Probing the cooperative mechanism of the μ-δ opioid receptor heterodimer by multiscale simulation.
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Yanzhi Guo | Meng-long Li | X. Pu | Yuan Yuan | Chuan Li | Longrong Wang | Xin Chen | Jiangfan Chen
[1] M. Filizola,et al. Insights into the function of opioid receptors from molecular dynamics simulations of available crystal structures , 2018, British journal of pharmacology.
[2] Yanzhi Guo,et al. Use multiscale simulation to explore the effects of the homodimerizations between different conformation states on the activation and allosteric pathway for the μ-opioid receptor. , 2018, Physical chemistry chemical physics : PCCP.
[3] Jianrong Xu,et al. AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses , 2018, Nucleic Acids Res..
[4] Feng Zhu,et al. Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations. , 2018, ACS chemical neuroscience.
[5] Shaoyong Lu,et al. Small Molecule Allosteric Modulators of G-Protein-Coupled Receptors: Drug-Target Interactions. , 2018, Journal of medicinal chemistry.
[6] S. Yokoyama,et al. Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1. , 2018, Nature chemical biology.
[7] Chun Wu,et al. Investigating detailed interactions between novel PAR1 antagonist F16357 and the receptor using docking and molecular dynamic simulations. , 2017, Journal of molecular graphics & modelling.
[8] G. Schulte,et al. Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling , 2017, Nature Communications.
[9] Peter V Coveney,et al. An Ensemble-Based Protocol for the Computational Prediction of Helix–Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics , 2017, Journal of chemical theory and computation.
[10] P. Carloni,et al. Structural heterogeneity of the μ-opioid receptor’s conformational ensemble in the apo state , 2017, Scientific Reports.
[11] Nicolas Floquet,et al. Coarse-Grained Prediction of Peptide Binding to G-Protein Coupled Receptors , 2017, J. Chem. Inf. Model..
[12] Naomi R. Latorraca,et al. GPCR Dynamics: Structures in Motion. , 2017, Chemical reviews.
[13] Xavier Periole,et al. Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations. , 2017, Chemical reviews.
[14] Yanzhi Guo,et al. Use of network model to explore dynamic and allosteric properties of three GPCR homodimers , 2016 .
[15] Yanzhi Guo,et al. Exploring the mechanism of F282L mutation-caused constitutive activity of GPCR by a computational study. , 2016, Physical chemistry chemical physics : PCCP.
[16] A. J. Venkatakrishnan,et al. Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region , 2016, Nature.
[17] Stavros J. Hamodrakas,et al. Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions , 2016, Journal of Computer-Aided Molecular Design.
[18] A. Kolinski,et al. Coarse-Grained Protein Models and Their Applications. , 2016, Chemical reviews.
[19] L. Pardo,et al. The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor , 2016, Scientific Reports.
[20] L. Devi,et al. G Protein-Coupled Receptor Heteromers. , 2016, Annual review of pharmacology and toxicology.
[21] M. Sansom,et al. Organization and Dynamics of Receptor Proteins in a Plasma Membrane. , 2015, Journal of the American Chemical Society.
[22] Brian D. Weitzner,et al. An Integrated Framework Advancing Membrane Protein Modeling and Design , 2015, PLoS Comput. Biol..
[23] Aashish Manglik,et al. Propagation of conformational changes during μ-opioid receptor activation , 2015, Nature.
[24] Stephen M. Husbands,et al. Structural insights into μ-opioid receptor activation , 2015, Nature.
[25] J Andrew McCammon,et al. Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. , 2015, Biophysical journal.
[26] Stefan Dove,et al. Multi‐Component Protein – Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein‐Coupled Receptors , 2015, Molecular informatics.
[27] Davide Provasi,et al. Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association , 2015, PLoS Comput. Biol..
[28] Jianfeng Liu,et al. Major ligand-induced rearrangement of the heptahelical domain interface in a GPCR dimer. , 2015, Nature chemical biology.
[29] S. Filipek,et al. W246(6.48) opens a gate for a continuous intrinsic water pathway during activation of the adenosine A2A receptor. , 2014, Angewandte Chemie.
[30] Helgi I Ingólfsson,et al. Lipid organization of the plasma membrane. , 2014, Journal of the American Chemical Society.
[31] L. Devi,et al. Revolution in GPCR signalling: opioid receptor heteromers as novel therapeutic targets: IUPHAR Review 10 , 2014, British journal of pharmacology.
[32] N. Vaidehi,et al. Differences in allosteric communication pipelines in the inactive and active states of a GPCR. , 2014, Biophysical journal.
[33] Benjamin G Tehan,et al. Unifying family A GPCR theories of activation. , 2014, Pharmacology & therapeutics.
[34] Vadim Cherezov,et al. Allosteric sodium in class A GPCR signaling. , 2014, Trends in biochemical sciences.
[35] Martin J. Lohse,et al. G Protein–Coupled Receptor Oligomerization Revisited: Functional and Pharmacological Perspectives , 2014, Pharmacological Reviews.
[36] Siewert J Marrink,et al. Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. , 2014, Journal of chemical theory and computation.
[37] J. Wess,et al. Activation and allosteric modulation of a muscarinic acetylcholine receptor , 2013, Nature.
[38] Jing Huang,et al. CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data , 2013, J. Comput. Chem..
[39] Shuguang Yuan,et al. The role of water and sodium ions in the activation of the μ-opioid receptor. , 2013, Angewandte Chemie.
[40] L. Devi,et al. Identification of a μ-δ opioid receptor heteromer-biased agonist with antinociceptive activity , 2013, Proceedings of the National Academy of Sciences.
[41] M. Babu,et al. Molecular signatures of G-protein-coupled receptors , 2013, Nature.
[42] L. Devi,et al. Dimerization with Cannabinoid Receptors Allosterically Modulates Delta Opioid Receptor Activity during Neuropathic Pain , 2012, PloS one.
[43] Durba Sengupta,et al. Identification of cholesterol binding sites in the serotonin1A receptor. , 2012, The journal of physical chemistry. B.
[44] Hao Wang,et al. Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors , 2012, PLoS Comput. Biol..
[45] Siewert J Marrink,et al. Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers. , 2012, Journal of the American Chemical Society.
[46] Jingjing Guo,et al. Exploring structural and thermodynamic stabilities of human prion protein pathogenic mutants D202N, E211Q and Q217R. , 2012, Journal of structural biology.
[47] Aashish Manglik,et al. Structure of the δ-opioid receptor bound to naltrindole , 2012, Nature.
[48] L. Pardo,et al. Crystal structure of the μ-opioid receptor bound to a morphinan antagonist , 2012, Nature.
[49] Bryan L. Roth,et al. Structure of the human kappa opioid receptor in complex with JDTic , 2012, Nature.
[50] Roy G. Smith,et al. Apo-Ghrelin Receptor Forms Heteromers with DRD2 in Hypothalamic Neurons and Is Essential for Anorexigenic Effects of DRD2 Agonism , 2012, Neuron.
[51] Jeffery B. Klauda,et al. Update of the cholesterol force field parameters in CHARMM. , 2012, The journal of physical chemistry. B.
[52] Albert C. Pan,et al. Activation mechanism of the β2-adrenergic receptor , 2011, Proceedings of the National Academy of Sciences.
[53] R. Jockers,et al. Asymmetry of GPCR oligomers supports their functional relevance. , 2011, Trends in pharmacological sciences.
[54] Julie C. Mitchell,et al. KFC2: A knowledge‐based hot spot prediction method based on interface solvation, atomic density, and plasticity features , 2011, Proteins.
[55] J. Simms,et al. Lifting the lid on GPCRs: the role of extracellular loops , 2011, British journal of pharmacology.
[56] S. Rasmussen,et al. Crystal Structure of the β2Adrenergic Receptor-Gs protein complex , 2011, Nature.
[57] P. Kiss,et al. Sources of the deficiencies in the popular SPC/E and TIP3P models of water. , 2011, The Journal of chemical physics.
[58] Shaoqiu He,et al. Facilitation of μ-Opioid Receptor Activity by Preventing δ-Opioid Receptor-Mediated Codegradation , 2011, Neuron.
[59] Bryan L Roth,et al. Strategies to discover unexpected targets for drugs active at G protein-coupled receptors. , 2011, Annual review of pharmacology and toxicology.
[60] Francesca Fanelli,et al. Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces , 2010, J. Comput. Chem..
[61] N. Birdsall. Class A GPCR heterodimers: evidence from binding studies. , 2010, Trends in pharmacological sciences.
[62] M. Filizola,et al. Lessons from Free Energy Simulations of δ-Opioid Receptor Homodimers Involving the Fourth Transmembrane Helix† , 2010, Biochemistry.
[63] George Khelashvili,et al. GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base , 2010, Bioinform..
[64] I. Tavernelli,et al. Role of aggregation in rhodopsin signal transduction. , 2010, Biochemistry.
[65] Samuel L. DeLuca,et al. Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You , 2010, Biochemistry.
[66] Ming Kai,et al. Molecular modeling studies to predict the possible binding modes of endomorphin analogs in mu opioid receptor. , 2009, Bioorganic & medicinal chemistry letters.
[67] Xavier Periole,et al. Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. , 2009, Journal of chemical theory and computation.
[68] Irina S. Moreira,et al. Allosteric communication between protomers of dopamine Class A GPCR dimers modulates activation , 2009, Nature chemical biology.
[69] Gabriele Costantino,et al. Molecular Dynamics Simulation of the Heterodimeric mGluR2/5HT2A Complex. An Atomistic Resolution Study of a Potential New Target in Psychiatric Conditions , 2009, J. Chem. Inf. Model..
[70] S. Vishveshwara,et al. Intra and inter-molecular communications through protein structure network. , 2009, Current protein & peptide science.
[71] Xin Liu,et al. Computational study of the heterodimerization between μ and δ receptors , 2009, J. Comput. Aided Mol. Des..
[72] Oliver P. Ernst,et al. Crystal structure of opsin in its G-protein-interacting conformation , 2008, Nature.
[73] Julie C. Mitchell,et al. KFC Server: interactive forecasting of protein interaction hot spots , 2008, Nucleic Acids Res..
[74] Graeme Milligan,et al. Identification of a serotonin/glutamate receptor complex implicated in psychosis , 2008, Nature.
[75] K. Lorenz,et al. Conformational cross-talk between alpha2A-adrenergic and mu-opioid receptors controls cell signaling. , 2008, Nature chemical biology.
[76] G. Milligan,et al. Allosteric modulation of heterodimeric G-protein-coupled receptors. , 2007, Trends in pharmacological sciences.
[77] M. Burghammer,et al. Crystal structure of the human β2 adrenergic G-protein-coupled receptor , 2007, Nature.
[78] Amedeo Caflisch,et al. Wordom: a program for efficient analysis of molecular dynamics simulations , 2007, Bioinform..
[79] Pedro A Fernandes,et al. Hot spots—A review of the protein–protein interface determinant amino‐acid residues , 2007, Proteins.
[80] David J. Daniels,et al. Absence of conditioned place preference or reinstatement with bivalent ligands containing mu-opioid receptor agonist and delta-opioid receptor antagonist pharmacophores. , 2007, European journal of pharmacology.
[81] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[82] Richard N. Zare,et al. A monomeric G protein-coupled receptor isolated in a high-density lipoprotein particle efficiently activates its G protein , 2007, Proceedings of the National Academy of Sciences.
[83] J. Wess,et al. Multiple Residues in the Second Extracellular Loop Are Critical for M3 Muscarinic Acetylcholine Receptor Activation* , 2007, Journal of Biological Chemistry.
[84] Syma Khalid,et al. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. , 2007, Journal of structural biology.
[85] B. Bie,et al. Trafficking of central opioid receptors and descending pain inhibition , 2007, Molecular pain.
[86] Ben M. Webb,et al. Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.
[87] Graeme Milligan,et al. G-protein-coupled receptor heterodimers: pharmacology, function and relevance to drug discovery. , 2006, Drug discovery today.
[88] A. Engel,et al. Functional and Structural Characterization of Rhodopsin Oligomers* , 2006, Journal of Biological Chemistry.
[89] Guang Song,et al. An enhanced elastic network model to represent the motions of domain‐swapped proteins , 2006, Proteins.
[90] S. Vishveshwara,et al. A network representation of protein structures: implications for protein stability. , 2005, Biophysical journal.
[91] Gerrit Groenhof,et al. GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..
[92] Marta Filizola,et al. Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[93] Francesca Fanelli,et al. Computational modeling approaches to structure-function analysis of G protein-coupled receptors. , 2005, Chemical reviews.
[94] R. Nussinov,et al. Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. , 2005, Journal of molecular biology.
[95] Lakshmi A. Devi,et al. A role for heterodimerization of μ and δ opiate receptors in enhancing morphine analgesia , 2004 .
[96] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[97] Jeffrey J. Gray,et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.
[98] D. Bailey,et al. The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfaces , 2003, Bioinform..
[99] Krzysztof Palczewski,et al. Organization of the G Protein-coupled Receptors Rhodopsin and Opsin in Native Membranes* , 2003, Journal of Biological Chemistry.
[100] T. Rogers,et al. Interactions between opioid and chemokine receptors: heterologous desensitization. , 2002, Cytokine & growth factor reviews.
[101] Ka Yee Yeung,et al. Principal component analysis for clustering gene expression data , 2001, Bioinform..
[102] Kurt S. Thorn,et al. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions , 2001, Bioinform..
[103] Lakshmi A. Devi,et al. Heterodimerization of μ and δ Opioid Receptors: A Role in Opiate Synergy , 2000, The Journal of Neuroscience.
[104] Ivet Bahar,et al. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α‐amylase inhibitor , 2000, Proteins.
[105] E I Canela,et al. Dopamine D1 and adenosine A1 receptors form functionally interacting heteromeric complexes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[106] J. Wess,et al. Identification and Molecular Characterization of m3 Muscarinic Receptor Dimers* , 1999, The Journal of Biological Chemistry.
[107] A. Bogan,et al. Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.
[108] T. Sakmar,et al. Spectroscopic evidence for interaction between transmembrane helices 3 and 5 in rhodopsin. , 1998, Biochemistry.
[109] L. Devi,et al. Dimerization of the delta opioid receptor: implication for a role in receptor internalization. , 1997, The Journal of biological chemistry.
[110] C. Romano,et al. Metabotropic Glutamate Receptor 5 Is a Disulfide-linked Dimer* , 1996, The Journal of Biological Chemistry.
[111] P. Seeman,et al. Dopamine D2 receptor dimers and receptor-blocking peptides. , 1996, Biochemical and biophysical research communications.
[112] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[113] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[114] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[115] Jürgen Bajorath,et al. Design of chemical space networks on the basis of Tversky similarity , 2015, Journal of Computer-Aided Molecular Design.
[116] Michel Bouvier,et al. Dimerization: an emerging concept for G protein-coupled receptor ontogeny and function. , 2002, Annual review of pharmacology and toxicology.