,
Structural mechanism of G protein activation by G protein-coupled receptor, Eur. J. Pharmacol, vol.763, pp.214-222, 2015. ,
Structural mechanism of GPCRarrestin interaction: recent breakthroughs, Arch. Pharm. Res, vol.39, pp.293-301, 2016. ,
Structure and dynamics of GPCR signaling complexes, Nat. Struct. Mol. Biol, vol.25, pp.4-12, 2018. ,
Fingerprinting G-protein-coupled receptors, Protein Eng. Des. Sel, vol.7, pp.195-203, 1994. ,
The G-Protein-Coupled Receptors in the Human Genome Form Five Main Families. Phylogenetic Analysis, Paralogon Groups, and Fingerprints, Mol. Pharmacol, vol.63, pp.1256-1272, 2003. ,
Trends in GPCR drug discovery: new agents, targets and indications, Nat. Rev. Drug Discov, vol.16, pp.829-842, 2017. ,
, Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor, vol.289, 2000.
High-Resolution Crystal Structure of an Engineered Human 2-Adrenergic G Protein-Coupled Receptor, Science, vol.318, pp.1258-1265, 2007. ,
The 2.6 A Crystal Structure of a Human A2A Adenosine Receptor bound to ZM241385, vol.322, pp.1211-1217, 2008. ,
Structure of the human smoothened receptor bound to an antitumour agent, Nature, vol.497, pp.338-343, 2013. ,
Engineering a minimal G protein to facilitate crystallisation of G protein-coupled receptors in their active conformation, Protein Eng. Des. Sel, vol.29, pp.583-594, 2016. ,
Structure of a nanobody-stabilized active state of the ?2 adrenoceptor, Nature, vol.469, pp.175-180, 2011. ,
Crystal structure of the ?2 adrenergic receptor-Gs protein complex, Nature, vol.477, pp.549-555, 2011. ,
Gain-of-function mutations in G-protein-coupled receptor genes associated with human endocrine disorders, Clin. Endocrinol. (Oxf.), vol.88, pp.351-359, 2018. ,
How genetic errors in GPCRs affect their function: Possible therapeutic strategies, Genes Dis, vol.2, pp.108-132, 2015. ,
A Constitutively Activating Mutation Alters the Dynamics and Energetics of a Key Conformational Change in a Ligand-free G Protein-coupled Receptor, J. Biol. Chem, vol.288, pp.28207-28216, 2013. ,
Identification of Two Distinct Sites for Antagonist and Biased Agonist Binding to the Human Chemokine Receptor CXCR3, Angew. Chem. Int. Ed, vol.55, pp.15277-15281, 2016. ,
Coarse-Grained Prediction of Peptide Binding to G-Protein Coupled Receptors, J. Chem. Inf. Model, vol.57, pp.562-571, 2017. ,
Molecular mechanism of GPCR-mediated arrestin activation, Nature, vol.557, pp.452-456, 2018. ,
Activation mechanism of the ?2-adrenergic receptor, Proc. Natl. Acad. Sci, vol.108, pp.18684-18689, 2011. ,
Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor, Proc. Natl. Acad. Sci, vol.113, pp.12162-12167, 2016. ,
The chemokine receptor CCR5 in the central nervous system, Prog. Neurobiol, vol.93, pp.297-311, 2011. ,
CCR5/CCL5 axis interaction promotes migratory and invasiveness of pancreatic cancer cells, Sci. Rep, vol.8, 2018. ,
CCR5 Governs DNA Damage Repair and Breast Cancer Stem Cell Expansion, Cancer Res, vol.78, pp.1657-1671, 2018. ,
Identification of a major co-receptor for primary isolates of HIV-1, Nature, vol.381, pp.661-666, 1996. ,
Palmitoylation of CCR5 Is Critical for Receptor Trafficking and Efficient Activation of Intracellular Signaling Pathways, J. Biol. Chem, vol.276, pp.23795-23804, 2001. ,
Differential Effects of CC Chemokines on CC Chemokine Receptor 5 (CCR5) Phosphorylation and Identification of Phosphorylation Sites on the CCR5 Carboxyl Terminus, J. Biol. Chem, vol.274, pp.8875-8885, 1999. ,
Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene, Nature, vol.382, pp.722-725, 1996. ,
Allosteric Model of Maraviroc Binding to CC Chemokine Receptor 5 (CCR5), J. Biol. Chem, vol.286, pp.33409-33421, 2011. ,
Structure of the CCR5 Chemokine Receptor-HIV Entry Inhibitor Maraviroc Complex, Science, vol.341, pp.1387-1390, 2013. ,
Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV, Immunity, vol.46, p.5, 2017. ,
Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations, Sci. Rep, vol.5, 2015. ,
Molecular Recognition of CCR5 by an HIV-1 gp120 V3 Loop, PLoS ONE, vol.9, p.95767, 2014. ,
A single-residue change in the HIV-1 V3 loop associated with maraviroc resistance impairs CCR5 binding affinity while increasing replicative capacity, Retrovirology, vol.12, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01174427
,
, Cell Binding and Entry. Cold Spring Harb. Perspect. Med, vol.2, pp.6866-006866, 2012.
UK-427,857), a Potent, Orally Bioavailable, and Selective SmallMolecule Inhibitor of Chemokine Receptor CCR5 with Broad-Spectrum Anti-Human Immunodeficiency Virus Type 1 Activity, Antimicrob. Agents Chemother, vol.49, pp.4721-4732, 2005. ,
A Maraviroc-Resistant HIV-1 with Narrow Cross-Resistance to Other CCR5 Antagonists Depends on both N-Terminal and Extracellular Loop Domains of Drug-Bound CCR5, J. Virol, vol.84, pp.10863-10876, 2010. ,
A single-residue change in the HIV-1 V3 loop associated with maraviroc resistance impairs CCR5 binding affinity while increasing replicative capacity, Retrovirology, vol.12, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01174427
Structure of the CCR5 Chemokine Receptor-HIV Entry Inhibitor Maraviroc Complex, Science, vol.341, pp.1387-1390, 2013. ,
Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV, Immunity, vol.46, p.5, 2017. ,
Allosteric Model of Maraviroc Binding to CC Chemokine Receptor 5 (CCR5), J. Biol. Chem, vol.286, pp.33409-33421, 2011. ,
Biased Signaling at Chemokine Receptors, J. Biol. Chem, vol.290, pp.9542-9554, 2015. ,
Biased and Constitutive Signaling in the CC-chemokine Receptor CCR5 by Manipulating the Interface between Transmembrane Helices 6 and 7, J. Biol. Chem, vol.288, pp.12511-12521, 2013. ,
Constitutive Activation of CCR5 and CCR2 Induced by Conformational Changes in the Conserved T X P Motif in Transmembrane Helix 2, J. Biol. Chem, vol.278, pp.36513-36521, 2003. ,
Mutation of the DRY Motif Reveals Different Structural Requirements for the CC Chemokine Receptor 5-Mediated Signaling and Receptor Endocytosis, Mol. Pharmacol, vol.67, pp.1966-1976, 2005. ,
The T X P Motif in the Second Transmembrane Helix of CCR5: A STRUCTURAL DETERMINANT OF CHEMOKINE-INDUCED ACTIVATION, J. Biol. Chem, vol.276, pp.13217-13225, 2001. ,
Molecular dynamics simulations of biomolecules, Nat. Struct. Biol, vol.9, p.7, 2002. ,
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins, Chem. Rev, vol.106, pp.1589-1615, 2006. ,
Theory of protein folding, Curr. Opin. Struct. Biol, vol.14, pp.70-75, 2004. ,
Dynamic personalities of proteins, Nature, vol.450, pp.964-972, 2007. ,
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules, J. Chem. Phys, vol.120, pp.11919-11929, 2004. ,
Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position: AMD Simulations of a GPCR Using GPUs, Proteins Struct. Funct. Bioinforma, vol.84, pp.1480-1489, 2016. ,
Activation and dynamic network of the M2 muscarinic receptor, Proc. Natl. Acad. Sci, vol.110, pp.10982-10987, 2013. ,
Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter, Molecular Modeling of Proteins, vol.1215, pp.253-287, 2015. ,
Studying functional dynamics in bio-molecules using accelerated molecular dynamics, Phys. Chem. Chem. Phys, vol.13, p.20053, 2011. ,
CCR5 adopts three homodimeric conformations that control cell surface delivery, Sci. Signal, vol.11, p.2869, 2018. ,
Structures of the CCR5 N Terminus and of a Tyrosine-Sulfated Antibody with HIV-1 gp120 and CD4, Science, vol.317, pp.1930-1934, 2007. ,
Comparative Protein Modelling by Satisfaction of Spatial Restraints, J. Mol. Biol, vol.234, pp.779-815, 1993. ,
Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine, Science, vol.347, pp.1117-1122, 2015. ,
Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3, Proc. Natl. Acad. Sci, vol.113, pp.5000-5005, 2016. ,
DOI : 10.1073/pnas.1523981113
URL : https://www.pnas.org/content/pnas/113/18/5000.full.pdf
A web-based graphical user interface for CHARMM, J. Comput. Chem, vol.29, pp.1859-1865, 2008. ,
DOI : 10.1002/jcc.20945
, , 2018.
Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics, Phys. Chem. Chem. Phys, vol.16, pp.6398-6406, 2014. ,
Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computationalexperimental approach, Malar. J, vol.13, p.434, 2014. ,
Software for Processing and Analysis of Molecular Dynamics Trajectory Data, J. Chem. Theory Comput, vol.9, pp.3084-3095, 2013. ,
VMD -Visual Molecular Dynamics, J. Mol. Graph, vol.14, pp.33-38, 1996. ,
DOI : 10.1016/0263-7855(96)00018-5
Integrating protein structural dynamics and evolutionary analysis with Bio3D, BMC Bioinformatics, vol.15, 2014. ,
Bio3d: an R package for the comparative analysis of protein structures, Bioinformatics, vol.22, pp.2695-2696, 2006. ,
, R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2017.
GPCRdb in 2018: adding GPCR structure models and ligands, Nucleic Acids Res, vol.46, pp.440-446, 2018. ,
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.22, pp.2577-2637, 1983. ,
IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein-Ligand Interactions, ChemMedChem, vol.13, pp.507-510, 2018. ,
Hierarchical Grouping to Optimize an Objective Function, J. Am. Stat. Assoc, vol.58, pp.236-244, 1963. ,
DOI : 10.2307/2282967
Ward's Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward's Criterion?, J. Classif, vol.31, pp.274-295, 2014. ,
DOI : 10.1007/s00357-014-9161-z
URL : http://arxiv.org/pdf/1111.6285
How the ubiquitous GPCR receptor family selectively activates signalling pathways, Nature, vol.558, pp.529-530, 2018. ,
DOI : 10.1038/d41586-018-05503-4
URL : https://www.nature.com/magazine-assets/d41586-018-05503-4/d41586-018-05503-4.pdf
Molecular signatures of G-protein-coupled receptors, Nature, vol.494, pp.185-194, 2013. ,
Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations, Sci. Rep, vol.5, 2015. ,
, une partie de ECL2 (résidus 171-176) et de ECL3 (résidus 266-269) et le haut de TM 6 et de TM 7 (résidus 263 et 272). Les résidus C20, vol.15, pp.19-25
, N258(6.58) et T259(6.59), qui exposent des groupements pharmacophoriques dans la cavité
, Résidus à 4,5 Å des points de la cavité sélectionnée pour le dimère I56. Les résidus colorés en bleu sont issus de la chaîne A du dimère, les résidus en rouge, de la chaîne B et les résidus en violet des deux chaînes, pp.4-12
, W190(5.34), K191(5.35) impacte de manière significative la liaison de ligand "drug-like, D'après les données de la littérature résumées par le site GPCRdb, la mutation des résidus G163(4.60), T177, C178, S180, S185, Y187(5.31)
,
Dimers and beyond: The functional puzzles of class C GPCRs, Pharmacol. Ther, vol.130, pp.9-25, 2011. ,
Receptor oligomerization: from early evidence to current understanding in class B, GPCRs. Front. Endocrinol, vol.3, 2013. ,
A Trafficking Checkpoint Controls GABAB Receptor Heterodimerization, Neuron, vol.27, pp.97-106, 2000. ,
Basic Pharmacological and Structural Evidence for Class A G-Protein-Coupled Receptor Heteromerization ,
, , 2016.
Structure-Function of the G Protein-Coupled Receptor Superfamily, Annu. Rev. Pharmacol. Toxicol, vol.53, pp.531-556, 2013. ,
Crystal structure of oligomeric ?1-adrenergic G protein-coupled receptors in ligand-free basal state, Nat. Struct. Mol. Biol, vol.20, pp.419-425, 2013. ,
Crystal structure of a photoactivated deprotonated intermediate of rhodopsin, Proc. Natl. Acad. Sci, vol.103, pp.16123-16128, 2006. ,
Structure of the human kappa opioid receptor in complex with JDTic, Nature, vol.485, pp.327-332, 2012. ,
Crystal structure of the µ-opioid receptor bound to a morphinan antagonist, Nature, vol.485, pp.321-326, 2012. ,
Structure of the human smoothened receptor bound to an antitumour agent, Nature, vol.497, pp.338-343, 2013. ,
High-Resolution Crystal Structure of an Engineered Human 2-Adrenergic G Protein-Coupled Receptor, Science, vol.318, pp.1258-1265, 2007. ,
Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists, Science, vol.330, pp.1066-1071, 2010. ,
Allosteric Modulation of Binding Properties between Units of Chemokine Receptor Homo-and Hetero-Oligomers, Mol. Pharmacol, vol.69, pp.1652-1661, 2006. ,
Hetero-oligomerization of CCR2, CCR5, and CXCR4 and the Protean Effects of "Selective, Antagonists. J. Biol. Chem, vol.284, pp.31270-31279, 2009. ,
Constitutive Agonist-independent CCR5 Oligomerization and Antibodymediated Clustering Occurring at Physiological Levels of Receptors, J. Biol. Chem, vol.277, pp.34666-34673, 2002. ,
Evidence for Negative Binding Cooperativity within CCR5-CCR2b Heterodimers, Mol. Pharmacol, vol.67, pp.460-469, 2004. ,
CCR5/CD4/CXCR4 oligomerization prevents HIV-1 gp120IIIB binding to the cell surface, Proc. Natl. Acad. Sci, vol.111, pp.1960-1969, 2014. ,
CCR5 adopts three homodimeric conformations that control cell surface delivery, Sci. Signal, vol.11, p.2869, 2018. ,
un inventaire de molécules commercialement disponibles à des fins de criblage biologique ,
,
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures, J. Chem. Inf. Model, vol.34, pp.1000-1008, 1994. ,
Conformations and 3D pharmacophore searching, Drug Discov. Today Technol, vol.7, pp.245-253, 2010. ,
, 3D Structure Generator CORINA Classic. (Molecular Networks GmbH)
A web-based graphical user interface for CHARMM, J. Comput. Chem, vol.29, pp.1859-1865, 2008. ,
, , 2018.
Software for Processing and Analysis of Molecular Dynamics Trajectory Data, J. Chem. Theory Comput, vol.9, pp.3084-3095, 2013. ,
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints, J. Chem. Inf. Model, vol.47, pp.195-207, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00195175
IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein-Ligand Interactions, ChemMedChem, vol.13, pp.507-510, 2018. ,
IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein-Protein Interfaces, J. Chem. Inf. Model, vol.55, 2005. ,
Comparison and Druggability Prediction of Protein-Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes ,
, J. Chem. Inf. Model, vol.52, pp.2287-2299, 2012.
Comparison of Shape-Matching and Docking as Virtual Screening Tools, J. Med. Chem, vol.50, pp.74-82, 2007. ,
,
,
,
Allosteric Model of Maraviroc Binding to CC Chemokine Receptor 5 (CCR5), J. Biol. Chem, vol.286, pp.33409-33421, 2011. ,
Structural and Molecular Interactions of CCR5 Inhibitors with CCR5, J. Biol. Chem, vol.281, pp.12688-12698, 2006. ,
Chemokine G Protein-Coupled Receptor (Gpcr) Mutation Data Set, 2016. ,
Molecular Recognition of CCR5 by an HIV-1 gp120 V3 Loop, PLoS ONE, vol.9, p.95767, 2014. ,
Structure-based discovery of 2-adrenergic receptor ligands, Proc. Natl. Acad. Sci, vol.106, pp.6843-6848, 2009. ,
Structure-Based Discovery of Selective Serotonin 5-HT 1B Receptor Ligands, Structure, vol.22, pp.1140-1151, 2014. ,
Identification of Nonpeptide CCR5 Receptor Agonists by Structurebased Virtual Screening, J. Med. Chem, vol.50, pp.1294-1303, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00174008
A benchmarking study on virtual ligand screening against homology models of human GPCRs, Proteins Struct. Funct. Bioinforma, 2018. ,
Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations ,
, Monatshefte Für Chem. -Chem. Mon, vol.147, pp.553-563, 2016.
A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor ?, ChemMedChem, vol.12, pp.1399-1407, 2017. ,
, Carte de corrélations des mouvements dans CCR5. Les barres noires annotées de 1 à 7 définissent les hélices transmembranaires du récepteur. Les valeurs de corrélation des mouvements des résidus vont de 1 (couleur cyan), pour des mouvements corrélés, vol.4