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Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, Aranda-García D, Ramírez-Anguita JM, Stepniewski TM, Worp N, Varela-Rial A, Morales-Pastor A, Medel-Lacruz B, Pándy-Szekeres G, Mayol E, Giorgino T, Carlsson J, Deupi X, Filipek S, Filizola M, Gómez-Tamayo JC, Gonzalez A, Gutiérrez-de-Terán H, Jiménez-Rosés M, Jespers W, Kapla J, Khelashvili G, Kolb P, Latek D, Marti-Solano M, Matricon P, Matsoukas MT, Miszta P, Olivella M, Perez-Benito L, Provasi D, Ríos S, R Torrecillas I, Sallander J, Sztyler A, Vasile S, Weinstein H, Zachariae U, Hildebrand PW, De Fabritiis G, Sanz F, Gloriam DE, Cordomi A, Guixà-González R, Selent J. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat Methods 2020; 17:777-787. [PMID: 32661425 DOI: 10.1038/s41592-020-0884-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/29/2020] [Indexed: 11/08/2022]
Abstract
G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.
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Affiliation(s)
- Ismael Rodríguez-Espigares
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Mariona Torrens-Fontanals
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, Charite University Medicine Berlin, Berlin, Germany
- Institute of Medical Physics and Biophysics, Medical University Leipzig, Leipzig, Sachsen, Germany
| | - David Aranda-García
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Juan Manuel Ramírez-Anguita
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Nathalie Worp
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Alejandro Varela-Rial
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
- Acellera, Barcelona, Spain
| | - Adrián Morales-Pastor
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Brian Medel-Lacruz
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - Gáspár Pándy-Szekeres
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Eduardo Mayol
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Toni Giorgino
- Biophysics Institute, National Research Council of Italy, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen PSI, Switzerland
- Condensed Matter Theory Group, PSI, Villigen PSI, Switzerland
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - José Carlos Gómez-Tamayo
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Mireia Jiménez-Rosés
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Willem Jespers
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Jon Kapla
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Dorota Latek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Maria Marti-Solano
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Minos-Timotheos Matsoukas
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Przemyslaw Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Mireia Olivella
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Laura Perez-Benito
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Santiago Ríos
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Iván R Torrecillas
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jessica Sallander
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Agnieszka Sztyler
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Silvana Vasile
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Charite University Medicine Berlin, Berlin, Germany
- Institute of Medical Physics and Biophysics, Medical University Leipzig, Leipzig, Sachsen, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Gianni De Fabritiis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
- Acellera, Barcelona, Spain
| | - Ferran Sanz
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Arnau Cordomi
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Ramon Guixà-González
- Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen PSI, Switzerland.
- Condensed Matter Theory Group, PSI, Villigen PSI, Switzerland.
| | - Jana Selent
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
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Bissaro M, Bolcato G, Deganutti G, Sturlese M, Moro S. Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A 2A Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations. Molecules 2019; 24:E2752. [PMID: 31362426 PMCID: PMC6695830 DOI: 10.3390/molecules24152752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 11/24/2022] Open
Abstract
One of the most intriguing findings highlighted from G protein-coupled receptor (GPCR) crystallography is the presence, in many members of class A, of a partially hydrated sodium ion in the middle of the seven transmembrane helices (7TM) bundle. In particular, the human adenosine A2A receptor (A2A AR) is the first GPCR in which a monovalent sodium ion was crystallized in a distal site from the canonical orthosteric one, corroborating, from a structural point of view, its role as a negative allosteric modulator. However, the molecular mechanism by which the sodium ion influences the recognition of the A2A AR agonists is not yet fully understood. In this study, the supervised molecular dynamics (SuMD) technique was exploited to analyse the sodium ion recognition mechanism and how its presence influences the binding of the endogenous agonist adenosine. Due to a higher degree of flexibility of the receptor extracellular (EC) vestibule, we propose the sodium-bound A2A AR as less efficient in stabilizing the adenosine during the different steps of binding.
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Affiliation(s)
- Maicol Bissaro
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giovanni Bolcato
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giuseppe Deganutti
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Mattia Sturlese
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy.
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