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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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Martínez-Archundia M, Correa-Basurto J, Montaño S, Rosas-Trigueros JL. Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis. J Biomol Struct Dyn 2019; 37:4685-4700. [DOI: 10.1080/07391102.2018.1564700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sarita Montaño
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacan, Sinaloa, Mexico
| | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Cómputo, Instituto Politécnico Nacional, Mexico City, Mexico
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Retinal Conformation Changes Rhodopsin's Dynamic Ensemble. Biophys J 2016; 109:608-17. [PMID: 26244742 DOI: 10.1016/j.bpj.2015.06.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 11/23/2022] Open
Abstract
G protein-coupled receptors are vital membrane proteins that allosterically transduce biomolecular signals across the cell membrane. However, the process by which ligand binding induces protein conformation changes is not well understood biophysically. Rhodopsin, the mammalian dim-light receptor, is a unique test case for understanding these processes because of its switch-like activity; the ligand, retinal, is bound throughout the activation cycle, switching from inverse agonist to agonist after absorbing a photon. By contrast, the ligand-free opsin is outside the activation cycle and may behave differently. We find that retinal influences rhodopsin dynamics using an ensemble of all-atom molecular dynamics simulations that in aggregate contain 100 μs of sampling. Active retinal destabilizes the inactive state of the receptor, whereas the active ensemble was more structurally homogenous. By contrast, simulations of an active-like receptor without retinal present were much more heterogeneous than those containing retinal. These results suggest allosteric processes are more complicated than a ligand inducing protein conformational changes or simply capturing a shifted ensemble as outlined in classic models of allostery.
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Caliman AD, Swift SE, Wang Y, Miao Y, McCammon JA. Investigation of the conformational dynamics of the apo A2A adenosine receptor. Protein Sci 2015; 24:1004-12. [PMID: 25761901 PMCID: PMC4456113 DOI: 10.1002/pro.2681] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/08/2015] [Indexed: 12/19/2022]
Abstract
The activation/deactivation processes for G-protein coupled receptors (GPCRs) have been computationally studied for several different classes, including rhodopsin, the β2 adrenergic receptor, and the M2 muscarinic receptor. Despite determined cocrystal structures of the adenosine A2A receptor (A2A AR) in complex with antagonists, agonists and an antibody, the deactivation process of this GPCR is not completely understood. In this study, we investigate the convergence of two apo simulations, one starting with an agonist-bound conformation (PDB: 3QAK)(14) and the other starting with an antagonist-bound conformation (PDB: 3EML)(11) . Despite the two simulations not completely converging, we were able to identify distinct intermediate steps of the deactivation process characterized by the movement of Y288(7.53) in the NPxxY motif. We find that Y288(7.53) contributes to the process by forming hydrogen bonds to residues in transmembrane helices 2 and 7 and losing these interactions upon full deactivation. Y197(5.58) also plays a role in the process by forming a hydrogen bond only once the side chain moves from the lipid interface to the middle of the helical bundle.
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Affiliation(s)
- Alisha D Caliman
- Department of Pharmacology, University of California at San DiegoLa Jolla, California, 92093
| | - Sara E Swift
- Department of Pharmacology, University of California at San DiegoLa Jolla, California, 92093
| | - Yi Wang
- Howard Hughes Medical Institute, University of California at San DiegoLa Jolla, California, 92093
| | - Yinglong Miao
- Howard Hughes Medical Institute, University of California at San DiegoLa Jolla, California, 92093
| | - J Andrew McCammon
- Department of Pharmacology, University of California at San DiegoLa Jolla, California, 92093
- Howard Hughes Medical Institute, University of California at San DiegoLa Jolla, California, 92093
- Department of Chemistry and Biochemistry, University of California at San DiegoLa Jolla, California, 92093
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Ghanemi A, Hu X. Elements toward novel therapeutic targeting of the adrenergic system. Neuropeptides 2015; 49:25-35. [PMID: 25481798 DOI: 10.1016/j.npep.2014.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/30/2014] [Accepted: 11/19/2014] [Indexed: 01/14/2023]
Abstract
Adrenergic receptors belong to the family of the G protein coupled receptors that represent important targets in the modern pharmacotherapies. Studies on different physiological and pathophysiological properties of the adrenergic system have led to novel evidences and theories that suggest novel possible targeting of such system in a variety of pathologies and disorders, even beyond the classical known therapeutic possibilities. Herein, those advances have been illustrated with selected concepts and different examples. Furthermore, we illustrated the applications and the therapeutic implications that such findings and advances might have in the contexts of experimental pharmacology, therapeutics and clinic. We hope that the content of this work will guide researches devoted to the adrenergic aspects that combine neurosciences with pharmacology.
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Affiliation(s)
- Abdelaziz Ghanemi
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; University of Chinese Academy of Science, Beijing, China.
| | - Xintian Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; Key State Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Science, Beijing, China.
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Romo TD, Leioatts N, Grossfield A. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations. J Comput Chem 2014; 35:2305-18. [PMID: 25327784 PMCID: PMC4227929 DOI: 10.1002/jcc.23753] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/07/2014] [Indexed: 01/13/2023]
Abstract
LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development.
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Affiliation(s)
- Tod D Romo
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, 14642
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