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Brigitte Murat
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Robert E Jefferson
- Interfaculty Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Badr Sokrat
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Martyna Szpakowska
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Mireille Hogue
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Nick D Bergkamp
- Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Franziska M Heydenreich
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Martine J Smit
- Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Andy Chevigné
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC, H3T 1J4, Canada.
| | - Patrick Barth
- Interfaculty Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
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7
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Caniceiro AB, Bueschbell B, Schiedel AC, Moreira IS. Class A and C GPCR Dimers in Neurodegenerative Diseases. Curr Neuropharmacol 2022; 20:2081-2141. [PMID: 35339177 PMCID: PMC9886835 DOI: 10.2174/1570159x20666220327221830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 11/22/2022] Open
Abstract
Neurodegenerative diseases affect over 30 million people worldwide with an ascending trend. Most individuals suffering from these irreversible brain damages belong to the elderly population, with onset between 50 and 60 years. Although the pathophysiology of such diseases is partially known, it remains unclear upon which point a disease turns degenerative. Moreover, current therapeutics can treat some of the symptoms but often have severe side effects and become less effective in long-term treatment. For many neurodegenerative diseases, the involvement of G proteincoupled receptors (GPCRs), which are key players of neuronal transmission and plasticity, has become clearer and holds great promise in elucidating their biological mechanism. With this review, we introduce and summarize class A and class C GPCRs, known to form heterodimers or oligomers to increase their signalling repertoire. Additionally, the examples discussed here were shown to display relevant alterations in brain signalling and had already been associated with the pathophysiology of certain neurodegenerative diseases. Lastly, we classified the heterodimers into two categories of crosstalk, positive or negative, for which there is known evidence.
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Affiliation(s)
- Ana B. Caniceiro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Beatriz Bueschbell
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Anke C. Schiedel
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany;
| | - Irina S. Moreira
- University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; ,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal,Address correspondence to this author at the Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal; E-mail:
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8
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Ricci V, Ronco F, Musilova Z, Salzburger W. Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika. Mol Ecol 2022; 31:2882-2897. [PMID: 35302684 PMCID: PMC9314932 DOI: 10.1111/mec.16429] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/11/2022] [Accepted: 03/04/2022] [Indexed: 11/29/2022]
Abstract
The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim‐light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in virtually the entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the environmental light with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth‐related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability and 11 sites that may be functionally important on the basis of their physicochemical properties. Among the strongest candidate sites for deep‐water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is the first comprehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.
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Affiliation(s)
- Virginie Ricci
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Fabrizia Ronco
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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9
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Ito RK, Harada S, Tabata R, Watanabe K. Molecular evolution and convergence of the rhodopsin gene in Gymnogobius, a goby group having diverged into coastal to freshwater habitats. J Evol Biol 2021; 35:333-346. [PMID: 34689368 DOI: 10.1111/jeb.13955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022]
Abstract
Adaptive evolution of vision-related genes has been frequently observed in the process of invasion of new environments in a wide range of animal taxa. The typical example is that of the molecular evolution of rhodopsin associated with habitat changes in aquatic animals. However, few studies have investigated rhodopsin evolution during adaptive radiation across various habitats. In the present study, we examined the link between molecular evolutionary patterns in the rhodopsin gene and macroscopic habitat changes in Gymnogobius species (Gobiidae), which have adaptively radiated to diverse aquatic habitats including the sea, brackish waters, rivers and lakes. Analysis of amino acid substitutions in rhodopsin in the phylogenetic framework revealed convergent substitutions in 4-5 amino acids in three groups (four species), including two spectral tuning amino acid sites known to change rhodopsin's absorption wavelength. Positive selection was detected in the basal branches of each of these three groups, suggesting adaptive molecular convergence of rhodopsin. However, no significant correlation was observed between amino acid substitutions and the species' habitat changes, suggesting molecular adaptation to some unidentified micro-ecological environments. Taken together, these results emphasize the importance of considering not only macroscopic habitats but also micro-ecological environments when elucidating the driving forces of adaptive evolution of the visual system.
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Affiliation(s)
- Ryosuke K Ito
- Division of Biological Sciences, Department of Zoology, Graduate School of Science, Kyoto University, Kyoto City, Japan
| | - Shigeo Harada
- Resource Management Division, Fisheries Bureau, Agriculture, Forestry and Fisheries Department, Wakayama Prefectural Government, Wakayama City, Japan
| | | | - Katsutoshi Watanabe
- Division of Biological Sciences, Department of Zoology, Graduate School of Science, Kyoto University, Kyoto City, Japan
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10
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El Khamlichi C, Cobret L, Arrang JM, Morisset-Lopez S. BRET Analysis of GPCR Dimers in Neurons and Non-Neuronal Cells: Evidence for Inactive, Agonist, and Constitutive Conformations. Int J Mol Sci 2021; 22:ijms221910638. [PMID: 34638980 PMCID: PMC8508734 DOI: 10.3390/ijms221910638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) are dimeric proteins, but the functional consequences of the process are still debated. Active GPCR conformations are promoted either by agonists or constitutive activity. Inverse agonists decrease constitutive activity by promoting inactive conformations. The histamine H3 receptor (H3R) is the target of choice for the study of GPCRs because it displays high constitutive activity. Here, we study the dimerization of recombinant and brain H3R and explore the effects of H3R ligands of different intrinsic efficacy on dimerization. Co-immunoprecipitations and Western blots showed that H3R dimers co-exist with monomers in transfected HEK 293 cells and in rodent brains. Bioluminescence energy transfer (BRET) analysis confirmed the existence of spontaneous H3R dimers, not only in living HEK 293 cells but also in transfected cortical neurons. In both cells, agonists and constitutive activity of the H3R decreased BRET signals, whereas inverse agonists and GTPγS, which promote inactive conformations, increased BRET signals. These findings show the existence of spontaneous H3R dimers not only in heterologous systems but also in native tissues, which are able to adopt a number of allosteric conformations, from more inactive to more active states.
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Affiliation(s)
- Chayma El Khamlichi
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Université d’Orléans, Rue Charles Sadron, CEDEX 2, 45071 Orléans, France; (C.E.K.); (L.C.)
| | - Laetitia Cobret
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Université d’Orléans, Rue Charles Sadron, CEDEX 2, 45071 Orléans, France; (C.E.K.); (L.C.)
| | - Jean-Michel Arrang
- Centre de Psychiatrie et Neurosciences, 2 ter Rue d’Alésia, 75014 Paris, France;
- Institut de Psychiatrie et Neurosciences de Paris, UMR_S1266 INSERM, Université Paris Descartes, 102 Rue de la Santé, 75014 Paris, France
| | - Séverine Morisset-Lopez
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Université d’Orléans, Rue Charles Sadron, CEDEX 2, 45071 Orléans, France; (C.E.K.); (L.C.)
- Institut de Psychiatrie et Neurosciences de Paris, UMR_S1266 INSERM, Université Paris Descartes, 102 Rue de la Santé, 75014 Paris, France
- Correspondence: ; Tel.: +33-238257858
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11
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Plante A, Weinstein H. Ligand-Dependent Conformational Transitions in Molecular Dynamics Trajectories of GPCRs Revealed by a New Machine Learning Rare Event Detection Protocol. Molecules 2021; 26:molecules26103059. [PMID: 34065494 PMCID: PMC8161244 DOI: 10.3390/molecules26103059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 01/14/2023] Open
Abstract
Central among the tools and approaches used for ligand discovery and design are Molecular Dynamics (MD) simulations, which follow the dynamic changes in molecular structure in response to the environmental condition, interactions with other proteins, and the effects of ligand binding. The need for, and successes of, MD simulations in providing this type of essential information are well documented, but so are the challenges presented by the size of the resulting datasets encoding the desired information. The difficulty of extracting information on mechanistically important state-to-state transitions in response to ligand binding and other interactions is compounded by these being rare events in the MD trajectories of complex molecular machines, such as G-protein-coupled receptors (GPCRs). To address this problem, we have developed a protocol for the efficient detection of such events. We show that the novel Rare Event Detection (RED) protocol reveals functionally relevant and pharmacologically discriminating responses to the binding of different ligands to the 5-HT2AR orthosteric site in terms of clearly defined, structurally coherent, and temporally ordered conformational transitions. This information from the RED protocol offers new insights into specific ligand-determined functional mechanisms encoded in the MD trajectories, which opens a new and rigorously reproducible path to understanding drug activity with application in drug discovery.
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Affiliation(s)
- Ambrose Plante
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA;
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA;
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
- Correspondence: ; Tel.: +1-212-746-6358
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12
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Qian M, Ricarte A, Wouters E, Dalton JAR, Risseeuw MDP, Giraldo J, Van Calenbergh S. Discovery of a true bivalent dopamine D 2 receptor agonist. Eur J Med Chem 2021; 212:113151. [PMID: 33450620 DOI: 10.1016/j.ejmech.2020.113151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/06/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
Employing two different alkyne-modified dopamine agonists to construct bivalent compounds via click chemistry resulted in the identification of a bivalent ligand (11c) for dopamine D2 receptor homodimer, which, compared to its parent monomeric alkyne, showed a 16-fold higher binding affinity for the dopamine D2 receptor and a 5-fold higher potency in a cAMP assay in HEK 293T cells stably expressing D2R. Molecular modeling revealed that 11c can indeed bridge the orthosteric binding sites of a D2R homodimer in a relaxed conformation via the TM5-TM6 interface and allows to largely rationalize the results of the receptor assays.
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Affiliation(s)
- Mingcheng Qian
- Department of Medicinal Chemistry, School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China; Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Adrián Ricarte
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigaciói InnovacióParc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Elise Wouters
- Laboratory of Toxicology, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigaciói InnovacióParc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigaciói InnovacióParc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium.
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13
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Han X, Hofmann L, de la Fuente M, Alexander N, Palczewski K, Nieman MT. PAR4 activation involves extracellular loop 3 and transmembrane residue Thr153. Blood 2020; 136:2217-2228. [PMID: 32575122 PMCID: PMC7645988 DOI: 10.1182/blood.2019004634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/24/2020] [Indexed: 12/17/2022] Open
Abstract
Protease-activated receptor 4 (PAR4) mediates sustained thrombin signaling in platelets and is required for a stable thrombus. PAR4 is activated by proteolysis of the N terminus to expose a tethered ligand. The structural basis for PAR4 activation and the location of its ligand binding site (LBS) are unknown. Using hydrogen/deuterium exchange (H/D exchange), computational modeling, and signaling studies, we determined the molecular mechanism for tethered ligand-mediated PAR4 activation. H/D exchange identified that the LBS is composed of transmembrane 3 (TM3) domain and TM7. Unbiased computational modeling further predicted an interaction between Gly48 from the tethered ligand and Thr153 from the LBS. Mutating Thr153 significantly decreased PAR4 signaling. H/D exchange and modeling also showed that extracellular loop 3 (ECL3) serves as a gatekeeper for the interaction between the tethered ligand and LBS. A naturally occurring sequence variant (P310L, rs2227376) and 2 experimental mutations (S311A and P312L) determined that the rigidity conferred by prolines in ECL3 are essential for PAR4 activation. Finally, we examined the role of the polymorphism at position 310 in venous thromboembolism (VTE) using the International Network Against Venous Thrombosis (INVENT) consortium multi-ancestry genome-wide association study (GWAS) meta-analysis. Individuals with the PAR4 Leu310 allele had a 15% reduction in relative risk for VTE (odds ratio, 0.85; 95% confidence interval, 0.77-0.94) compared with the Pro310 allele. These data are consistent with our H/D exchange, molecular modeling, and signaling studies. In conclusion, we have uncovered the structural basis for PAR4 activation and identified a previously unrecognized role for PAR4 in VTE.
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Affiliation(s)
- Xu Han
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
| | - Lukas Hofmann
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
| | | | - Nathan Alexander
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
| | | | - Marvin T Nieman
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
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14
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Structural Complexity and Plasticity of Signaling Regulation at the Melanocortin-4 Receptor. Int J Mol Sci 2020; 21:ijms21165728. [PMID: 32785054 PMCID: PMC7460885 DOI: 10.3390/ijms21165728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
The melanocortin-4 receptor (MC4R) is a class A G protein-coupled receptor (GPCR), essential for regulation of appetite and metabolism. Pathogenic inactivating MC4R mutations are the most frequent cause of monogenic obesity, a growing medical and socioeconomic problem worldwide. The MC4R mediates either ligand-independent or ligand-dependent signaling. Agonists such as α-melanocyte-stimulating hormone (α-MSH) induce anorexigenic effects, in contrast to the endogenous inverse agonist agouti-related peptide (AgRP), which causes orexigenic effects by suppressing high basal signaling activity. Agonist action triggers the binding of different subtypes of G proteins and arrestins, leading to concomitant induction of diverse intracellular signaling cascades. An increasing number of experimental studies have unraveled molecular properties and mechanisms of MC4R signal transduction related to physiological and pathophysiological aspects. In addition, the MC4R crystal structure was recently determined at 2.75 Å resolution in an inactive state bound with a peptide antagonist. Underpinned by structural homology models of MC4R complexes simulating a presumably active-state conformation compared to the structure of the inactive state, we here briefly summarize the current understanding and key players involved in the MC4R switching process between different activity states. Finally, these perspectives highlight the complexity and plasticity in MC4R signaling regulation and identify gaps in our current knowledge.
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15
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Saito A, Tsuchiya D, Sato S, Okamoto A, Murakami Y, Mizuguchi K, Toh H, Nemoto W. Update of the GRIP web service. J Recept Signal Transduct Res 2020; 40:348-356. [PMID: 32148150 DOI: 10.1080/10799893.2020.1734821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
G protein-coupled receptors (GPCRs) can form homodimers, heterodimers, or higher-order molecular complexes (oligomers). The reports on the change of functions through the oligomerization have been accumulated. Inhibition of GPCR oligomerization without affecting the protomer's overall structure would clarify the oligomer-specific functions although inhibition experiments are costly and require accurate information about the interface location. Unfortunately, the number of experimentally determined interfaces is limited. The precise prediction of the oligomerization interfaces is, therefore, useful for inhibition experiments to examine the oligomer-specific functions, which would accelerate investigations of the GPCR signaling. However, interface prediction for GPCR oligomerization is difficult because different GPCR subtypes belonging to the same subfamily often use different structural regions as their interfaces. We previously developed a high-performance method to predict the interfaces for GPCR oligomerization, by identifying the conserved surfaces with the sequence and structure information. Then, the structural characteristic of a GPCR structure is regarded to be a thick-tube like conformation that is approximately perpendicular to the membrane plane. Our method had successfully predicted all of the interfaces available on that day. We had launched a web server for our interface prediction of GPCRs (GRIP). We have improved the previous version of GRIP server and enhanced its usability. First, we discarded the approximation of the GPCR structure as the thick-tube-like conformation. This improvement increased the number of structures for the prediction. Second, the FUGUE-based template recommendation service was introduced to facilitate the choice of an appropriate structure for the prediction. The new prediction server is available at http://grip.b.dendai.ac.jp/∼grip/.
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Affiliation(s)
- Akira Saito
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University (TDU), Tokyo, Japan
| | - Daiki Tsuchiya
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University (TDU), Tokyo, Japan
| | | | | | - Yoichi Murakami
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Institute for Protein Research, Osaka University, Osaka, Japan.,Department of Informatics, Tokyo University of Information Sciences, Tokyo, Japan
| | - Kenji Mizuguchi
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hiroyuki Toh
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Nishinomiya, Japan
| | - Wataru Nemoto
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University (TDU), Tokyo, Japan.,Department of Life Science and Engineering, Division of Life Science and Engineering, Tokyo Denki University (TDU), Tokyo, Japan
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16
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Firouzabadi N, Navabzadeh N, Moghimi-Sarani E, Haghnegahdar M. Orexin/Hypocretin Type 2 Receptor (HCRTR2) Gene as a Candidate Gene in Sertraline-Associated Insomnia in Depressed Patients. Neuropsychiatr Dis Treat 2020; 16:1121-1128. [PMID: 32440126 PMCID: PMC7210038 DOI: 10.2147/ndt.s250141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/22/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Selective serotonin reuptake inhibitors (SSRIs) are considered as first-line drugs for treating depressive disorders. Among the adverse effects reported with sertraline is sleep disturbances; however, the etiology lying beneath is obscure. Orexin, the most recently discovered neurotransmitter, is involved in the sleep cycle. It exerts its physiological actions through orexin or hypocretin type 1 and 2 receptors (HCRTR1 and HCRTR2). Dysfunction of the orexin system contributes to various psychiatric, neurologic and neuropsychiatric disorders. Thus, our study aimed to assess the possible association of genetic variation of HCRTR2 G1246A with hypersomnia reported with sertraline in a group of major depressive disorder (MDD) patients. PATIENTS AND METHODS Ninety-six newly diagnosed MDD patients were enrolled in our cohort study. MDD was assessed using DSM-V criteria. Insomnia Severity Index (ISI) was used to assess insomnia at baseline (week 0) and week 4. Blood samples were collected for further genotyping of HCRTR2 G1246A (rs2653349) using polymerase chain reaction-restriction fragment length polymorphism. RESULTS A significant association between G1264A polymorphism of HCRTR2 and insomnia was observed. Insomnia with sertraline happens by 2.5-fold (P=0.022; odds ratio (OR)=2.5; 95% confidence interval (CI): 1.1-5.7) in patients having GG genotype. Patients with G allele experience insomnia by 2.1-fold more than A allele carriers (P=0.022; OR=2.1; 95% CI= 1.1-4.0). Subgroup analysis showed a significant association between GG genotype as well as the G allele and insomnia only in female MDD patients (P=0.011; OR=4.0; 95% CI=1.3-12.0 and P=0.033; OR=2.4; 95% CI=1.02-5.7, respectively). CONCLUSION In conclusion, the G1246A variant might be a predictor for insomnia in MDD patients treated with sertraline. Our findings support the idea that some variants of the HCRTR might contribute to inter-individual variability in the sleep pattern of patients receiving antidepressants.
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Affiliation(s)
- Negar Firouzabadi
- Department of Pharmacology and Toxicology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Niloofar Navabzadeh
- Department of Pharmacology and Toxicology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ebrahim Moghimi-Sarani
- Department of Psychiatry, School of Medicine, Shiraz University of Medical Sciences, School of Medicine, Shiraz, Iran
| | - Maral Haghnegahdar
- Department of Pharmacology and Toxicology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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17
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Ferré S, Ciruela F, Casadó V, Pardo L. Oligomerization of G protein-coupled receptors: Still doubted? PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:297-321. [DOI: 10.1016/bs.pmbts.2019.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Li Y, Wang M, Gao N, Li D, Lin J. The effect of dimerization on the activation and conformational dynamics of adenosine A 1 receptor. Phys Chem Chem Phys 2019; 21:22763-22773. [PMID: 31595279 DOI: 10.1039/c9cp04060a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adenosine A1 receptor (A1R) is one of four adenosine receptors in humans, which are involved in the function of the cardiovascular, respiratory and central nervous systems. Experimental results indicate that A1R can form a homodimer and that the protomer-protomer interaction in the A1R dimer is related to certain pharmacological characteristics of A1R activation. In this work, we performed docking, metadynamics simulation, conventional molecular dynamics simulations, Gaussian-accelerated molecular dynamics simulations, potential of mean force calculations, dynamic cross-correlation motions analysis and community network analysis to study the binding mode of 5'-N-ethylcarboxamidoadenosine (NECA) to A1R and the effect of dimerization on the activation of A1R. Our results show that NECA binds to A1R in a similar mode to adenosine in the A1R crystal structure and NECA in the A2AR crystal structure. The A1R homodimer can be activated by one or two agonists with NECA occupying its orthosteric pockets in one (which we call the NECA-A1R system) or both protomers (which we call the dNECA-A1R system). In the NECA-A1R system, activation is predicated in the protomer without NECA bound. In the dNECA-A1R system, only one protomer achieves the active state. These findings suggest an asymmetrical activation mechanism of the homodimer and a negative cooperativity between the two protomers. We envision that our results may further facilitate the drug development of A1R.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
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19
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Zhao DY, Pöge M, Morizumi T, Gulati S, Van Eps N, Zhang J, Miszta P, Filipek S, Mahamid J, Plitzko JM, Baumeister W, Ernst OP, Palczewski K. Cryo-EM structure of the native rhodopsin dimer in nanodiscs. J Biol Chem 2019; 294:14215-14230. [PMID: 31399513 DOI: 10.1074/jbc.ra119.010089] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/02/2019] [Indexed: 02/03/2023] Open
Abstract
Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy and cryo-electron tomography has revealed that the visual pigment rhodopsin, a prototypical class A G protein-coupled receptor (GPCR), can organize as rows of dimers. GPCR dimerization and oligomerization offer possibilities for allosteric regulation of GPCR activity, but the detailed structures and mechanism remain elusive. In this investigation, we made use of the high rhodopsin density in the native disc membranes and of a bifunctional cross-linker that preserves the native rhodopsin arrangement by covalently tethering rhodopsins via Lys residue side chains. We purified cross-linked rhodopsin dimers and reconstituted them into nanodiscs for cryo-EM analysis. We present cryo-EM structures of the cross-linked rhodopsin dimer as well as a rhodopsin dimer reconstituted into nanodiscs from purified monomers. We demonstrate the presence of a preferential 2-fold symmetrical dimerization interface mediated by transmembrane helix 1 and the cytoplasmic helix 8 of rhodopsin. We confirmed this dimer interface by double electron-electron resonance measurements of spin-labeled rhodopsin. We propose that this interface and the arrangement of two protomers is a prerequisite for the formation of the observed rows of dimers. We anticipate that the approach outlined here could be extended to other GPCRs or membrane receptors to better understand specific receptor dimerization mechanisms.
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Affiliation(s)
- Dorothy Yanling Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthias Pöge
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jianye Zhang
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Przemyslaw Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697 .,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
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20
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Fongang B, Cunningham KA, Rowicka M, Kudlicki A. Coevolution of Residues Provides Evidence of a Functional Heterodimer of 5-HT 2AR and 5-HT 2CR Involving Both Intracellular and Extracellular Domains. Neuroscience 2019; 412:48-59. [PMID: 31158438 PMCID: PMC7299066 DOI: 10.1016/j.neuroscience.2019.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
Abstract
Serotonin is a neurotransmitter that plays a role in regulating activities such as sleep, appetite, mood and substance abuse disorders; serotonin receptors 5-HT2AR and 5-HT2CR are active within pathways associated with substance abuse. It has been suggested that 5-HT2AR and 5-HT2CR may form a dimer that affects behavioral processes. Here we study the coevolution of residues in 5-HT2AR and 5-HT2CR to identify potential interactions between residues in both proteins. Coevolution studies can detect protein interactions, and since the thus uncovered interactions are subject to evolutionary pressure, they are likely functional. We assessed the significance of the 5-HT2AR/5-HT2CR interactions using randomized phylogenetic trees and found the coevolution significant (p-value = 0.01). We also discuss how co-expression of the receptors suggests the predicted interaction is functional. Finally, we analyze how several single nucleotide polymorphisms for the 5-HT2AR and 5-HT2CR genes affect their interaction. Our findings are the first to characterize the binding interface of 5-HT2AR/5-HT2CR and indicate a correlation between this interface and location of SNPs in both proteins.
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MESH Headings
- Animals
- Databases, Genetic
- Evolution, Molecular
- Papio anubis
- Phosphorylation
- Receptor, Serotonin, 5-HT2A/genetics
- Receptor, Serotonin, 5-HT2A/metabolism
- Receptor, Serotonin, 5-HT2C/genetics
- Receptor, Serotonin, 5-HT2C/metabolism
- Transcriptome
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Affiliation(s)
- Bernard Fongang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UTHSCSA, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, UTHSCSA, San Antonio, TX 78229, USA; Department of Epidemiology and Biostatistics, UTHSCSA, San Antonio, TX 78229, USA.
| | - Kathryn A Cunningham
- Center for Addiction Research and Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrzej Kudlicki
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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Townsend-Nicholson A, Altwaijry N, Potterton A, Morao I, Heifetz A. Computational prediction of GPCR oligomerization. Curr Opin Struct Biol 2019; 55:178-184. [PMID: 31170578 DOI: 10.1016/j.sbi.2019.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 01/08/2023]
Abstract
There has been a recent and prolific expansion in the number of GPCR crystal structures being solved: in both active and inactive forms and in complex with ligand, with G protein and with each other. Despite this, there is relatively little experimental information about the precise configuration of GPCR oligomers during these different biologically relevant states. While it may be possible to identify the experimental conditions necessary to crystallize a GPCR preferentially in a specific structural conformation, computational approaches afford a potentially more tractable means of describing the probability of formation of receptor dimers and higher order oligomers. Ensemble-based computational methods based on structurally determined dimers, coupled with a computational workflow that uses quantum mechanical methods to analyze the chemical nature of the molecular interactions at a GPCR dimer interface, will generate the reproducible and accurate predictions needed to predict previously unidentified GPCR dimers and to inform future advances in our ability to understand and begin to precisely manipulate GPCR oligomers in biological systems. It may also provide information needed to achieve an increase in the number of experimentally determined oligomeric GPCR structures.
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Affiliation(s)
- Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
| | - Nojood Altwaijry
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Andrew Potterton
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Inaki Morao
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Alexander Heifetz
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
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22
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Pin JP, Kniazeff J, Prézeau L, Liu JF, Rondard P. GPCR interaction as a possible way for allosteric control between receptors. Mol Cell Endocrinol 2019; 486:89-95. [PMID: 30849406 DOI: 10.1016/j.mce.2019.02.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 12/17/2022]
Abstract
For more than twenty years now, GPCR dimers and larger oligomers have been the subject of intense debates. Evidence for a role of such complexes in receptor trafficking to and from the plasma membrane have been provided. However, one main issue is of course to determine whether or not such a phenomenon can be responsible for an allosteric and reciprocal control (allosteric control) of the subunits. Such a possibility would indeed add to the possible ways a cell integrates various signals targeting GPCRs. Among the large GPCR family, the class C receptors that include mGlu and GABAB receptors, represent excellent models to examine such a possibility as they are mandatory dimers. In the present review, we will report on the observed allosteric interaction between the subunits of class C GPCRs, both mGluRs and GABABRs, and on the structural bases of these interactions. We will then discuss these findings for other GPCR types such as the rhodopsin-like class A receptors. We will show that many of the observations made with class C receptors have also been reported with class A receptors, suggesting that the mechanisms involved in the allosteric control between subunits in GPCR dimers may not be unique to class C GPCRs.
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Affiliation(s)
- Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France.
| | - Julie Kniazeff
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Laurent Prézeau
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Jiang-Feng Liu
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
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23
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Zhang F, Yuan Y, Xiang M, Guo Y, Li M, Liu Y, Pu X. Molecular Mechanism Regarding Allosteric Modulation of Ligand Binding and the Impact of Mutations on Dimerization for CCR5 Homodimer. J Chem Inf Model 2019; 59:1965-1976. [DOI: 10.1021/acs.jcim.8b00850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Fuhui Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, People’s Republic of China
| | - Minghui Xiang
- College of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Yijing Liu
- College of Computer Science, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
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24
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Heyder N, Kleinau G, Szczepek M, Kwiatkowski D, Speck D, Soletto L, Cerdá-Reverter JM, Krude H, Kühnen P, Biebermann H, Scheerer P. Signal Transduction and Pathogenic Modifications at the Melanocortin-4 Receptor: A Structural Perspective. Front Endocrinol (Lausanne) 2019; 10:515. [PMID: 31417496 PMCID: PMC6685040 DOI: 10.3389/fendo.2019.00515] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) can be endogenously activated by binding of melanocyte-stimulating hormones (MSH), which mediates anorexigenic effects. In contrast, the agouti-related peptide (AgRP) acts as an endogenous inverse agonist and suppresses ligand-independent basal signaling activity (orexigenic effects). Binding of ligands to MC4R leads to the activation of different G-protein subtypes or arrestin and concomitant signaling pathways. This receptor is a key protein in the hypothalamic regulation of food intake and energy expenditure and naturally-occurring inactivating MC4R variants are the most frequent cause of monogenic obesity. In general, obesity is a growing problem on a global scale and is of social, medical, and economic relevance. A significant goal is to develop optimized pharmacological tools targeting MC4R without adverse effects. To date, this has not been achieved because of inter alia non-selective ligands across the five functionally different MCR subtypes (MC1-5R). This motivates further investigation of (i) the three-dimensional MC4R structure, (ii) binding mechanisms of various ligands, and (iii) the molecular transfer process of signal transduction, with the aim of understanding how structural features are linked with functional-physiological aspects. Unfortunately, experimentally elucidated structural information is not yet available for the MC receptors, a group of class A G-protein coupled receptors (GPCRs). We, therefore, generated MC4R homology models and complexes with interacting partners to describe approximate structural properties associated with signaling mechanisms. In addition, molecular insights from pathogenic mutations were incorporated to discriminate more precisely their individual malfunction of the signal transfer mechanism.
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Affiliation(s)
- Nicolas Heyder
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- *Correspondence: Gunnar Kleinau
| | - Michal Szczepek
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dennis Kwiatkowski
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Speck
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lucia Soletto
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - José Miguel Cerdá-Reverter
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Kühnen
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Patrick Scheerer
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25
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Qian M, Wouters E, Dalton JAR, Risseeuw MDP, Crans RAJ, Stove C, Giraldo J, Van Craenenbroeck K, Van Calenbergh S. Synthesis toward Bivalent Ligands for the Dopamine D 2 and Metabotropic Glutamate 5 Receptors. J Med Chem 2018; 61:8212-8225. [PMID: 30180563 DOI: 10.1021/acs.jmedchem.8b00671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this study, we designed and synthesized heterobivalent ligands targeting heteromers consisting of the metabotropic glutamate 5 receptor (mGluR5) and the dopamine D2 receptor (D2R). Bivalent ligand 22a with a linker consisting of 20 atoms showed 4-fold increase in affinity for cells coexpressing D2R and mGluR5 compared to cells solely expressing D2R. Likewise, the affinity of 22a for mGluR5 increased 2-fold in the coexpressing cells. Additionally, 22a exhibited a 5-fold higher mGluR5 affinity than its monovalent precursor 21a in cells coexpressing D2R and mGluR5. These results indicate that 22a is able to bridge binding sites on both receptors constituting the heterodimer. Likewise, cAMP assays revealed that 22a had a 4-fold higher potency in stable D2R and mGluR5 coexpressing cell lines than 1. Furthermore, molecular modeling reveals that 22a is able to simultaneously bind both receptors by passing between the TM5-TM6 interface and establishing six protein-ligand H-bonds.
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Affiliation(s)
- Mingcheng Qian
- Laboratory for Medicinal Chemistry (FFW) , Ghent University , Ottergemsesteenweg 460 , B-9000 Ghent , Belgium.,Laboratory of Toxicology , Ghent University , Ottergemsesteenweg 460 , B-9000 Ghent , Belgium
| | - Elise Wouters
- Laboratory of Toxicology , Ghent University , Ottergemsesteenweg 460 , B-9000 Ghent , Belgium
| | - James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry (FFW) , Ghent University , Ottergemsesteenweg 460 , B-9000 Ghent , Belgium
| | - René A J Crans
- Laboratory of Toxicology , Ghent University , Ottergemsesteenweg 460 , B-9000 Ghent , Belgium
| | - Christophe Stove
- Laboratory of Toxicology , Ghent University , Ottergemsesteenweg 460 , B-9000 Ghent , Belgium
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain.,Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain.,Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | | | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW) , Ghent University , Ottergemsesteenweg 460 , B-9000 Ghent , Belgium
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26
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Borroto-Escuela DO, Rodriguez D, Romero-Fernandez W, Kapla J, Jaiteh M, Ranganathan A, Lazarova T, Fuxe K, Carlsson J. Mapping the Interface of a GPCR Dimer: A Structural Model of the A 2A Adenosine and D 2 Dopamine Receptor Heteromer. Front Pharmacol 2018; 9:829. [PMID: 30214407 PMCID: PMC6125358 DOI: 10.3389/fphar.2018.00829] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The A2A adenosine (A2AR) and D2 dopamine (D2R) receptors form oligomers in the cell membrane and allosteric interactions across the A2AR–D2R heteromer represent a target for development of drugs against central nervous system disorders. However, understanding of the molecular determinants of A2AR–D2R heteromerization and the allosteric antagonistic interactions between the receptor protomers is still limited. In this work, a structural model of the A2AR–D2R heterodimer was generated using a combined experimental and computational approach. Regions involved in the heteromer interface were modeled based on the effects of peptides derived from the transmembrane (TM) helices on A2AR–D2R receptor–receptor interactions in bioluminescence resonance energy transfer (BRET) and proximity ligation assays. Peptides corresponding to TM-IV and TM-V of the A2AR blocked heterodimer interactions and disrupted the allosteric effect of A2AR activation on D2R agonist binding. Protein–protein docking was used to construct a model of the A2AR–D2R heterodimer with a TM-IV/V interface, which was refined using molecular dynamics simulations. Mutations in the predicted interface reduced A2AR–D2R interactions in BRET experiments and altered the allosteric modulation. The heterodimer model provided insights into the structural basis of allosteric modulation and the technique developed to characterize the A2AR–D2R interface can be extended to study the many other G protein-coupled receptors that engage in heteroreceptor complexes.
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Affiliation(s)
| | - David Rodriguez
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Wilber Romero-Fernandez
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jon Kapla
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mariama Jaiteh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anirudh Ranganathan
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Tzvetana Lazarova
- Department of Biochemistry and Molecular Biology, Institute of Neuroscience, Faculty of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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27
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The Heptahelical Domain of the Sweet Taste Receptor T1R2 Is a New Allosteric Binding Site for the Sweet Taste Modulator Amiloride That Modulates Sweet Taste in a Species-Dependent Manner. J Mol Neurosci 2018; 66:207-213. [PMID: 30120716 DOI: 10.1007/s12031-018-1156-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022]
Abstract
The activity of sweet taste receptor (heterodimeric T1R2 and T1R3) can be modulated by sweet regulators. The compound amiloride can inhibit the sweet sensitivity of the human sweet taste receptor. This study describes the species-dependent regulation of the response of sweet taste receptors by this sweet inhibitor. Amiloride inhibited the sweet taste response of humans and mice but not that of squirrel monkeys. Using human/squirrel monkey/mouse chimeric T1R2 and T1R3 receptors as well as the agonist perillartine (which can activate the single heptahelical domain of T1R2), we found that the heptahelical domain of T1R2 is the molecular determinant that mediates the species-dependent sensitivity to this sweet regulator. Compared to the sweet inhibitor lactisole (which acts on T1R3), amiloride has a different allosteric binding site on the sweet receptor, which is important new information for the design of novel sweet taste modulators that act on T1R2.
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28
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Jin J, Momboisse F, Boncompain G, Koensgen F, Zhou Z, Cordeiro N, Arenzana-Seisdedos F, Perez F, Lagane B, Kellenberger E, Brelot A. CCR5 adopts three homodimeric conformations that control cell surface delivery. Sci Signal 2018; 11:11/529/eaal2869. [DOI: 10.1126/scisignal.aal2869] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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29
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Dynamic tuneable G protein-coupled receptor monomer-dimer populations. Nat Commun 2018; 9:1710. [PMID: 29703992 PMCID: PMC5923235 DOI: 10.1038/s41467-018-03727-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 03/06/2018] [Indexed: 01/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of membrane receptors, playing a key role in the regulation of processes as varied as neurotransmission and immune response. Evidence for GPCR oligomerisation has been accumulating that challenges the idea that GPCRs function solely as monomeric receptors; however, GPCR oligomerisation remains controversial primarily due to the difficulties in comparing evidence from very different types of structural and dynamic data. Using a combination of single-molecule and ensemble FRET, double electron–electron resonance spectroscopy, and simulations, we show that dimerisation of the GPCR neurotensin receptor 1 is regulated by receptor density and is dynamically tuneable over the physiological range. We propose a “rolling dimer” interface model in which multiple dimer conformations co-exist and interconvert. These findings unite previous seemingly conflicting observations, provide a compelling mechanism for regulating receptor signalling, and act as a guide for future physiological studies. Evidence suggests oligomerisation of G protein-coupled receptors in membranes, but this is controversial. Here, authors use single-molecule and ensemble FRET, and spectroscopy to show that the neurotensin receptor 1 forms multiple dimer conformations that interconvert - “rolling” interfaces.
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30
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Salmas RE, Seeman P, Stein M, Durdagi S. Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2 HighR and D2 LowR States. J Chem Inf Model 2018. [PMID: 29537837 DOI: 10.1021/acs.jcim.7b00722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The active (D2HighR) and inactive (D2LowR) states of dimeric dopamine D2 receptor (D2R) models were investigated to clarify the binding mechanisms of the dopamine agonist bromocriptine, using Molecular Dynamics (MD) simulation. The aim of this comprehensive study was to investigate the critical effects of bromocriptine binding on each distinct receptor conformation. The different binding modes of the bromocriptine ligand in the active and inactive states have a significant effect on the conformational changes of the receptor. Based on the MM/GBSA approach, the calculated binding enthalpies of bromocriptine demonstrated selectivity toward the D2HighR active state. There is good agreement between the calculated and experimentally measured D2HighR selectivity. In the ligand-binding site, the key amino acids identified for D2HighR were Asp114(3.32) and Glu95(2.65), and for D2LowR, it was Ser193(5.42). Moreover, analysis of replicate MD trajectories demonstrated that the bromocriptine structure was more rigid at the D2HighR state and more flexible at the D2LowR state. However, the side chains of the ligand-receptor complex of D2HighR showed larger variations relative to the corresponding regions of D2LowR. The present study is part of an ongoing research program to study D2R conformational changes during ligand activation and to evaluate the conformational state selectivity for ligand binding.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey
| | - Philip Seeman
- Departments of Pharmacology and Psychiatry , University of Toronto , 260 Heath Street West, Unit 605 , M5P 3L6 Toronto , Ontario , Canada
| | - Matthias Stein
- Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1 , 39106 Magdeburg , Germany
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey.,Neuroscience Program, Graduate School of Health Sciences , Bahcesehir University , Istanbul 34349 , Turkey
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31
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Borroto-Escuela DO, Tarakanov AO, Brito I, Fuxe K. Glutamate heteroreceptor complexes in the brain. Pharmacol Rep 2018; 70:936-950. [PMID: 32002960 DOI: 10.1016/j.pharep.2018.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/26/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
Abstract
The existence of mGluR, NMDAR, AMPAR and putative KAR heteroreceptor complexes in synaptic and extrasynaptic regions of brain glutamate synapses represents a major integrative mechanism. Our aim in the current article is to analyze if the formation of the different types glutamate hetereceptor complexes involves the contribution of triplet amino acid homologies (protriplets) in a postulated receptor interface based on the triplet puzzle theory. Seven main sets (lists) of receptor pairs in databases were used containing various sets (lists) of human receptor heteromers and nonheteromers obtained from the available scientific publications including the publically available GPCR-hetnet database. Brain mGluR1-mGluR5 and mGluR2-mGluR4 isoreceptor complexes were demonstrated with a predominant extrasynaptic localization at a post- and prejunctional localization. The existence of putative mGluR4-mGluR7 heteroreceptor complexes in the basal ganglia is proposed. Metabotropic glutamate receptor subtypes also participated in the formation of a large number of heteroreceptor complexes like mGluR1-A1R, mGluR5-A2AR, mGluR5-D2R and D2R-A2AR-mGluR5, located in relation to glutamate synapses, especially in the basal ganglia. A putative mGluR1-GABAB1/2 heterocomplex may also exist. NMDAR heteroreceptor complexes were also demonstrated as a fundamental integrative mechanism in the glutamate synapse and its extrasynaptic membranes. It represented fundamental work on inter alia NMDAR-mGluR5, NMDAR-D1R and NMDAR-D2R heteroreceptor complexes involving both antagonistic and facilitatory allosteric receptor-receptor interactions. As to AMPA receptors, a heterocomplex was found for the interaction between IFNgR1 and the AMPAR mediated via the subunit GluA1 which may be of relevance for neuroinflammation. AMPAR-D2R heteroreceptor complexes were also demonstrated. Besides glutamate heteroreceptor complexes and their allosteric receptor-receptor interactions, a significant mechanism for the functional crosstalk can also be phosphorylation and/or reorganization of adapter proteins with dynamic binding to the two receptors modulating the allosteric receptor mechanism.
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Affiliation(s)
- Dasiel O Borroto-Escuela
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Department of Biomolecular Science, Section of Physiology, University of Urbino, Campus Scientifico Enrico Mattei, Urbino, Italy.,Grupo Bohío-Estudio, Observatorio Cubano de Neurociencias, Yaguajay, Cuba
| | - Alexander O Tarakanov
- St. Petersburg Institute for Informatics and Automation, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Ismel Brito
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Grupo Bohío-Estudio, Observatorio Cubano de Neurociencias, Yaguajay, Cuba
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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32
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Evidence for functional pre-coupled complexes of receptor heteromers and adenylyl cyclase. Nat Commun 2018; 9:1242. [PMID: 29593213 PMCID: PMC5871782 DOI: 10.1038/s41467-018-03522-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/21/2018] [Indexed: 01/13/2023] Open
Abstract
G protein-coupled receptors (GPCRs), G proteins and adenylyl cyclase (AC) comprise one of the most studied transmembrane cell signaling pathways. However, it is unknown whether the ligand-dependent interactions between these signaling molecules are based on random collisions or the rearrangement of pre-coupled elements in a macromolecular complex. Furthermore, it remains controversial whether a GPCR homodimer coupled to a single heterotrimeric G protein constitutes a common functional unit. Using a peptide-based approach, we here report evidence for the existence of functional pre-coupled complexes of heteromers of adenosine A2A receptor and dopamine D2 receptor homodimers coupled to their cognate Gs and Gi proteins and to subtype 5 AC. We also demonstrate that this macromolecular complex provides the necessary frame for the canonical Gs-Gi interactions at the AC level, sustaining the ability of a Gi-coupled GPCR to counteract AC activation mediated by a Gs-coupled GPCR. It is unclear whether GPCRs, G proteins and adenylyl cyclase (AC) associate through random collisions or defined pre-coupling mechanisms. Using a peptide-based approach, the authors show that heteromers of adenosine A2A and dopamine D2 receptors form pre-coupled complexes with their cognate G proteins and AC5.
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33
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Liao C, Zhao X, Liu J, Schneebeli ST, Shelley JC, Li J. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models. Phys Chem Chem Phys 2018; 19:9181-9188. [PMID: 28317993 DOI: 10.1039/c7cp00200a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.
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Affiliation(s)
- Chenyi Liao
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
| | - Xiaochuan Zhao
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
| | - Jiyuan Liu
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
| | | | - John C Shelley
- Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, OR 97204, USA
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, VT 05405, USA.
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34
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Wang L, Yuan Y, Chen X, Chen J, Guo Y, Li M, Li C, Pu X. Probing the cooperative mechanism of the μ–δ opioid receptor heterodimer by multiscale simulation. Phys Chem Chem Phys 2018; 20:29969-29982. [DOI: 10.1039/c8cp06652c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The activation-cooperativity of the μ–δ opioid receptor heterodimer was probed by multiscale simulation coupled with a protein structure network.
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Affiliation(s)
- Longrong Wang
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610041
- P. R. China
| | - Xin Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Jiangfan Chen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Menglong Li
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Chuan Li
- College of Computer Science
- Sichuan University
- Chengdu
- P. R. China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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35
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Pandey K, Ploier B, Goren MA, Levitz J, Khelashvili G, Menon AK. An engineered opsin monomer scrambles phospholipids. Sci Rep 2017; 7:16741. [PMID: 29196630 PMCID: PMC5711885 DOI: 10.1038/s41598-017-16842-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
The G protein-coupled receptor opsin is a phospholipid scramblase that facilitates rapid transbilayer phospholipid exchange in liposomes. The mechanism by which opsin scrambles lipids is unknown. It has been proposed that lipid translocation may occur at protein-protein interfaces of opsin dimers. To test this possibility, we rationally engineered QUAD opsin by tryptophan substitution of four lipid-facing residues in transmembrane helix 4 (TM4) that is known to be important for dimerization. Atomistic molecular dynamics simulations of wild type and QUAD opsins combined with continuum modeling revealed that the tryptophan substitutions lower the energetically unfavorable residual hydrophobic mismatch between TM4 and the membrane, reducing the drive of QUAD opsin to dimerize. We purified thermostable wild type and QUAD opsins, with or without a SNAP tag for fluorescence labeling. Single molecule fluorescence measurements of purified SNAP-tagged constructs revealed that both proteins are monomers. Fluorescence-based activity assays indicated that QUAD opsin is a fully functional scramblase. However, unlike wild type opsin which dimerizes en route to insertion into phospholipid vesicles, QUAD opsin reconstitutes as a monomer. We conclude that an engineered opsin monomer can scramble phospholipids, and that the lipid-exposed face of TM4 is unlikely to contribute to transbilayer phospholipid exchange.
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Affiliation(s)
- Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Birgit Ploier
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Michael A Goren
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
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36
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Kasai RS, Ito SV, Awane RM, Fujiwara TK, Kusumi A. The Class-A GPCR Dopamine D2 Receptor Forms Transient Dimers Stabilized by Agonists: Detection by Single-Molecule Tracking. Cell Biochem Biophys 2017; 76:29-37. [PMID: 29116599 PMCID: PMC5913388 DOI: 10.1007/s12013-017-0829-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/18/2017] [Indexed: 01/06/2023]
Abstract
Whether class-A G-protein coupled receptors (GPCRs) exist and work as monomers or dimers has drawn extensive attention. A class-A GPCR dopamine D2 receptor (D2R) is involved in many physiological and pathological processes and diseases, indicating its critical role in proper functioning of neuronal circuits. In particular, D2R homodimers might play key roles in schizophrenia development and amphetamine-induced psychosis. Here, using single-molecule imaging, we directly tracked single D2R molecules in the plasma membrane at a physiological temperature of 37 °C, and unequivocally determined that D2R forms transient dimers with a lifetime of 68 ms in its resting state. Agonist addition prolonged the dimer lifetime by a factor of ~1.5, suggesting the possibility that transient dimers might be involved in signaling.
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Affiliation(s)
- Rinshi S Kasai
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Shuichi V Ito
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Ryo M Awane
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Takahiro K Fujiwara
- Center for Meso-Bio Single-Molecule Imaging (CeMI), Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, 606-8507, Japan
| | - Akihiro Kusumi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan. .,Center for Meso-Bio Single-Molecule Imaging (CeMI), Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, 606-8507, Japan. .,Membrane Cooperativity Unit, Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.
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37
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Pediani JD, Ward RJ, Marsango S, Milligan G. Spatial Intensity Distribution Analysis: Studies of G Protein-Coupled Receptor Oligomerisation. Trends Pharmacol Sci 2017; 39:175-186. [PMID: 29032835 PMCID: PMC5783713 DOI: 10.1016/j.tips.2017.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/04/2017] [Accepted: 09/14/2017] [Indexed: 02/08/2023]
Abstract
Spatial intensity distribution analysis (SpIDA) is a recently developed approach for determining quaternary structure information on fluorophore-labelled proteins of interest in situ. It can be applied to live or fixed cells and native tissue. Using confocal images, SpIDA generates fluorescence intensity histograms that are analysed by super-Poissonian distribution functions to obtain density and quantal brightness values of the fluorophore-labelled protein of interest. This allows both expression level and oligomerisation state of the protein to be determined. We describe the application of SpIDA to investigate the oligomeric state of G protein-coupled receptors (GPCRs) at steady state and following cellular challenge, and consider how SpIDA may be used to explore GPCR quaternary organisation in pathophysiology and to stratify medicines. GPCRs may exist and function as monomers: however, abundant evidence suggests they can form dimers/oligomers. This concept has implications for drug discovery as it may offer opportunities to modulate the effects of known pharmaceuticals or identify new drug therapies. A variety of approaches have been applied to this issue from traditional biochemical techniques, via resonance energy transfer approaches to recently developed image analysis-based techniques such as SpIDA. This uses mathematical analysis of confocal microscopy images to generate quantal brightness and density information for a fluorophore-tagged receptor. SpIDA can be applied to live or fixed cells and native tissue. SpIDA has been applied to GPCRs from each of the major subfamilies to explore their oligomerisation status at steady state and their regulation by receptor density and ligand binding.
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Affiliation(s)
- John D Pediani
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Richard J Ward
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sara Marsango
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
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38
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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39
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Computer-Aided Drug Design Approaches to Study Key Therapeutic Targets in Alzheimer’s Disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-1-4939-7404-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Liu J, Zhang Z, Moreno-Delgado D, Dalton JA, Rovira X, Trapero A, Goudet C, Llebaria A, Giraldo J, Yuan Q, Rondard P, Huang S, Liu J, Pin JP. Allosteric control of an asymmetric transduction in a G protein-coupled receptor heterodimer. eLife 2017; 6:26985. [PMID: 28829739 PMCID: PMC5582870 DOI: 10.7554/elife.26985] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/03/2017] [Indexed: 01/30/2023] Open
Abstract
GPCRs play critical roles in cell communication. Although GPCRs can form heteromers, their role in signaling remains elusive. Here we used rat metabotropic glutamate (mGlu) receptors as prototypical dimers to study the functional interaction between each subunit. mGluRs can form both constitutive homo- and heterodimers. Whereas both mGlu2 and mGlu4 couple to G proteins, G protein activation is mediated by mGlu4 heptahelical domain (HD) exclusively in mGlu2-4 heterodimers. Such asymmetric transduction results from the action of both the dimeric extracellular domain, and an allosteric activation by the partially-activated non-functional mGlu2 HD. G proteins activation by mGlu2 HD occurs if either the mGlu2 HD is occupied by a positive allosteric modulator or if mGlu4 HD is inhibited by a negative modulator. These data revealed an oriented asymmetry in mGlu heterodimers that can be controlled with allosteric modulators. They provide new insight on the allosteric interaction between subunits in a GPCR dimer.
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Affiliation(s)
- Junke Liu
- College of Life Science and Technology, Collaborative Innovation Center for Genetics and Development, and Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Zongyong Zhang
- College of Life Science and Technology, Collaborative Innovation Center for Genetics and Development, and Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - David Moreno-Delgado
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - James Ar Dalton
- Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, Barcelona, Spain.,Network Biomedical Research Center on Mental Health, Barcelona, Spain
| | - Xavier Rovira
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Ana Trapero
- MCS, Laboratory of Medicinal Chemistry and Synthesis, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Cyril Goudet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Amadeu Llebaria
- MCS, Laboratory of Medicinal Chemistry and Synthesis, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Jesús Giraldo
- Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, Barcelona, Spain.,Network Biomedical Research Center on Mental Health, Barcelona, Spain
| | - Qilin Yuan
- College of Life Science and Technology, Collaborative Innovation Center for Genetics and Development, and Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Siluo Huang
- College of Life Science and Technology, Collaborative Innovation Center for Genetics and Development, and Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Jianfeng Liu
- College of Life Science and Technology, Collaborative Innovation Center for Genetics and Development, and Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
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41
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Salmas RE, Seeman P, Aksoydan B, Erol I, Kantarcioglu I, Stein M, Yurtsever M, Durdagi S. Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking. ACS Chem Neurosci 2017; 8:1404-1415. [PMID: 28272861 DOI: 10.1021/acschemneuro.7b00070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dopamine receptor D2 (D2R) plays an important role in the human central nervous system and is a focal target of antipsychotic agents. The D2HighR and D2LowR dimeric models previously developed by our group are used to investigate the prediction of binding affinity of the LY404,039 ligand and its binding mechanism within the catalytic domain. The computational data obtained using molecular dynamics simulations fit well with the experimental results. The calculated binding affinities of LY404,039 using MM/PBSA for the D2HighR and D2LowR targets were -12.04 and -9.11 kcal/mol, respectively. The experimental results suggest that LY404,039 binds to D2HighR and D2LowR with binding affinities (Ki) of 8.2 and 1640 nM, respectively. The high binding affinity of LY404,039 in terms of binding to [3H]domperidone was inhibited by the presence of a guanine nucleotide, indicating an agonist action of the drug at D2HighR. The interaction analysis demonstrated that while Asp114 was among the most critical amino acids for D2HighR binding, residues Ser193 and Ser197 were significantly more important within the binding cavity of D2LowR. Molecular modeling analyses are extended to ensemble docking as well as structure-based pharmacophore model (E-pharmacophore) development using the bioactive conformation of LY404,039 at the binding pocket as a template and screening of small-molecule databases with derived pharmacophore models.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, Toronto, Ontario M5P 3L6, Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Ismail Erol
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
- Department
of Chemistry, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Isik Kantarcioglu
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Matthias Stein
- Max-Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34469 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
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42
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Marsango S, Caltabiano G, Jiménez-Rosés M, Millan MJ, Pediani JD, Ward RJ, Milligan G. A Molecular Basis for Selective Antagonist Destabilization of Dopamine D 3 Receptor Quaternary Organization. Sci Rep 2017; 7:2134. [PMID: 28522847 PMCID: PMC5437050 DOI: 10.1038/s41598-017-02249-3] [Citation(s) in RCA: 16] [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: 11/15/2016] [Accepted: 04/07/2017] [Indexed: 12/17/2022] Open
Abstract
The dopamine D3 receptor (D3R) is a molecular target for both first-generation and several recently-developed antipsychotic agents. Following stable expression of this mEGFP-tagged receptor, Spatial Intensity Distribution Analysis indicated that a substantial proportion of the receptor was present within dimeric/oligomeric complexes and that increased expression levels of the receptor favored a greater dimer to monomer ratio. Addition of the antipsychotics, spiperone or haloperidol, resulted in re-organization of D3R quaternary structure to promote monomerization. This action was dependent on ligand concentration and reversed upon drug washout. By contrast, a number of other antagonists with high affinity at the D3R, did not alter the dimer/monomer ratio. Molecular dynamics simulations following docking of each of the ligands into a model of the D3R derived from the available atomic level structure, and comparisons to the receptor in the absence of ligand, were undertaken. They showed that, in contrast to the other antagonists, spiperone and haloperidol respectively increased the atomic distance between reference α carbon atoms of transmembrane domains IV and V and I and II, both of which provide key interfaces for D3R dimerization. These results offer a molecular explanation for the distinctive ability of spiperone and haloperidol to disrupt D3R dimerization.
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Affiliation(s)
- Sara Marsango
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
| | - Gianluigi Caltabiano
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Mireia Jiménez-Rosés
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Mark J Millan
- Institut de Recherches Servier, Centre for Innovation in Neuropsychiatry, 125 Chemin de Ronde, Croissy sur Seine, France, 78290
| | - John D Pediani
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Richard J Ward
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
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43
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Ekhteiari Salmas R, Seeman P, Aksoydan B, Stein M, Yurtsever M, Durdagi S. Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor. ACS Chem Neurosci 2017; 8:826-836. [PMID: 28001043 DOI: 10.1021/acschemneuro.6b00396] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The dopamine D2 receptor (D2R) plays an important part in the human central nervous system and it is considered to be a focal target of antipsychotic agents. It is structurally modeled in active and inactive states, in which homodimerization reaction of the D2R monomers is also applied. The ASP2314 (also known as ACR16) ligand, a D2R stabilizer, is used in tests to evaluate how dimerization and conformational changes may alter the ligand binding space and to provide information on alterations in inhibitory mechanisms upon activation. The administration of the D2R agonist ligand ACR16 [3H](+)-4-propyl-3,4,4a,5,6,10b-hexahydro-2H-naphtho[1,2-b][1,4]oxazin-9-ol ((+)PHNO) revealed Ki values of 32 nM for the D2highR and 52 μM for the D2lowR. The calculated binding affinities of ACR16 with post processing molecular dynamics (MD) simulations analyses using MM/PBSA for the monomeric and homodimeric forms of the D2highR were -9.46 and -8.39 kcal/mol, respectively. The data suggests that the dimerization of the D2R leads negative cooperativity for ACR16 binding. The dimerization reaction of the D2highR is energetically favorable by -22.95 kcal/mol. The dimerization reaction structurally and thermodynamically stabilizes the D2highR conformation, which may be due to the intermolecular forces formed between the TM4 of each monomer, and the result strongly demonstrates dimerization essential for activation of the D2R.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, M5P 3L6 Toronto, Ontario Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Max-Planck
Institute
for Dynamics of Complex Technical Systems, Molecular Simulations and
Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34467 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
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44
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Scholler P, Moreno-Delgado D, Lecat-Guillet N, Doumazane E, Monnier C, Charrier-Savournin F, Fabre L, Chouvet C, Soldevila S, Lamarque L, Donsimoni G, Roux T, Zwier JM, Trinquet E, Rondard P, Pin JP. HTS-compatible FRET-based conformational sensors clarify membrane receptor activation. Nat Chem Biol 2017; 13:372-380. [DOI: 10.1038/nchembio.2286] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
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45
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Kleinau G, Worth CL, Kreuchwig A, Biebermann H, Marcinkowski P, Scheerer P, Krause G. Structural-Functional Features of the Thyrotropin Receptor: A Class A G-Protein-Coupled Receptor at Work. Front Endocrinol (Lausanne) 2017; 8:86. [PMID: 28484426 PMCID: PMC5401882 DOI: 10.3389/fendo.2017.00086] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
The thyroid-stimulating hormone receptor (TSHR) is a member of the glycoprotein hormone receptors, a sub-group of class A G-protein-coupled receptors (GPCRs). TSHR and its endogenous ligand thyrotropin (TSH) are of essential importance for growth and function of the thyroid gland and proper function of the TSH/TSHR system is pivotal for production and release of thyroid hormones. This receptor is also important with respect to pathophysiology, such as autoimmune (including ophthalmopathy) or non-autoimmune thyroid dysfunctions and cancer development. Pharmacological interventions directly targeting the TSHR should provide benefits to disease treatment compared to currently available therapies of dysfunctions associated with the TSHR or the thyroid gland. Upon TSHR activation, the molecular events conveying conformational changes from the extra- to the intracellular side of the cell across the membrane comprise reception, conversion, and amplification of the signal. These steps are highly dependent on structural features of this receptor and its intermolecular interaction partners, e.g., TSH, antibodies, small molecules, G-proteins, or arrestin. For better understanding of signal transduction, pathogenic mechanisms such as autoantibody action and mutational modifications or for developing new pharmacological strategies, it is essential to combine available structural data with functional information to generate homology models of the entire receptor. Although so far these insights are fragmental, in the past few decades essential contributions have been made to investigate in-depth the involved determinants, such as by structure determination via X-ray crystallography. This review summarizes available knowledge (as of December 2016) concerning the TSHR protein structure, associated functional aspects, and based on these insights we suggest several receptor complex models. Moreover, distinct TSHR properties will be highlighted in comparison to other class A GPCRs to understand the molecular activation mechanisms of this receptor comprehensively. Finally, limitations of current knowledge and lack of information are discussed highlighting the need for intensified efforts toward TSHR structure elucidation.
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Affiliation(s)
- Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
- Group Protein X-Ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany
| | | | - Annika Kreuchwig
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
| | | | - Patrick Scheerer
- Group Protein X-Ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany
| | - Gerd Krause
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
- *Correspondence: Gerd Krause,
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46
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Beta 2-adrenergic receptor homodimers: Role of transmembrane domain 1 and helix 8 in dimerization and cell surface expression. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:1445-1455. [PMID: 27993566 DOI: 10.1016/j.bbamem.2016.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/05/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
Even though there are hundreds of reports in the published literature supporting the hypothesis that G protein-coupled receptors (GPCR) form and function as dimers this remains a highly controversial area of research and mechanisms governing homodimer formation are poorly understood. Crystal structures revealing homodimers have been reported for many different GPCR. For adrenergic receptors, a potential dimer interface involving transmembrane domain 1 (TMD1) and helix 8 (H8) was identified in crystal structures of the beta1-adrenergic (β1-AR) and β2-AR. The purpose of this study was to investigate a potential role for TMD1 and H8 in dimerization and plasma membrane expression of functional β2-AR. Charged residues at the base of TMD1 and in the distal portion of H8 were replaced, singly and in combination, with non-polar residues or residues of opposite charge. Wild type and mutant β2-AR, tagged with YFP and expressed in HEK293 cells, were evaluated for plasma membrane expression and function. Homodimer formation was evaluated using bioluminescence resonance energy transfer, bimolecular fluorescence complementation, and fluorescence correlation spectroscopy. Amino acid substitutions at the base of TMD1 and in the distal portion of H8 disrupted homodimer formation and caused receptors to be retained in the endoplasmic reticulum. Mutations in the proximal region of H8 did not disrupt dimerization but did interfere with plasma membrane expression. This study provides biophysical evidence linking a potential TMD1/H8 interface with ER export and the expression of functional β2-AR on the plasma membrane. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.
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Marino KA, Prada-Gracia D, Provasi D, Filizola M. Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model. PLoS Comput Biol 2016; 12:e1005240. [PMID: 27959924 PMCID: PMC5154498 DOI: 10.1371/journal.pcbi.1005240] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/07/2016] [Indexed: 11/21/2022] Open
Abstract
The lipid composition of cell membranes has increasingly been recognized as playing an important role in the function of various membrane proteins, including G Protein-Coupled Receptors (GPCRs). For instance, experimental and computational evidence has pointed to lipids influencing receptor oligomerization directly, by physically interacting with the receptor, and/or indirectly, by altering the bulk properties of the membrane. While the exact role of oligomerization in the function of class A GPCRs such as the μ-opioid receptor (MOR) is still unclear, insight as to how these receptors oligomerize and the relevance of the lipid environment to this phenomenon is crucial to our understanding of receptor function. To examine the effect of lipids and different MOR conformations on receptor oligomerization we carried out extensive coarse-grained molecular dynamics simulations of crystal structures of inactive and/or activated MOR embedded in an idealized mammalian plasma membrane composed of 63 lipid types asymmetrically distributed across the two leaflets. The results of these simulations point, for the first time, to specific direct and indirect effects of the lipids, as well as the receptor conformation, on the spatio-temporal organization of MOR in the plasma membrane. While sphingomyelin-rich, high-order lipid regions near certain transmembrane (TM) helices of MOR induce an effective long-range attractive force on individual protomers, both long-range lipid order and interface formation are found to be conformation dependent, with a larger number of different interfaces formed by inactive MOR compared to active MOR. The μ-opioid receptor (MOR) is an important pharmaceutical target in the treatment of pain. In order to develop novel pain therapies, devoid of the serious side-effects of present opioid analgesics, we need to understand the fundamentals of how MOR works on the molecular level. While some studies suggest that oligomers of MOR could play a role in signaling, how MOR forms dimers, which interfaces form, and the exact role of oligomers in MOR function remain unclear. While research has shown that the membrane environment can affect membrane protein function, most previous computational work to study oligomerization has been performed in a very simple membrane. Here, we use molecular dynamics simulations of MOR in a heterogeneous plasma membrane model (comprising 63 lipid types) to investigate how the presence of the protein modulates its lipid environment, affecting species distribution and sculpting characteristic order and thickness profiles around the receptors. Such modulations, in turn, induce long-range interactions between the proteins and favor the formation of specific dimeric conformations.
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Affiliation(s)
- Kristen A. Marino
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Diego Prada-Gracia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States of America
- * E-mail:
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Müller A, Berkmann JC, Scheerer P, Biebermann H, Kleinau G. Insights into Basal Signaling Regulation, Oligomerization, and Structural Organization of the Human G-Protein Coupled Receptor 83. PLoS One 2016; 11:e0168260. [PMID: 27936173 PMCID: PMC5148169 DOI: 10.1371/journal.pone.0168260] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022] Open
Abstract
The murine G-protein coupled receptor 83 (mGPR83) is expressed in the hypothalamus and was previously suggested to be involved in the regulation of metabolism. The neuropeptide PEN has been recently identified as a potent GPR83 ligand. Moreover, GPR83 constitutes functionally relevant hetero-oligomers with other G-protein coupled receptors (GPCR) such as the ghrelin receptor (GHSR) or GPR171. Previous deletion studies also revealed that the long N-terminal extracellular receptor domain (eNDo) of mGPR83 may act as an intra-molecular ligand, which participates in the regulation of basal signaling activity, which is a key feature of GPCR function. Here, we investigated particular amino acids at the eNDo of human GPR83 (hGPR83) by side-directed mutagenesis to identify determinants of the internal ligand. These studies were accompanied by structure homology modeling to combine functional insights with structural information. The capacity for hetero-oligomer formation of hGPR83 with diverse family A GPCRs such as the melanocortin-4 receptor (MC4R) was also investigated, with a specific emphasis on the impact of the eNDo on oligomerization and basal signaling properties. Finally, we demonstrate that hGPR83 exhibits an unusual basal signaling for different effectors, which also supports signaling promiscuity. hGPR83 interacts with a variety of hypothalamic GPCRs such as the MC4R or GHSR. These interactions are not dependent on the ectodomain and most likely occur at interfaces constituted in the transmembrane regions. Moreover, several amino acids at the transition between the eNDo and transmembrane helix 1 were identified, where mutations lead also to biased basal signaling modulation.
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Affiliation(s)
- Anne Müller
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Julia Catherine Berkmann
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- * E-mail:
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Pluhackova K, Gahbauer S, Kranz F, Wassenaar TA, Böckmann RA. Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4. PLoS Comput Biol 2016; 12:e1005169. [PMID: 27812115 PMCID: PMC5094716 DOI: 10.1371/journal.pcbi.1005169] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/27/2016] [Indexed: 12/15/2022] Open
Abstract
G protein coupled receptors (GPCRs) allow for the transmission of signals across biological membranes. For a number of GPCRs, this signaling was shown to be coupled to prior dimerization of the receptor. The chemokine receptor type 4 (CXCR4) was reported before to form dimers and their functionality was shown to depend on membrane cholesterol. Here, we address the dimerization pattern of CXCR4 in pure phospholipid bilayers and in cholesterol-rich membranes. Using ensembles of molecular dynamics simulations, we show that CXCR4 dimerizes promiscuously in phospholipid membranes. Addition of cholesterol dramatically affects the dimerization pattern: cholesterol binding largely abolishes the preferred dimer motif observed for pure phospholipid bilayers formed mainly by transmembrane helices 1 and 7 (TM1/TM5-7) at the dimer interface. In turn, the symmetric TM3,4/TM3,4 interface is enabled first by intercalating cholesterol molecules. These data provide a molecular basis for the modulation of GPCR activity by its lipid environment.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Stefan Gahbauer
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Franziska Kranz
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Computer Graphics, Department of Computer Science, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Tsjerk A. Wassenaar
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Groningen Biomolecular Sciences and Biotechnology and Zernike Institute of Advanced Materials, University of Groningen, The Netherlands
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
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Gahbauer S, Böckmann RA. Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function. Front Physiol 2016; 7:494. [PMID: 27826255 PMCID: PMC5078798 DOI: 10.3389/fphys.2016.00494] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/11/2016] [Indexed: 12/18/2022] Open
Abstract
The dimerization or even oligomerization of G protein coupled receptors (GPCRs) causes ongoing, controversial debates about its functional role and the coupled biophysical, biochemical or biomedical implications. A continously growing number of studies hints to a relation between oligomerization and function of GPCRs and strengthens the assumption that receptor assembly plays a key role in the regulation of protein function. Additionally, progress in the structural analysis of GPCR-G protein and GPCR-ligand interactions allows to distinguish between actively functional and non-signaling complexes. Recent findings further suggest that the surrounding membrane, i.e., its lipid composition may modulate the preferred dimerization interface and as a result the abundance of distinct dimeric conformations. In this review, the association of GPCRs and the role of the membrane in oligomerization will be discussed. An overview of the different reported oligomeric interfaces is provided and their capability for signaling discussed. The currently available data is summarized with regard to the formation of GPCR oligomers, their structures and dependency on the membrane microenvironment as well as the coupling of oligomerization to receptor function.
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Affiliation(s)
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-NürnbergErlangen, Germany
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