Molecular mechanisms of allosteric probe dependence in μ opioid receptor

References

• Anandakrishnan, R., Aguilar, B., & Onufriev, A. V. (2012). H++ 3.0: Automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Research, 40(Web Server issue), W537–W541. https://doi.org/10.1093/nar/gks37510.1093/nar/gks375
   PubMed Web of Science ®Google Scholar
• Ballesteros, J. A., & Weinstein, H. (1995). [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. In S. C. Sealfon (Ed.), Methods in Neurosciences, Vol. 25 (pp. 366–428). San Diego, CA: Academic Press. Retrieved from http://www.sciencedirect.com/science/article/pii/S1043947105800497.
   Google Scholar
• Bartuzi, D., Kaczor, A. A., & Matosiuk, D. (2015). Activation and allosteric modulation of human μ opioid receptor in molecular dynamics. Journal of Chemical Information and Modeling, 55(11), 2421–2434. doi:10.1021/acs.jcim.5b00280
   PubMed Web of Science ®Google Scholar
• Bartuzi, D., Kaczor, A. A., & Matosiuk, D. (2016). Interplay between two allosteric sites and their influence on agonist binding in human μ opioid receptor. Journal of Chemical Information and Modeling, 56(3), 563–570. doi:10.1021/acs.jcim.5b00705
   PubMed Web of Science ®Google Scholar
• Bernat, V., Brox, R., Heinrich, M. R., Auberson, Y. P., & Tschammer, N. (2015). Ligand-biased and probe-dependent modulation of chemokine receptor CXCR3 signaling by negative allosteric modulators. ChemMedChem, 10(3), 566–574. doi:10.1002/cmdc.201402507
   PubMed Web of Science ®Google Scholar
• Chakrabarti, S., Chang, A., & Gintzler, A. R. (2010). Subcellular localization of mu-opioid receptor G(s) signaling. The Journal of Pharmacology and Experimental Therapeutics, 333(1), 193–200. doi:10.1124/jpet.109.165142
   PubMed Web of Science ®Google Scholar
• Hertig, S., Latorraca, N. R., & Dror, R. O. (2016). Revealing atomic-level mechanisms of protein allostery with molecular dynamics simulations. PLoS Computational Biology, 12(6), e1004746. doi:10.1371/journal.pcbi.1004746
   PubMed Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. doi:10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38, 27–28.10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Jämbeck, J. P. M., & Lyubartsev, A. P. (2012a). An extension and further validation of an all-atomistic force field for biological membranes. Journal of Chemical Theory and Computation, 8(8), 2938–2948. doi:10.1021/ct300342n
   PubMed Web of Science ®Google Scholar
• Jämbeck, J. P. M., & Lyubartsev, A. P. (2012b). Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. The Journal of Physical Chemistry. B, 116(10), 3164–3179. doi:10.1021/jp212503e
   PubMed Web of Science ®Google Scholar
• Jämbeck, J. P. M., & Lyubartsev, A. P. (2013). Another piece of the membrane puzzle: Extending slipids further. Journal of Chemical Theory and Computation, 9(1), 774–784. doi:10.1021/ct300777p
   PubMed Web of Science ®Google Scholar
• Katritch, V., Cherezov, V., & Stevens, R. C. (2013). Structure-function of the G protein–coupled receptor superfamily. Annual Review of Pharmacology and Toxicology, 53, 531–556. doi:10.1146/annurev-pharmtox-032112-135923
   PubMed Web of Science ®Google Scholar
• Liu, J. J., Horst, R., Katritch, V., Stevens, R. C., & Wüthrich, K. (2012). Biased signaling pathways in β2-adrenergic receptor characterized by 19F-NMR. Science, 335(6072), 1106–1110. doi:10.1126/science.1215802
   PubMed Web of Science ®Google Scholar
• Livingston, K. E., & Traynor, J. R. (2014). Disruption of the Na+ ion binding site as a mechanism for positive allosteric modulation of the mu-opioid receptor. Proceedings of the National Academy of Sciences of the United States of America, 111(51), 18369–18374. doi:10.1073/pnas.1415013111
   PubMed Web of Science ®Google Scholar
• Lomize, M. A., Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. (2006). OPM: Orientations of proteins in membranes database. Bioinformatics, 22(5), 623–625.10.1093/bioinformatics/btk023
   PubMed Web of Science ®Google Scholar
• Mahmood, I., Liu, X., Neya, S., & Hoshino, T. (2013). Influence of lipid composition on the structural stability of G-protein coupled receptor. Chemical & Pharmaceutical Bulletin, 61(4), 426–437.10.1248/cpb.c12-01059
   PubMed Web of Science ®Google Scholar
• Monod, J. (1972). Chance and necessity: Essay on the natural philosophy of modern biology. (HarperCollins Distribution Services, 1972).
   Google Scholar
• Paloncýová, M., Fabre, G., DeVane, R. H., Trouillas, P., Berka, K., & Otyepka, M. (2014). Benchmarking of force fields for molecule-membrane interactions. Journal of Chemical Theory and Computation, 10(9), 4143–4151. doi:10.1021/ct500419b
   PubMed Web of Science ®Google Scholar
• Pennisi, E. (2003). Human genome: A low number wins the genesweep pool. Science, 300(5625), 1484b. doi:10.1126/science.300.5625.1484b
   PubMed Web of Science ®Google Scholar
• Perez-Aguilar, J. M., Shan, J., LeVine, M. V., Khelashvili, G., & Weinstein, H. (2014). A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2. Journal of the American Chemical Society, 136(45), 16044–16054. doi:10.1021/ja508394x
   PubMed Web of Science ®Google Scholar
• Pike, L. J., Han, X., Chung, K.-N., & Gross, R. W. (2002). Lipid rafts are enriched in arachidonic acid and plasmenylethanolamine and their composition is independent of caveolin-1 expression: A quantitative electrospray ionization/mass spectrometric analysis. Biochemistry, 41(6), 2075–2088.10.1021/bi0156557
   PubMed Web of Science ®Google Scholar
• Rahmeh, R., Damian, M., Cottet, M., Orcel, H., Mendre, C., Durroux, T., … Granier, S. (2012). Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopy. Proceedings of the National Academy of Sciences of the United States of America, 109(17), 6733–6738. doi:10.1073/pnas.1201093109
   PubMed Web of Science ®Google Scholar
• Rask-Andersen, M., Almén, M. S., & Schiöth, H. B. (2011). Trends in the exploitation of novel drug targets. Nature Reviews. Drug Discovery, 10(8), 579–590. doi:10.1038/nrd3478
   PubMed Web of Science ®Google Scholar
• Rasmussen, S. G. F., DeVree, B. T., Zou, Y., Kruse, A. C., Chung, K. Y., Kobilka, T. S., … Kobilka, B. K. (2011). Crystal structure of the β2 adrenergic receptor-Gs protein complex. Nature, 477(7366), 549–555. doi:10.1038/nature10361
   PubMed Web of Science ®Google Scholar
• Salmas, R. E., Yurtsever, M., & Durdagi, S. (2015). Investigation of inhibition mechanism of Chemokine receptor CCR5 by micro-second molecular dynamics simulations. Scientific Reports, 5, 13180. doi:10.1038/srep13180
   PubMed Web of Science ®Google Scholar
• Saulière-Nzeh Ndong, A., Saulière-Nzeh, A. N., Millot, C., Corbani, M., Mazères, S., Lopez, A., & Salomé, L. (2010). Agonist-selective dynamic compartmentalization of human mu opioid receptor as revealed by resolutive FRAP analysis. The Journal of Biological Chemistry, 285(19), 14514–14520. doi:10.1074/jbc.M109.076695
   PubMed Web of Science ®Google Scholar
• Sekercioglu, N., Busse, J. W., Mustafa, R. A., Guyatt, G. H., & Thabane, L. (2016). Cinacalcet versus standard treatment for chronic kidney disease: A protocol for a systematic review and meta-analysis. Systematic Reviews, 5, 2. doi:10.1186/s13643-015-0177-1
   PubMed Web of Science ®Google Scholar
• Shang, Y., Yeatman, H. R., Provasi, D., Alt, A., Christopoulos, A., Canals, M., & Filizola, M. (2016). Proposed mode of binding and action of positive allosteric modulators at opioid receptors. ACS Chemical Biology,. doi:10.1021/acschembio.5b00712
   Web of Science ®Google Scholar
• Small-Molecule Drug Discovery Suite 2015-3: Glide. (2015). (Version version 6.8). New York, NY: Schrödinger, LLC.
   Google Scholar
• Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE – AnteChamber PYthon Parser interfacE. BMC Research Notes, 5, 367. doi:10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Spartan ‘10. (2010). Irvine. CA: Wavefunction Inc.
   Google Scholar
• SYBYL-X 1.3. (2009). St. Louis, MO: Tripos International.
   Google Scholar
• The PyMOL Molecular Graphics System. (2012). (Version Version 1.5.0.4). Schrödinger, LLC.
   Google Scholar
• Trzaskowski, B., Latek, D., Yuan, S., Ghoshdastider, U., Debinski, A., & Filipek, S. (2012). Action of molecular switches in GPCRs – Theoretical and experimental studies. Current Medicinal Chemistry, 19(8), 1090–1109.10.2174/092986712799320556
   PubMed Web of Science ®Google Scholar
• Valant, C., Felder, C. C., Sexton, P. M., & Christopoulos, A. (2012). Probe dependence in the allosteric modulation of a G protein-coupled receptor: Implications for detection and validation of allosteric ligand effects. Molecular Pharmacology, 81(1), 41–52. doi:10.1124/mol.111.074872
   PubMed Web of Science ®Google Scholar
• van der Westhuizen, E. T., Valant, C., Sexton, P. M., & Christopoulos, A. (2015). Endogenous allosteric modulators of G protein-coupled receptors. The Journal of Pharmacology and Experimental Therapeutics, 353(2), 246–260. doi:10.1124/jpet.114.221606
   PubMed Web of Science ®Google Scholar
• Vanquelef, E., Simon, S., Marquant, G., Garcia, E., Klimerak, G., Delepine, J. C., … Dupradeau, F.-Y. (2011). R.E.D. Server: A web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. Nucleic Acids Research, 39(Web Server issue), W511–W517. https://doi.org/10.1093/nar/gkr28810.1093/nar/gkr288
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Webb, B, & Sali, A. (2014). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [et Al.], 47, 5.6.1–5.6.32. https://doi.org/10.1002/0471250953.bi0506s4710.1002/0471250953.bi0506s47
   Google Scholar
• Woollard, S. M., & Kanmogne, G. D. (2015). Maraviroc: A review of its use in HIV infection and beyond. Drug Design, Development and Therapy, 9, 5447–5468. doi:10.2147/DDDT.S90580
   PubMed Web of Science ®Google Scholar
• Yuan, S., Filipek, S., Palczewski, K., & Vogel, H. (2014). Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway. Nature Communications, 5, 4733. doi:10.1038/ncomms5733
   PubMed Web of Science ®Google Scholar