32 results on '"Maria Marti-Solano"'
Search Results
2. Human MC4R variants affect endocytosis, trafficking and dimerization revealing multiple cellular mechanisms involved in weight regulation
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Bas Brouwers, Edson Mendes de Oliveira, Maria Marti-Solano, Fabiola B.F. Monteiro, Suli-Anne Laurin, Julia M. Keogh, Elana Henning, Rebecca Bounds, Carole A. Daly, Shane Houston, Vikram Ayinampudi, Natalia Wasiluk, David Clarke, Bianca Plouffe, Michel Bouvier, M. Madan Babu, I. Sadaf Farooqi, and Jacek Mokrosiński
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obesity ,MC4R ,therapy ,weight loss ,GPCRs ,β-arrestin ,Biology (General) ,QH301-705.5 - Abstract
Summary: The Melanocortin-4 Receptor (MC4R) plays a pivotal role in energy homeostasis. We used human MC4R mutations associated with an increased or decreased risk of obesity to dissect mechanisms that regulate MC4R function. Most obesity-associated mutations impair trafficking to the plasma membrane (PM), whereas obesity-protecting mutations either accelerate recycling to the PM or decrease internalization, resulting in enhanced signaling. MC4R mutations that do not affect canonical Gαs protein-mediated signaling, previously considered to be non-pathogenic, nonetheless disrupt agonist-induced internalization, β-arrestin recruitment, and/or coupling to Gαs, establishing their causal role in severe obesity. Structural mapping reveals ligand-accessible sites by which MC4R couples to effectors and residues involved in the homodimerization of MC4R, which is disrupted by multiple obesity-associated mutations. Human genetic studies reveal that endocytosis, intracellular trafficking, and homodimerization regulate MC4R function to a level that is physiologically relevant, supporting the development of chaperones, agonists, and allosteric modulators of MC4R for weight loss therapy.
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- 2021
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3. A multi-dimensional view of context-dependent G protein-coupled receptor function
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Maria Marti-Solano
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Biochemistry - Abstract
G protein-coupled receptor (GPCR) family members can sense an extraordinary variety of biomolecules to activate intracellular signalling cascades that modulate key aspects of cell physiology. Apart from their crucial role in maintaining cell homeostasis, these critical sensory and modulatory properties have made GPCRs the most successful drug target class to date. However, establishing direct links between receptor activation of specific intracellular partners and individual physiological outcomes is still an ongoing challenge. By studying this receptor signalling complexity at increasing resolution through the development of novel biosensors and high-throughput techniques, a growing number of studies are revealing how receptor function can be diversified in a spatial, temporal or cell-specific manner. This mini-review will introduce recent examples of this context-dependent receptor signalling and discuss how it can impact our understanding of receptor function in health and disease, and contribute to the search of more selective, efficacious and safer GPCR drug candidates.
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- 2023
4. Cancer-Associated Mutations Enhance The Sensitivity Of The Trupath GαQ/11 System
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Dewi Safitri, Matthew Harris, Abigail Pearce, Xianglin Huang, Matthew Rosa, Kerry Barkan, Edward Wills, Maria Marti-Solano, Matthew D. Falk, and Graham Ladds
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G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and are a common drug target. They can be stabilised in different conformational states by ligands to activate multiple transducers and effectors leading to a variety of cellular responses. The potential of agonists to activate select pathways has important implications for drug discovery. Thus, there is a clear need to profile the initial GPCR signal transduction event, activation of G proteins, to enhance understanding of receptor coupling and guide drug design. The BRET-based biosensor suite, TRUPATH, was recently developed to enable quantification of the activation profiles of all non-visual G proteins (excluding Golf and G14) and has since been utilised in numerous studies. However, it fails to detect Gq/11 activation for a number of GPCRs previously reported to display promiscuous secondary coupling to Gq/11. Here we report modifications to the Gαq and Gα11 biosensors in the switch I region that prevent intrinsic GTPase activity (R183C/Q). Except for the PAC1R, substitution with cancer-associated mutations, Cys or Gln, significantly increased sensitivity to allow detection of robust, reliable, and representative Gq/11 responses to Class B1 GPCRs. We also demonstrate the utility of these modified biosensors for promiscuously coupled class A GPCR that have primary Gs-coupling. Thus, we propose that modification to Gαq/11 may also be necessary in other biosensor systems to enable detection of Gq/11 activation.
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- 2022
5. A highly conserved δ‐opioid receptor region determines RGS4 interaction
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Zafiroula Georgoussi, Alexandra Symeonof, Maria Marti-Solano, Tomasz Maciej Stepniewski, Christos Karoussiotis, and Jana Selent
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Protein Conformation, alpha-Helical ,0301 basic medicine ,G protein ,medicine.drug_class ,Genetic Vectors ,Regulator ,Gene Expression ,GTP-Binding Protein alpha Subunits, Gi-Go ,Molecular Dynamics Simulation ,Crystallography, X-Ray ,Biochemistry ,RGS4 ,03 medical and health sciences ,0302 clinical medicine ,Opioid receptor ,Receptors, Opioid, delta ,Escherichia coli ,medicine ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Cloning, Molecular ,Receptor ,Molecular Biology ,Ternary complex ,Conserved Sequence ,Regulation of gene expression ,Binding Sites ,Sequence Homology, Amino Acid ,biology ,Chemistry ,Cell Biology ,Recombinant Proteins ,Cell biology ,030104 developmental biology ,030220 oncology & carcinogenesis ,Mutation ,biology.protein ,Cattle ,Protein Conformation, beta-Strand ,Salt bridge ,Sequence Alignment ,RGS Proteins ,Protein Binding - Abstract
The δ-opioid receptor (δ-OR) couples to Gi/Go proteins to modulate a variety of responses in the nervous system. Τhe regulator of G protein signalling 4 (RGS4) was previously shown to directly interact within the C-terminal region of δ-OR using its N-terminal domain to negatively modulate opioid receptor signalling. Herein, using molecular dynamics simulations and in vitro pull-down experiments we delimit this interaction to 12 helix 8 residues of δ-ΟR and to the first 17 N-terminal residues (NT) of RGS4. Monitoring the complex arrangement and stabilization between RGS4 and δ-OR by molecular dynamics simulations combined with mutagenesis studies, we defined that two critical interactions are formed: one between Phe329 of helix8 of δ-ΟR and Pro9 of the NT of RGS4 and the other a salt bridge between Glu323 of δ-ΟR and Lys17 of RGS4. Our observations allow drafting for the first time a structural model of a ternary complex including the δ-opioid receptor, a G protein and a RGS protein. Furthermore, the high degree of conservation among opioid receptors of the RGS4-binding region, points to a conserved interaction mode between opioid receptors and this important regulatory protein.
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- 2019
6. A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection
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David Rodríguez, Katerina Strakova, Gunnar Schulte, Julian Petersen, Belma Hot, Maria Kowalski-Jahn, M. Madan Babu, Carl-Fredrik Bowin, Jens Carlsson, Jana Valnohova, Najeah Okashah, Paweł Kozielewicz, Greg Slodkowicz, Nevin A. Lambert, Maria Marti-Solano, and Shane C. Wright
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0301 basic medicine ,Models, Molecular ,G protein ,Protein Conformation ,Science ,Population ,Immunoblotting ,General Physics and Astronomy ,02 engineering and technology ,Plasma protein binding ,Molecular Dynamics Simulation ,General Biochemistry, Genetics and Molecular Biology ,Article ,Receptors, G-Protein-Coupled ,03 medical and health sciences ,Protein structure ,Functional selectivity ,Humans ,Receptor ,education ,lcsh:Science ,Phylogeny ,Molecular switch ,chemistry.chemical_classification ,Mitogen-Activated Protein Kinase 1 ,education.field_of_study ,Multidisciplinary ,Mitogen-Activated Protein Kinase 3 ,Chemistry ,Biochemistry and Molecular Biology ,General Chemistry ,Models, Theoretical ,021001 nanoscience & nanotechnology ,Flow Cytometry ,Dishevelled ,Cell biology ,030104 developmental biology ,HEK293 Cells ,lcsh:Q ,0210 nano-technology ,Biokemi och molekylärbiologi ,Protein Binding - Abstract
Class F receptors are considered valuable therapeutic targets due to their role in human disease, but structural changes accompanying receptor activation remain unexplored. Employing population and cancer genomics data, structural analyses, molecular dynamics simulations, resonance energy transfer-based approaches and mutagenesis, we identify a conserved basic amino acid in TM6 in Class F receptors that acts as a molecular switch to mediate receptor activation. Across all tested Class F receptors (FZD4,5,6,7, SMO), mutation of the molecular switch confers an increased potency of agonists by stabilizing an active conformation as assessed by engineered mini G proteins as conformational sensors. Disruption of the switch abrogates the functional interaction between FZDs and the phosphoprotein Dishevelled, supporting conformational selection as a prerequisite for functional selectivity. Our studies reveal the molecular basis of a common activation mechanism conserved in all Class F receptors, which facilitates assay development and future discovery of Class F receptor-targeting drugs., Class F receptors are therapeutic targets in human disease and understanding their structural changes during receptor activation may provide important pharmacological insight. Here, the authors combine computational and experimental methods to identify a molecular switch in TM6/7 of Class F receptors that mediates receptor activation.
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- 2019
7. Human MC4R variants affect endocytosis, trafficking and dimerization revealing multiple cellular mechanisms involved in weight regulation
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M. Madan Babu, Elana Henning, Maria Marti-Solano, Bianca Plouffe, Carole A. Daly, Julia M. Keogh, Michel Bouvier, Bas Brouwers, Rebecca Bounds, Jacek Mokrosinski, Fabiola B.F. Monteiro, I. Sadaf Farooqi, Suli-Anne Laurin, Vikram Ayinampudi, David Clarke, Natalia Wasiluk, Edson Mendes de Oliveira, Shane Houston, Farooqi, Ismaa [0000-0001-7609-3504], and Apollo - University of Cambridge Repository
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0301 basic medicine ,obesity ,MC4R ,Energy homeostasis ,Gα(s) ,0302 clinical medicine ,Chlorocebus aethiops ,Cyclic AMP ,GTP-Binding Protein alpha Subunits, Gs ,Phosphorylation ,Internalization ,Extracellular Signal-Regulated MAP Kinases ,lcsh:QH301-705.5 ,beta-Arrestins ,media_common ,Chemistry ,Effector ,16. Peace & justice ,Endocytosis ,Cell biology ,COS Cells ,Receptor, Melanocortin, Type 4 ,Signal Transduction ,Gs alpha subunit ,media_common.quotation_subject ,Allosteric regulation ,Biology ,Affect (psychology) ,Models, Biological ,General Biochemistry, Genetics and Molecular Biology ,Article ,GPCRs ,03 medical and health sciences ,SDG 3 - Good Health and Well-being ,Animals ,Humans ,melanocortin ,MSH ,G protein-coupled receptor ,therapy ,β-arrestin ,Gαs ,Body Weight ,Cell Membrane ,Genetic Variation ,030104 developmental biology ,HEK293 Cells ,lcsh:Biology (General) ,Mutation ,Mutant Proteins ,weight loss ,Protein Multimerization ,030217 neurology & neurosurgery ,Function (biology) - Abstract
Summary The Melanocortin-4 Receptor (MC4R) plays a pivotal role in energy homeostasis. We used human MC4R mutations associated with an increased or decreased risk of obesity to dissect mechanisms that regulate MC4R function. Most obesity-associated mutations impair trafficking to the plasma membrane (PM), whereas obesity-protecting mutations either accelerate recycling to the PM or decrease internalization, resulting in enhanced signaling. MC4R mutations that do not affect canonical Gαs protein-mediated signaling, previously considered to be non-pathogenic, nonetheless disrupt agonist-induced internalization, β-arrestin recruitment, and/or coupling to Gαs, establishing their causal role in severe obesity. Structural mapping reveals ligand-accessible sites by which MC4R couples to effectors and residues involved in the homodimerization of MC4R, which is disrupted by multiple obesity-associated mutations. Human genetic studies reveal that endocytosis, intracellular trafficking, and homodimerization regulate MC4R function to a level that is physiologically relevant, supporting the development of chaperones, agonists, and allosteric modulators of MC4R for weight loss therapy., Graphical abstract, Highlights • Obesity-associated MC4R mutations that do not reduce cAMP disrupt other processes • MC4R mutations impact receptor homodimerization, endocytosis, and trafficking • Obesity-protecting mutations increase plasma membrane MC4Rs and enhance signaling • Multiple mechanisms regulate melanocortin tone to a physiologically relevant level, Using mutations in the human Melanocortin-4 Receptor (MC4R), Brouwers et al. identify receptor trafficking and endocytosis, coupling to Gαs/β-arrestins, and homodimerization as mechanisms involved in the regulation of body weight that may be targeted for weight loss therapy.
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- 2021
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8. GPCRmd uncovers the dynamics of the 3D-GPCRome
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Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, Johanna K.S. Tiemann, David Aranda-García, Juan Manuel Ramírez-Anguita, Tomasz Maciej Stepniewski, Nathalie Worp, Alejandro Varela-Rial, Adrián Morales-Pastor, Brian Medel Lacruz, Gáspár Pándy-Szekeres, Eduardo Mayol, Toni Giorgino, Jens Carlsson, Xavier Deupi, Slawomir Filipek, Marta Filizola, José Carlos Gómez-Tamayo, Angel Gonzalez, Hugo Gutierrez-de-Teran, Mireia Jimenez, Willem Jespers, Jon Kapla, George Khelashvili, Peter Kolb, Dorota Latek, Maria Marti-Solano, Pierre Matricon, Minos-Timotheos Matsoukas, Przemyslaw Miszta, Mireia Olivella, Laura Perez-Benito, Davide Provasi, Santiago Ríos, Iván Rodríguez-Torrecillas, Jessica Sallander, Agnieszka Sztyler, Nagarajan Vaidehi, Silvana Vasile, Harel Weinstein, Ulrich Zachariae, Peter W. Hildebrand, Gianni De Fabritiis, Ferran Sanz, David E. Gloriam, Arnau Cordomi, Ramon Guixà-González, and Jana Selent
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Flexibility (engineering) ,0303 health sciences ,Protein family ,Computer science ,media_common.quotation_subject ,Context (language use) ,Data science ,Visualization ,03 medical and health sciences ,Molecular dynamics ,0302 clinical medicine ,Resource (project management) ,Function (engineering) ,030217 neurology & neurosurgery ,030304 developmental biology ,media_common ,G protein-coupled receptor - 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 3D molecular structures of GPCRs (3D-GPCRome) during the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. While experimentally-resolved structures undoubtedly provide valuable snapshots of specific GPCR conformational states, they give only limited information on their flexibility and dynamics associated with function. Molecular dynamics (MD) simulations have become a widely established technique to explore the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations requires efficient storage resources and specialized software, hence limiting the dissemination of these data to specialists in the field. Here we present the 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, analyse and share GPCR MD data. GPCRmd originates from a community-driven effort to create the first open, interactive, and standardized database of GPCR MD simulations. We demonstrate the power of this resource by performing comparative analyses of multiple GPCR simulations on two mechanisms critical to receptor function: internal water networks and sodium ion interaction.
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- 2020
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9. GPCRmd uncovers the dynamics of the 3D-GPCRome
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Minos-Timotheos Matsoukas, David E. Gloriam, Ismael Rodríguez-Espigares, Agnieszka Sztyler, Davide Provasi, Arnau Cordomí, Peter Kolb, David Aranda-García, Toni Giorgino, Ferran Sanz, Mariona Torrens-Fontanals, Peter W. Hildebrand, Maria Marti-Solano, Mireia Olivella, Alejandro Varela-Rial, Gianni De Fabritiis, José Carlos Gómez-Tamayo, Laura Pérez-Benito, Tomasz Maciej Stepniewski, Eduardo Mayol, Silvana Vasile, Slawomir Filipek, Ulrich Zachariae, Jens Carlsson, Dorota Latek, Harel Weinstein, Gáspár Pándy-Szekeres, Przemyslaw Miszta, Willem Jespers, Nathalie Worp, Mireia Jiménez-Rosés, Juan Manuel Ramírez-Anguita, Marta Filizola, George Khelashvili, Angel Gonzalez, Brian Medel Lacruz, Pierre Matricon, Iván Rodríguez-Torrecillas, Xavier Deupi, Adrián Morales-Pastor, Jessica Sallander, Hugo Gutiérrez-de-Terán, Johanna K. S. Tiemann, Jana Selent, Jon Kapla, Ramon Guixà-González, and Santiago Ríos
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Models, Molecular ,0303 health sciences ,model ,business.industry ,Computer science ,Extramural ,Protein Conformation ,Protein database ,Cell Biology ,Molecular Dynamics Simulation ,simulation ,Biochemistry ,Data science ,molecular dynamics ,Visualization ,Receptors, G-Protein-Coupled ,03 medical and health sciences ,Software ,GPCR ,Metabolome ,business ,Molecular Biology ,030304 developmental biology ,Biotechnology - 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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- 2020
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10. The allosteric site regulates the voltage sensitivity of muscarinic receptors
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Matthäus Drabek, Anika Hoppe, Maria Marti-Solano, Andreas Rinne, Moritz Bünemann, and Peter Kolb
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0301 basic medicine ,Patch-Clamp Techniques ,Allosteric modulator ,Recombinant Fusion Proteins ,Allosteric regulation ,Gene Expression ,Biosensing Techniques ,Molecular Dynamics Simulation ,Protein Structure, Secondary ,Membrane Potentials ,03 medical and health sciences ,Bacterial Proteins ,Muscarinic acetylcholine receptor ,Fluorescence Resonance Energy Transfer ,Humans ,Protein Interaction Domains and Motifs ,Receptor ,Binding Sites ,Gallamine Triethiodide ,biology ,Chimera ,Chemistry ,Cell Biology ,Receptors, Muscarinic ,Acetylcholine ,Kinetics ,Luminescent Proteins ,Transmembrane domain ,Crosstalk (biology) ,HEK293 Cells ,030104 developmental biology ,Biochemistry ,Gq alpha subunit ,Allosteric enzyme ,Hydroxyquinolines ,biology.protein ,Biophysics ,GTP-Binding Protein alpha Subunits, Gq-G11 ,Allosteric Site ,Protein Binding - Abstract
Muscarinic receptors (M-Rs) for acetylcholine (ACh) belong to the class A of G protein-coupled receptors. M-Rs are activated by orthosteric agonists that bind to a specific site buried in the M-R transmembrane helix bundle. In the active conformation, receptor function can be modulated either by allosteric modulators, which bind to the extracellular receptor surface or by the membrane potential via an unknown mechanism. Here, we compared the modulation of M1-Rs and M3-Rs induced by changes in voltage to their allosteric modulation by chemical compounds. We quantified changes in receptor signaling in single HEK 293 cells with a FRET biosensor for the Gq protein cycle. In the presence of ACh, M1-R signaling was potentiated by voltage, similarly to positive allosteric modulation by benzyl quinolone carboxylic acid. Conversely, signaling of M3-R was attenuated by voltage or the negative allosteric modulator gallamine. Because the orthosteric site is highly conserved among M-Rs, but allosteric sites vary, we constructed "allosteric site" M3/M1-R chimeras and analyzed their voltage dependencies. Exchanging the entire allosteric sites eliminated the voltage sensitivity of ACh responses for both receptors, but did not affect their modulation by allosteric compounds. Furthermore, a point mutation in M3-Rs caused functional uncoupling of the allosteric and orthosteric sites and abolished voltage dependence. Molecular dynamics simulations of the receptor variants indicated a subtype-specific crosstalk between both sites, involving the conserved tyrosine lid structure of the orthosteric site. This molecular crosstalk leads to receptor subtype-specific voltage effects.
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- 2018
11. Serotonin 2A receptor disulfide bridge integrity is crucial for ligand binding to different signalling states but not for its homodimerization
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María Isabel Loza, María Isabel Cadavid, Jana Selent, Marta Cimadevila, Marián Castro, Maria Marti-Solano, José Brea, Rocio A. de la Fuente, and Alba Iglesias
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Models, Molecular ,0301 basic medicine ,Allosteric regulation ,CHO Cells ,Ligands ,Dithiothreitol ,03 medical and health sciences ,chemistry.chemical_compound ,Cricetulus ,0302 clinical medicine ,Radioligand binding ,Phospholipase C ,Cricetinae ,Functional selectivity ,Animals ,Humans ,Receptor, Serotonin, 5-HT2A ,Amino Acid Sequence ,Disulfides ,Phospholipase ,Serotonina--Receptors ,Binding site ,Protein Structure, Quaternary ,Receptor ,Clozapine ,Serotonin hydrochloride ,G protein-coupled receptor ,Pharmacology ,Methysergide maleate ,Binding Sites ,Chemistry ,Serotonin 2(A) receptor ,Nuclear Proteins ,Disulfide bridges ,Ligand (biochemistry) ,030104 developmental biology ,Biochemistry ,DL-1,4-Dithiothreitol ,Biophysics ,Protein Multimerization ,030217 neurology & neurosurgery ,Protein Binding ,Signal Transduction ,Cysteine - Abstract
The serotonin 2A (5-HT2A) receptor is a G-protein coupled receptor (GPCR) with a conserved disulfide bridge formed by Cys148 (transmembrane helix 3, TM3) and Cys227 (extracellular loop 2, ECL-2). We hypothesized that disulfide bridges may determine serotonin 5-HT2A receptor functions such as receptor activation, functional selectivity and ligand recognition. We used the reducing agent dithiothreitol (DTT) to determine how the reduction of disulfide bridges affects radioligand binding, second messenger mobilization and receptor dimerization. A DTT-induced decrease in the number of binding sites (1190 ± 63.55 fmol/mg protein for control cells compared with 921.2 ± 60.84 fmol/mg protein for DTT-treated cells) as well as in the efficacy of both signalling pathways characterized was observed, although the affinity and potency were unchanged. Bioluminiscence resonance energy transfer (BRET) assays revealed the DTT treatment did not modify the homodimeric nature of serotonin 5-HT2A receptors. In molecular dynamic simulations, the ECL-2 of the receptor with a broken cysteine bond adopts a wider variety of conformations, some of which protrude deeper into the receptor orthosteric binding pocket leading to collapse of the pocket. A shrunken binding pocket would be incapable of accommodating lysergic acid diethylamide (LSD). Our findings suggest that the decrease of efficacy may be due to disruption of disulfide bridge between TM3 and ECL-2. This reveals the integrity of the ECL-2 epitope, which should be explored in the development of novel ligands acting as allosteric modulators of serotonin 5-HT2A receptors. his work was supported by Ministerio de Ciencia e Innovacion (SAF2009-13609-C04-01), Ministerio de Economia y Competitividad (SAF2014-57138-C2-2R), and Innopharma project (PI12/00742; Ministerio de Economía y Competitividad -FEDER). A.I. was recipient of a FPI fellowship from Ministerio de Ciencia e Innovacion. M. Cimadevila is recipient of a financial support from the Xunta de Galicia (ED481A-2016/096) and the European Union (European Social Fund - ESF).
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- 2017
12. POLEandPOLD1screening in 155 patients with multiple polyps and early-onset colorectal cancer
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Clara Esteban-Jurado, Sebastià Franch-Expósito, Clara Ruiz-Ponte, Sergi Castellví-Bel, Maria Marti-Solano, Sabela Carballal, Joaquín Cubiella, David Giménez-Zaragoza, Teresa Ocaña, Gemma Llort, Jenifer Muñoz, Rosa Aligué, María López-Cerón, Francesc Balaguer, Tom van Wezel, Luis Bujanda, Miriam Cuatrecasas, Judith Balmaña, Victoria Gonzalo, Antoni Castells, Miriam Alvarez-Barona, and Marcos Díaz-Gay
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Male ,Models, Molecular ,0301 basic medicine ,Protein Conformation ,Colorectal cancer ,0302 clinical medicine ,Medicine ,Age of Onset ,Multiple Polyps ,Child ,Poly-ADP-Ribose Binding Proteins ,Early onset ,Aged, 80 and over ,colorectal adenoma ,Middle Aged ,University hospital ,Pedigree ,Adenomatous Polyposis Coli ,Oncology ,Child, Preschool ,030220 oncology & carcinogenesis ,POLE ,Female ,Colorectal Neoplasms ,Research Paper ,Adult ,medicine.medical_specialty ,Adolescent ,Colorectal adenoma ,POLD1 ,Young Adult ,03 medical and health sciences ,Protein Domains ,Humans ,Genetic Testing ,Alleles ,Genetic Association Studies ,Aged ,DNA Polymerase III ,genetic predisposition to disease ,Gynecology ,Cancer prevention ,business.industry ,Infant, Newborn ,Infant ,DNA Polymerase II ,medicine.disease ,030104 developmental biology ,Amino Acid Substitution ,Colorectal neoplasm ,Mutation ,colorectal neoplasm ,business - Abstract
// Clara Esteban-Jurado 1 , David Gimenez-Zaragoza 2 , Jenifer Munoz 1 , Sebastia Franch-Exposito 1 , Miriam Alvarez-Barona 3 , Teresa Ocana 1 , Miriam Cuatrecasas 4 , Sabela Carballal 1 , Maria Lopez-Ceron 1 , Maria Marti-Solano 5 , Marcos Diaz-Gay 1 , Tom van Wezel 6 , Antoni Castells 1 , Luis Bujanda 7 , Judith Balmana 8 , Victoria Gonzalo 9 , Gemma Llort 10 , Clara Ruiz-Ponte 3 , Joaquin Cubiella 11 , Francesc Balaguer 1 , Rosa Aligue 2 , Sergi Castellvi-Bel 1 1 Gastroenterology Department, Hospital Clinic, Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain 2 Biomedical Sciences Department, School of Medicine, University de Barcelona, Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain 3 Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clinico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain 4 Department of Pathology, Hospital Clinic, Biobanc Clinic-IDIBAPS, Barcelona, Catalonia, Spain 5 Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany 6 Leiden University Medical Center (LUMC), Leiden, Netherlands 7 Gastroenterology Department, Hospital Donostia–Instituto Biodonostia, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas (CIBEREHD), Basque Country University (UPV/EHU), San Sebastian, Spain 8 High Risk and Cancer Prevention Unit, Medical Oncology Department, University Hospital Vall d’Hebron and Vall d’Hebron Institute of Oncology, Barcelona, Spain 9 Gastroenterology Department, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain 10 Clinical Oncology Department, Corporacio Parc Tauli, Sabadell, Barcelona, Spain 11 Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigacion Biomedica Ourense, Pontevedra y Vigo, Ourense, Spain Correspondence to: Sergi Castellvi-Bel, email: sbel@clinic.cat Keywords: colorectal neoplasm, colorectal adenoma, genetic predisposition to disease, POLE, POLD1 Received: January 04, 2017 Accepted: February 18, 2017 Published: March 01, 2017 ABSTRACT Germline mutations in POLE and POLD1 have been shown to cause predisposition to colorectal multiple polyposis and a wide range of neoplasms, early-onset colorectal cancer being the most prevalent. In order to find additional mutations affecting the proofreading activity of these polymerases, we sequenced its exonuclease domain in 155 patients with multiple polyps or an early-onset colorectal cancer phenotype without alterations in the known hereditary colorectal cancer genes. Interestingly, none of the previously reported mutations in POLE and POLD1 were found. On the other hand, among the genetic variants detected, only two of them stood out as putative pathogenic in the POLE gene, c.1359 + 46del71 and c.1420G > A (p.Val474Ile). The first variant, detected in two families, was not proven to alter correct RNA splicing. Contrarily, c.1420G > A (p.Val474Ile) was detected in one early-onset colorectal cancer patient and located right next to the exonuclease domain. The pathogenicity of this change was suggested by its rarity and bioinformatics predictions, and it was further indicated by functional assays in Schizosaccharomyces pombe . This is the first study to functionally analyze a POLE genetic variant outside the exonuclease domain and widens the spectrum of genetic changes in this DNA polymerase that could lead to colorectal cancer predisposition.
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- 2017
13. Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome
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Johanna K. S. Tiemann, George Khelashvili, Brian Medel-Lacruz, Ramon Guixà-González, Alejandro Varela-Rial, José Carlos Gómez-Tamayo, Marta Filizola, Dorota Latek, Gianni De Fabritiis, David Aranda-García, Juan Manuel Ramírez-Anguita, Santiago Ríos, Davide Provasi, David E. Gloriam, Jana Selent, Minos-Timotheos Matsoukas, Toni Giorgino, Ferran Sanz, Jon Kapla, Silvana Vasile, Slawomir Filipek, Xavier Deupi, Adrián Morales-Pastor, Przemyslaw Miszta, Àngel Puyol González, Mireia Jiménez-Rosés, Harel Weinstein, Peter Kolb, Agnieszka Sztyler, Nathalie Worp, Maria Marti-Solano, Arnau Cordomí, Ulrich Zachariae, Ismael Rodríguez-Espigares, Pierre Matricon, Ivan R. Torrecillas, Tomasz Maciej Stepniewski, Eduardo Mayol, Gáspár Pándy-Szekeres, Peter W. Hildebrand, Mireia Olivella, Mariona Torrens-Fontanals, Hugo Gutiérrez-de-Terán, Laura Pérez-Benito, Jens Carlsson, Willem Jespers, and Jessica Sallander
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Published Erratum ,Protein database ,Cell Biology ,Computational biology ,Biology ,Molecular Biology ,Biochemistry ,Membrane biophysics ,Biotechnology - Published
- 2020
14. Combinatorial expression of GPCR isoforms affects signalling and drug responses
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Junmin Peng, Graham Ladds, Manojkumar A. Puthenveedu, Amanda E. Mackenzie, Christian Munk, Matthew Harris, Xusheng Wang, Graeme Milligan, Tezz Quon, Stephanie E Crilly, M. Madan Babu, David E. Gloriam, Andrew B. Tobin, Maria Marti-Solano, Duccio Malinverni, Abigail Pearce, Marti-Solano, Maria [0000-0003-0373-8927], Pearce, Abigail [0000-0001-9845-0541], Peng, Junmin [0000-0003-0472-7648], Tobin, Andrew B [0000-0002-1807-3123], Ladds, Graham [0000-0001-7320-9612], Milligan, Graeme [0000-0002-6946-3519], Gloriam, David E [0000-0002-4299-7561], Puthenveedu, Manojkumar A [0000-0002-3177-4231], Babu, M Madan [0000-0003-0556-6196], and Apollo - University of Cambridge Repository
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0301 basic medicine ,Gene isoform ,Proteomics ,Databases, Factual ,Computational biology ,Biology ,Article ,Receptors, G-Protein-Coupled ,03 medical and health sciences ,0302 clinical medicine ,Single-cell analysis ,Humans ,Protein Isoforms ,Molecular Targeted Therapy ,Receptor ,G protein-coupled receptor ,Multidisciplinary ,Gene Expression Profiling ,HEK 293 cells ,Gene expression profiling ,030104 developmental biology ,HEK293 Cells ,Membrane protein ,Organ Specificity ,Single-Cell Analysis ,Transcriptome ,030217 neurology & neurosurgery ,Signal Transduction - Abstract
G protein-coupled receptors (GPCRs) are transmembrane proteins that modulate physiology across diverse tissues in response to extracellular signals. GPCR signalling can differ due to variation in the sequence (e.g. polymorphisms) or in the expression of receptors in different tissues. The resulting differences in response are an important source of physiological signalling bias. An underexplored source of such bias is the generation of functionally diverse GPCR isoforms that can have distinct patterns of expression in human tissues. Here, we report the findings from a comprehensive study, integrating data from human tissue-level transcriptomes, GPCR sequences and structures, functional annotations, proteomics, single-cell RNA sequencing, population-wide genetic association studies, and pharmacological experiments. Our results show how a single GPCR gene can diversify into multiple isoforms with distinct structural and signalling properties, and how unique combinations of these isoforms can be expressed in different human tissues, contributing to differences in physiological signalling. Based on their structural changes and expression patterns, some of the detected isoforms may also influence drug response and represent new drug targets with improved tissue selectivity. Our findings highlight the need to move from a canonical to a context-specific view of GPCR signalling, in which one considers how the combinatorial expression of receptor isoforms in a specific system (i.e. a particular cell type, tissue, or organism) collectively impacts receptor signalling. These observations pave the way for understanding the impact of isoform variation on GPCR signalling response and have implications for exploiting such variation as a source of GPCR selectivity in drug development.
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- 2019
15. Context-Specific Striatal Astrocyte Molecular Responses Are Phenotypically Exploitable
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Xinzhu Yu, Maria Marti-Solano, M. Madan Babu, Giovanni Coppola, Baljit S. Khakh, Joselyn S. Soto, and Jun Nagai
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HD ,Huntington's Disease ,0301 basic medicine ,striatum ,Synaptogenesis ,Stimulation ,Striatum ,Neurodegenerative ,Mice ,synaptogenic ,GPCR ,0302 clinical medicine ,Data Mining ,Psychology ,context-specific ,Neurons ,General Neuroscience ,RNA sequencing ,Phenotype ,Huntington Disease ,medicine.anatomical_structure ,Neurological ,Cognitive Sciences ,Signal transduction ,Signal Transduction ,Astrocyte ,neuroimmune ,perturbation ,Central nervous system ,Biology ,Article ,03 medical and health sciences ,astrocyte ,Rare Diseases ,Genetics ,medicine ,Animals ,Humans ,G protein-coupled receptor ,calcium ,Neurology & Neurosurgery ,behavior ,Neurosciences ,Corpus Striatum ,Brain Disorders ,030104 developmental biology ,Astrocytes ,Synapses ,Neuroscience ,030217 neurology & neurosurgery - Abstract
Summary Astrocytes tile the central nervous system and are widely implicated in brain diseases, but the molecular mechanisms by which astrocytes contribute to brain disorders remain incompletely explored. By performing astrocyte gene expression analyses following 14 experimental perturbations of relevance to the striatum, we discovered that striatal astrocytes mount context-specific molecular responses at the level of genes, pathways, and upstream regulators. Through data mining, we also identified astrocyte pathways in Huntington’s disease (HD) that were reciprocally altered with respect to the activation of striatal astrocyte G protein-coupled receptor (GPCR) signaling. Furthermore, selective striatal astrocyte stimulation of the Gi-GPCR pathway in vivo corrected several HD-associated astrocytic, synaptic, and behavioral phenotypes, with accompanying improvement of HD-associated astrocyte signaling pathways, including those related to synaptogenesis and neuroimmune functions. Overall, our data show that astrocytes are malleable, using context-specific responses that can be dissected molecularly and used for phenotypic benefit in brain disorders.
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- 2020
16. Drugging specific conformational states of GPCRs: challenges and opportunities for computational chemistry
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Jana Selent, Denis Schmidt, Maria Marti-Solano, and Peter Kolb
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0301 basic medicine ,Pharmacology ,Protein Conformation ,Nanotechnology ,Context (language use) ,Computational biology ,Molecular Dynamics Simulation ,Biology ,Receptors, G-Protein-Coupled ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Drug development ,Structural biology ,Drug Design ,Drug Discovery ,030217 neurology & neurosurgery ,G protein-coupled receptor - Abstract
Current advances in structural biology for membrane proteins support the existence of multiple Gprotein-coupled receptor (GPCR) conformations. These conformations can be associated to particular receptor states with definite coupling and signaling capacities. Drugging such receptor states represents an opportunity to discover a new generation of GPCR drugs with unprecedented specificity. However, exploiting recently available structural information to develop these drugs is still challenging. In this context, computational structure-based approaches can inform such drug development. In this review, we examine the potential of these approaches and the challenges they will need to overcome to guide the rational discovery of drugs targeting specific GPCR states.
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- 2016
17. Unbiased dynamic characterization of RNA-protein interactions by OOPS
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Dan-Mircea Mirea, E A Willis, Manasa Ramakrishna, H G Thomas, Veronica Dezi, Lennart Martens, Sven Degroeve, Mariavittoria Pizzinga, Maria Marti-Solano, L M R Queiroz, S K Lilley, Mie Monti, Eneko Villanueva, Tom Smith, and F R Harvey
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0303 health sciences ,Rna protein ,Computer science ,Free protein ,RNA ,Single sample ,Computational biology ,Limiting ,Human cell ,Proteomics ,03 medical and health sciences ,0302 clinical medicine ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Current methods for the identification of RNA–protein interactions require a quantity and quality of sample that hinders their application, especially for dynamic biological systems or when sample material is limiting. Here, we present a new approach to enrich RNA-Binding Proteins (RBPs): Orthogonal Organic Phase Separation (OOPS), which is compatible with downstream proteomics and RNA sequencing. OOPS enables recovery of RBPs and free protein, or protein-bound RNA and free RNA, from a single sample in an unbiased manner. By applying OOPS to human cell lines, we extract the majority of known RBPs, and importantly identify additional novel RBPs, including those from previously under-represented cellular compartments. The high yield and unbiased nature of OOPS facilitates its application in both dynamic and inaccessible systems. Thus, we have identified changes in RNA-protein interactions in mammalian cells following nocodazole cell-cycle arrest, and defined the first bacterial RNA-interactome. Overall, OOPS provides an easy-to-use and flexible technique that opens new opportunities to characterize RNA-protein interactions and explore their dynamic behaviour.
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- 2018
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18. Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)
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Rayner M L, Queiroz, Tom, Smith, Eneko, Villanueva, Maria, Marti-Solano, Mie, Monti, Mariavittoria, Pizzinga, Dan-Mircea, Mirea, Manasa, Ramakrishna, Robert F, Harvey, Veronica, Dezi, Gavin H, Thomas, Anne E, Willis, and Kathryn S, Lilley
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Proteomics ,Proteome ,Sequence Analysis, RNA ,Nocodazole ,RNA-Binding Proteins ,RNA, Bacterial ,Cross-Linking Reagents ,HEK293 Cells ,Cell Line, Tumor ,Escherichia coli ,Cluster Analysis ,Humans ,RNA ,RNA, Long Noncoding ,RNA, Messenger ,Transcriptome ,Glycoproteins ,Protein Binding ,Thymidine - Abstract
Existing high-throughput methods to identify RNA-binding proteins (RBPs) are based on capture of polyadenylated RNAs and cannot recover proteins that interact with nonadenylated RNAs, including long noncoding RNA, pre-mRNAs and bacterial RNAs. We present orthogonal organic phase separation (OOPS), which does not require molecular tagging or capture of polyadenylated RNA, and apply it to recover cross-linked protein-RNA and free protein, or protein-bound RNA and free RNA, in an unbiased way. We validated OOPS in HEK293, U2OS and MCF10A human cell lines, and show that 96% of proteins recovered were bound to RNA. We show that all long RNAs can be cross-linked to proteins, and recovered 1,838 RBPs, including 926 putative novel RBPs. OOPS is approximately 100-fold more efficient than existing methods and can enable analyses of dynamic RNA-protein interactions. We also characterize dynamic changes in RNA-protein interactions in mammalian cells following nocodazole arrest, and present a bacterial RNA-interactome for Escherichia coli. OOPS is compatible with downstream proteomics and RNA sequencing, and can be applied in any organism.
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- 2018
19. Membrane cholesterol access into a G-protein-coupled receptor
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Jana Selent, Ramon Guixà-González, Ismael Rodríguez-Espigares, Manuel Pastor, José Luis Albasanz, Maria Marti-Solano, Ferran Sanz, Hector Martinez-Seara, Moutusi Manna, Peter W. Hildebrand, Mairena Martín, Tampere University, Physics, and Research area: Computational Physics
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0301 basic medicine ,Receptor, Adenosine A2A ,Membrane lipids ,Science ,Allosteric regulation ,General Physics and Astronomy ,Adenosine A2A receptor ,Plasma protein binding ,Molecular dynamics ,Biology ,Molecular Dynamics Simulation ,Binding, Competitive ,114 Physical sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,Receptors, G-Protein-Coupled ,03 medical and health sciences ,0302 clinical medicine ,G protein-coupled receptors ,Protein Domains ,Cell Line, Tumor ,Animals ,Binding site ,Receptor ,G protein-coupled receptor ,Multidisciplinary ,Binding Sites ,Cell Membrane ,membrane lipids ,General Chemistry ,3. Good health ,Cell biology ,Rats ,030104 developmental biology ,Cholesterol ,Biotinylation ,lipids (amino acids, peptides, and proteins) ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Cholesterol is a key component of cell membranes with a proven modulatory role on the function and ligand-binding properties of G-protein-coupled receptors (GPCRs). Crystal structures of prototypical GPCRs such as the adenosine A2A receptor (A2AR) have confirmed that cholesterol finds stable binding sites at the receptor surface suggesting an allosteric role of this lipid. Here we combine experimental and computational approaches to show that cholesterol can spontaneously enter the A2AR-binding pocket from the membrane milieu using the same portal gate previously suggested for opsin ligands. We confirm the presence of cholesterol inside the receptor by chemical modification of the A2AR interior in a biotinylation assay. Overall, we show that cholesterol's impact on A2AR-binding affinity goes beyond pure allosteric modulation and unveils a new interaction mode between cholesterol and the A2AR that could potentially apply to other GPCRs., G-protein-coupled receptors trigger several signalling pathways and their activity was proposed to be allosteric modulated by cholesterol. Here the authors use molecular dynamics simulations and ligand binding assays to show that membrane cholesterol can bind to adenosine A2A receptor orthosteric site.
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- 2017
20. Author Correction: Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)
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Veronica Dezi, Robert F. Harvey, Manasa Ramakrishna, Kathryn S. Lilley, Maria Marti-Solano, Tom Smith, Anne E. Willis, Eneko Villanueva, Gavin H. Thomas, Dan-Mircea Mirea, Mie Monti, Rayner M. L. Queiroz, and Mariavittoria Pizzinga
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Rna protein ,Chemistry ,Biomedical Engineering ,Molecular Medicine ,RNA ,Bioengineering ,Identification (biology) ,Computational biology ,Proteomics ,Applied Microbiology and Biotechnology ,Article ,Organism ,Biotechnology - Abstract
Existing high-throughput methods to identify RNA-binding proteins (RBPs) involving capture of polyadenylated RNAs can not recover proteins that interact with non-adenylated RNAs, including lncRNA, pre-mRNA and bacterial RNAs. We present orthogonal organic phase separation (OOPS) which does not require molecular tagging or capture of polyadenylated RNA. We verify OOPS in HEK293, U2OS and MCF10A human cell lines, finding 96% of proteins recovered are bound to RNA. We demonstrate that all long RNAs can be crosslinked to proteins and recover 1838 RBPs, including 926 putative novel RBPs. Importantly, OOPS is approximately 100-fold more efficient than current techniques, enabling analysis of dynamic RNA-protein interactions. We identified 749 proteins with altered RNA binding following release from nocodazole arrest. Finally, OOPS allowed the characterisation of the first RNA-interactome for a bacterium, Escherichia coli. OOPS is an easy to use and flexible technique, compatible with downstream proteomics and RNA sequencing and applicable to any organism.
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- 2019
21. Novel Insights into Biased Agonism at G Protein-Coupled Receptors and their Potential for Drug Design
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Manuel Pastor, Ramon Guixà-González, Ferran Sanz, Maria Marti-Solano, and Jana Selent
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Pharmacology ,Binding Sites ,Effector ,Drug Agonism ,Molecular Conformation ,Rational design ,Computational Biology ,Nanotechnology ,Computational biology ,Biology ,Ligands ,Models, Biological ,Receptors, G-Protein-Coupled ,Drug Design ,Drug Discovery ,Functional selectivity ,Animals ,Humans ,Binding site ,Signal transduction ,Function (biology) ,Signal Transduction ,G protein-coupled receptor - Abstract
G-protein coupled receptors (GPCRs) are the most important class of current pharmacological targets. However, it is now widely acknowledged that their regulation is more complex than previously thought: the evidence that GPCRs can couple to several effector pathways, and the existence of biased agonists able to activate them differentially, has introduced a new level of complexity in GPCR drug research. Considering bias represents a challenge for the research of new GPCR modulators, because it demands a detailed characterization of compound properties for several effector pathways. Still, biased ligands could provide an opportunity to modulate GPCR function in a finer way and to separate therapeutic from side effects. Nowadays, a variety of agonists for GPCRs have been described, which differ in their ability to promote receptor coupling to different Gprotein families or even subunits, recruit signal transducers such as arrestins, activate a variety of downstream molecular pathways and induce certain phosphorylation signatures or gene expression patterns. In this review, we will cover some of the experimental techniques currently used to understand and characterize biased agonism and discuss their strengths and limitations. Additionally, we will comment on the computational efforts that are being devoted to study ligand-induced bias and on the potential they hold for rationalizing its structural determinants. Finally, we will discuss which of these strategies could be used for the rational design of biased ligands and give some examples of the potential therapeutic value of this class of compounds.
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- 2013
22. Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness
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Maria Marti-Solano, Eneko Villanueva, and Cristina Fillat
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Gene Expression Regulation, Viral ,0301 basic medicine ,Protein Folding ,viruses ,Green Fluorescent Proteins ,Context (language use) ,Genome, Viral ,Biology ,medicine.disease_cause ,Genome ,Article ,Adenoviridae ,Viral Proteins ,03 medical and health sciences ,0302 clinical medicine ,Neoplasms ,medicine ,Humans ,Virotherapy ,Codon ,Oncolytic Virotherapy ,Genetics ,Regulation of gene expression ,Principal Component Analysis ,Multidisciplinary ,Genomes bacterians ,HEK293 Cells ,030104 developmental biology ,Lytic cycle ,A549 Cells ,030220 oncology & carcinogenesis ,Codon usage bias ,Capsid Proteins ,Genetic Engineering ,Function (biology) ,HeLa Cells ,Plasmids - Abstract
Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development. This work was supported by grants from the Spanish Ministry of Economia y Competitividad BIO2014-57716-C2-2-R and receives partial support from the Generalitat de Catalunya SGR14/248. CIBER de Enfermedades Raras is an initiative of the ISCIII. CF group is partially financed by the Instituto de Salud Carlos III (IIS10/00014) and co-financed by Fondo Europeo de Desarrollo Regional (FEDER). We also acknowledge the support of COST Action BM1204 EUPancreas. E.V. was supported by a fellowship from the Gobierno Vasco, Spain.
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- 2016
23. Detection of new biased agonists for the serotonin 5-HT2A receptor: modeling and experimental validation
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Ferran Sanz, Jana Selent, Gianni De Fabritiis, Manuel Pastor, M. Isabel Loza, Alba Iglesias, Maria Marti-Solano, and José Brea
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Pharmacology ,Serotonin ,Rational design ,Experimental validation ,Computational biology ,CHO Cells ,Biology ,Molecular Dynamics Simulation ,Ligand (biochemistry) ,Molecular Docking Simulation ,Binding, Competitive ,Cricetulus ,Drug Design ,Functional selectivity ,Molecular Medicine ,Animals ,Humans ,Receptor, Serotonin, 5-HT2A ,Receptor ,Serotonin 5-HT2 Receptor Agonists ,Antipsychotic Agents - Abstract
Detection of biased agonists for the serotonin 5-HT2A receptor can guide the discovery of safer and more efficient antipsychotic drugs. However, the rational design of such drugs has been hampered by the difficulty detecting the impact of small structural changes on signaling bias. To overcome these difficulties, we characterized the dynamics of ligand-receptor interactions of known biased and balanced agonists using molecular dynamics simulations. Our analysis revealed that interactions with residues S5.46 and N6.55 discriminate compounds with different functional selectivity. Based on our computational predictions, we selected three derivatives of the natural balanced ligand serotonin and experimentally validated their ability to act as biased agonists. Remarkably, our approach yielded compounds promoting an unprecedented level of signaling bias at the 5-HT2A receptor, which could help interrogate the importance of particular pathways in conditions like schizophrenia.
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- 2015
24. A Dynamic View of Molecular Switch Behavior at Serotonin Receptors: Implications for Functional Selectivity
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Ferran Sanz, Manuel Pastor, Jana Selent, and Maria Marti-Solano
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Biophysical Simulations ,G protein ,Biophysics ,lcsh:Medicine ,Molecular Dynamics Simulation ,Biochemistry ,Protein structure ,Neuropharmacology ,Computational Chemistry ,Chemical Biology ,Receptor, Serotonin, 5-HT2B ,Functional selectivity ,Macromolecular Structure Analysis ,Medicine and Health Sciences ,Ergotamine ,Biomacromolecule-Ligand Interactions ,lcsh:Science ,Receptor ,Databases, Protein ,Intracellular part ,Molecular Biology ,5-HT receptor ,G protein-coupled receptor ,Multidisciplinary ,Binding Sites ,Protein Stability ,lcsh:R ,Biology and Life Sciences ,Computational Biology ,Serotonina -- Receptors ,Protein Structure, Tertiary ,Serotonin Receptor Agonists ,Chemistry ,Neurology ,Helix ,Physical Sciences ,Receptor, Serotonin, 5-HT1B ,Thermodynamics ,lcsh:Q ,Proteïnes ,Hydrophobic and Hydrophilic Interactions ,Research Article - Abstract
Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity. This work was funded by the Ministerio de Educación y Ciencia, grant number SAF2009-13609-C04-04, and La MARATÓ de TV3 Foundation, grant number 091010. MM-S is supported by a doctoral fellowship from the University and Research Secretariat of the Catalan Government and the European Social Fund (2013FI_B 00143). JS acknowledges support from the Instituto de Salud Carlos III FEDER (CP12/03139) and the GLISTEN European Research Network
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- 2014
25. Integrative knowledge management to enhance pharmaceutical R&D
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Barend Mons, Oscar Della Pasqua, Maria Marti-Solano, Ioannis Xenarios, Hiroaki Kitano, Antoine Bril, Ferran Sanz, and Ewan Birney
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Pharmacology ,Information management ,Knowledge management ,Drug Industry ,Information Management ,business.industry ,Process (engineering) ,Computer science ,Research ,Information technology ,General Medicine ,Knowledge Management ,Drug Discovery ,Key (cryptography) ,Humans ,Technology, Pharmaceutical ,Cooperative behavior ,Cooperative Behavior ,business - Abstract
Information technologies already have a key role in pharmaceutical research and development (R&D), but achieving substantial advances in their use and effectiveness will depend on overcoming current challenges in sharing, integrating and jointly analysing the range of data generated at different stages of the R&D process.
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- 2014
26. Application of BRET for studying G protein-coupled receptors
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Magdalena Makarska-Bialokoz, Agnieszka A. Kaczor, Rocio A. de la Fuente, Maria Marti-Solano, Marián Castro, and Jana Selent
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Pharmacology ,Bioluminescence Resonance Energy Transfer Techniques ,Models, Molecular ,biology ,Kinase ,G protein ,Chemistry ,Energy transfer ,General Medicine ,Computational biology ,Bioinformatics ,Receptor tyrosine kinase ,Receptors, G-Protein-Coupled ,Cell surface receptor ,Drug Discovery ,biology.protein ,Animals ,Humans ,Receptor ,Function (biology) ,G protein-coupled receptor - Abstract
G protein-coupled receptors (GPCRs) constitute one of the largest classes of cell surface receptors. GPCR biology has been a subject of widespread interest owing to the functional relevance of these receptors and their potential importance in the development of new drugs. At present, over 30% of all launched drugs target these receptors. GPCRs have been considered for a long time to function as monomeric entities and the idea of GPCR dimerization and oligomerization was initially accepted with disbelief. However, a significant amount of experimental and molecular modeling evidence accumulated during the last several years suggests that the process of GPCRs dimer or oligomer formation is a general phenomenon, in some cases even essential for receptor function. Among the many methods to study GPCR dimerization and oligomerization, modern biophysical techniques such as those based on resonance energy transfer (RET) and particularly bioluminescence resonance energy transfer (BRET) have played a leading role. RET methods are commonly applied as non-destructive indicators of specific protein-protein interactions (PPIs) in living cells. Data from numerous BRET experiments support the idea that the process of GPCR oligomerization may be relevant in many physiological and pathological conditions. The application of BRET to the study of GPCRs is not only limited to the assessment of receptor oligomerization but also expands to the investigation of the interactions of GPCRs with other proteins, including G proteins, G protein-coupled receptor kinases, β-arrestins or receptor tyrosine kinases, as well as to the characterization of GPCR activation and signaling. In this review, we briefly summarize the fundaments of BRET, discuss new trends in this technology and describe the wide range of applications of BRET to study GPCRs.
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- 2013
27. Novel insights on the structural determinants of clozapine and olanzapine multi-target binding profiles
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Jana Selent, Patricio Atanes, Manuel Pastor, José Brea, M. Isabel Loza, Javier Maseda Rodríguez, Ferran Sanz, Maria Marti-Solano, and Marián Castro
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Olanzapine ,Models, Molecular ,Stereochemistry ,Mutagenesis (molecular biology technique) ,Computational biology ,Ligands ,Binding, Competitive ,Benzodiazepines ,Structure-Activity Relationship ,Multi target ,Drug Discovery ,medicine ,Humans ,Site-directed mutagenesis ,Clozapine ,G protein-coupled receptor ,Pharmacology ,Dose-Response Relationship, Drug ,Molecular Structure ,Chemistry ,Receptors, Dopamine D2 ,Organic Chemistry ,Hydrogen Bonding ,General Medicine ,Affinities ,Transmembrane domain ,Receptor, Serotonin, 5-HT1A ,Mutagenesis, Site-Directed ,Hydrophobic and Hydrophilic Interactions ,medicine.drug ,Antipsychotic Agents ,Protein Binding - Abstract
The clinical efficacy of antipsychotic drugs has been associated with a certain binding profile for a set of G protein-coupled receptors (GPCR)s. In this work, we use the structurally-related clozapine-olanzapine pair to progress in the understanding of the structural properties that determine their divergent binding profiles and, thereby, their differing therapeutic efficacy. First, we present novel site-directed mutagenesis results that confirm our previous hypothesis on the importance of ligand interaction with positions 5.42 and 5.46 in transmembrane helix 5. Then, we use refined models of ligand-receptor complexes, built from recently published GPCR crystal structures, to gain further insight into the molecular mechanisms responsible for the observed experimental outcomes. In particular, we observe that preventing or potentiating hydrogen bonding with position 5.46, could allow obtaining ligands with, respectively, clozapine or olanzapine-like affinities. Results presented in this study could guide the design of antipsychotic candidates with tailored binding profiles. © 2014 Elsevier Masson SAS. All rights reserved.
- Published
- 2013
28. Treatment with a sphingosine-1-phosphate analog inhibits airway remodeling following repeated allergen exposure
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Kimitake Tsuchiya, Harry Karmouty-Quintana, Maria Marti-Solano, Sana Siddiqui, Paul Andre Risse, Laura Xicota-Vila, Muhannad Hassan, and James G. Martin
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Pulmonary and Respiratory Medicine ,Male ,CD3 Complex ,Physiology ,Lymphocyte ,T cell ,Bronchi ,Severity of Illness Index ,chemistry.chemical_compound ,Smooth muscle ,Sphingosine ,hemic and lymphatic diseases ,Physiology (medical) ,medicine ,Animals ,Sphingosine-1-phosphate ,Anti-Asthmatic Agents ,medicine.diagnostic_test ,business.industry ,Fingolimod Hydrochloride ,Muscle, Smooth ,Cell Biology ,Lipid signaling ,respiratory system ,Allergens ,Asthma ,respiratory tract diseases ,Rats ,medicine.anatomical_structure ,Bronchoalveolar lavage ,Treatment Outcome ,chemistry ,Propylene Glycols ,Immunology ,Airway Remodeling ,ALLERGEN EXPOSURE ,Lysophospholipids ,Airway ,business ,Bronchoalveolar Lavage Fluid ,Immunosuppressive Agents - Abstract
Sphingosine-1-phosphate (S1P) is an immunomodulatory lipid mediator that plays an important role in lymphocyte trafficking. Elevated levels of S1P are found in bronchoalveolar lavage (BAL) fluid of patients with asthma; however, its role in disease is not known. FTY720, a synthetic analog of S1P, has been shown to abrogate allergic inflammation and airway hyperresponsiveness following acute allergen challenge. However, its effects on asthmatic airway remodeling induced by repeated allergen exposure are unknown. Ovalbumin (OVA)-sensitized rats were challenged on days 14, 19, and 24 after sensitization. FTY720 or vehicle (PBS) therapy was administered 1 h prior to each challenge. BAL fluid and quantitative histological analysis were performed 48 h after the last challenge. FTY720 inhibited OVA-induced features of airway remodeling including increased airway smooth muscle mass and bronchial neovascularization, without affecting lymphocyte numbers in secondary lymphoid organs. Furthermore, CD3+ cells adjacent to airway smooth muscle bundles were increased in OVA-challenged rats but the increase was inhibited by FTY720. There was an expansion of bronchus-associated lymphoid tissue following FTY720 treatment of OVA-challenged animals. Real-time quantitative PCR revealed that Th2-associated transcription factors were inhibited following FTY720 therapy. Airway remodeling is a cardinal feature of severe asthma. These results demonstrate that allergen-driven airway remodeling can be inhibited by FTY720, offering potential new therapies for the treatment of severe asthma.
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- 2012
29. Crosstalk within GPCR heteromers in schizophrenia and Parkinson's disease: physical or just functional?
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Maria Marti-Solano, Jana Selent, Ramon Guixà-González, and Agostino Bruno
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Pharmacology ,Models, Molecular ,Drug discovery ,Organic Chemistry ,Parkinson Disease ,Disease ,Biology ,Bioinformatics ,Biochemistry ,Receptors, G-Protein-Coupled ,Crosstalk (biology) ,Drug Discovery ,Schizophrenia ,Molecular Medicine ,Animals ,Humans ,Signal transduction ,Neuroscience ,G protein-coupled receptor ,Signal Transduction - Abstract
Crosstalk between G protein-coupled receptors (GPCRs) is one of the key mechanisms used by the cell for integrating multiple signaling pathways. Functional crosstalk at the level of signaling pathways was initially thought to regulate receptor function. Importantly, the existence of GPCR heteromers demonstrates that direct physical interactions between GPCRs could also be behind the crosstalk phenomenon. Neurological disorders such as Parkinson's disease (PD) and schizophrenia have been linked to a dysfunctional communication between certain GPCRs. In this review, we discuss functional and physical crosstalk of the main GPCR families involved in the aforementioned disorders. In addition, we analyze the available structural information on physical crosstalk and highlight some strategies in drug discovery based on these crosstalk mechanisms.
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- 2011
30. Membrane cholesterol access into a G-protein-coupled receptor
- Author
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Ramon Guixà-González, José L. Albasanz, Ismael Rodriguez-Espigares, Manuel Pastor, Ferran Sanz, Maria Martí-Solano, Moutusi Manna, Hector Martinez-Seara, Peter W. Hildebrand, Mairena Martín, and Jana Selent
- Subjects
Science - Abstract
G-protein-coupled receptors trigger several signalling pathways and their activity was proposed to be allosteric modulated by cholesterol. Here the authors use molecular dynamics simulations and ligand binding assays to show that membrane cholesterol can bind to adenosine A2Areceptor orthosteric site.
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- 2017
- Full Text
- View/download PDF
31. Analyzing Kinase Similarity in Small Molecule and Protein Structural Space to Explore the Limits of Multi-Target Screening
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Denis Schmidt, Magdalena M. Scharf, Dominique Sydow, Eva Aßmann, Maria Martí-Solano, Marina Keul, Andrea Volkamer, and Peter Kolb
- Subjects
multi-target ligands ,docking ,chemoinformatics ,bioinformatics ,kinases ,binding site comparison ,Organic chemistry ,QD241-441 - Abstract
While selective inhibition is one of the key assets for a small molecule drug, many diseases can only be tackled by simultaneous inhibition of several proteins. An example where achieving selectivity is especially challenging are ligands targeting human kinases. This difficulty arises from the high structural conservation of the kinase ATP binding sites, the area targeted by most inhibitors. We investigated the possibility to identify novel small molecule ligands with pre-defined binding profiles for a series of kinase targets and anti-targets by in silico docking. The candidate ligands originating from these calculations were assayed to determine their experimental binding profiles. Compared to previous studies, the acquired hit rates were low in this specific setup, which aimed at not only selecting multi-target kinase ligands, but also designing out binding to anti-targets. Specifically, only a single profiled substance could be verified as a sub-micromolar, dual-specific EGFR/ErbB2 ligand that indeed avoided its selected anti-target BRAF. We subsequently re-analyzed our target choice and in silico strategy based on these findings, with a particular emphasis on the hit rates that can be expected from a given target combination. To that end, we supplemented the structure-based docking calculations with bioinformatic considerations of binding pocket sequence and structure similarity as well as ligand-centric comparisons of kinases. Taken together, our results provide a multi-faceted picture of how pocket space can determine the success of docking in multi-target drug discovery efforts.
- Published
- 2021
- Full Text
- View/download PDF
32. A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.
- Author
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Maria Martí-Solano, Ferran Sanz, Manuel Pastor, and Jana Selent
- Subjects
Medicine ,Science - Abstract
Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity.
- Published
- 2014
- Full Text
- View/download PDF
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