1.
Wu, F., Song, G., de Graaf, C. & Stevens, R. C. Structure and Function of
Peptide-Binding G Protein-Coupled Receptors. J. Mol. Biol. 429, 2726–2745
(2017).
2.
Kamato, D. et al. Structure, Function, Pharmacology, and Therapeutic Potential
of the G Protein, Gα/q,11. Front. Cardiovasc. Med. 2, 1–11 (2015).
3.
Suzuki, N., Hajicek, N. & Kozasa, T. Regulation and physiological functions of
G12/13-mediated signaling pathways. NeuroSignals 17, 55–70 (2009).
4.
Rosenbaum, D. M. et al. Structure and function of an irreversible agonist-β2
adrenoceptor complex. Nature 469, 236–242 (2011).
5.
Kolakowski, L. F. GCRDb: A G-protein-coupled receptor database. Recept.
Channels 2, 1–7 (1994).
6.
Dixon, R. A. F. et al. Cloning of the gene and cDNA for mammalian βadrenergic receptor and homology with rhodopsin. 321, 75–79 (1986).
7.
Unger, V. M., Hargrave, P. A., Baldwin, J. M. & Schertler, G. F. X. Arrangement
of rhodopsin transmembrane α-helices. Nature 389, 203–206 (1997).
8.
Palczewski, K. et al. Crystal structure of rhodopsin: A G protein-coupled
receptor. Science (80-. ). 289, 739–745 (2000).
9.
Juan A., B. . H. W. . Integrated methods for the construction of three-dimensional
models and computational probing of structure-function relations in G proteincoupled receptors. Methods Neurosci. 25, 366–428 (1995).
10.
Zhou, Q. et al. Common activation mechanism of class A GPCRs. Elife 8, 1–31
(2019).
11.
White, K. L. et al. Structural Connection between Activation Microswitch and
Allosteric Sodium Site in GPCR Signaling. Structure 26, 259-269.e5 (2018).
12.
Shihoya, W. et al. Activation mechanism of endothelin ET B receptor by
endothelin-1. Nature 537, 363–368 (2016).
13.
Yanagisawa, M. et al. A novel potent vasoconstrictor peptide produced by
vascular endothelial cells. Nature 332, 411–415 (1988).
14.
Arai, H., Hori, S., Aramori, I., Ohkubo, H. & Nakanishi, S. Cloning and
expression of a cDNA encoding an endothelin receptor. Nature 348, 730–732
(1990).
15.
Sakurai, T. et al. Cloning of a cDNA encoding a non-isopeptide-selective
71
subtype of the endothelin receptor. Nature 348, 732–735 (1990).
16.
Remuzzi, G., Perico, N. & Benigni, A. New therapeutics that antagonize
endothelin: Promises and frustrations. Nat. Rev. Drug Discov. 1, 986–1001
(2002).
17.
Hiyama, T. Y. et al. Endothelin-3 expression in the subfornical organ enhances
the sensitivity of Nax, the brain sodium-level sensor, to suppress salt intake. Cell
Metab. 17, 507–519 (2013).
18.
Takai, M. et al. A potent and specific agonist, Suc-[Glu9,Ala11,15]-endothelin1(8-21), IRL 1620, for the ETB receptor. Biochem. Biophys. Res. Commun. 184,
953–959 (1992).
19.
Gulati, N. V. R., Matwyshyn, G. & Gulanti, A. IRL-1620, a tumor selective
vasodilator, augments the uptake and efficacy of chemotherapeutic agents in
prostate tumor rats. Prostate 67, 701–713 (2007).
20.
Rajeshkumar, N. V., Rai, A. & Gulati, A. Endothelin B receptor agonist, IRL
1620, enhances the anti-tumor efficacy of paclitaxel in breast tumor rats. Breast
Cancer Res. Treat. 94, 237–247 (2005).
21.
Leonard, M. G., Briyal, S. & Gulati, A. Endothelin B receptor agonist, IRL-1620,
provides long-term neuroprotection in cerebral ischemia in rats. Brain Res. 1464,
14–23 (2012).
22.
Briyal, S., Shepard, C. & Gulati, A. Endothelin receptor type B agonist, IRL1620, prevents beta amyloid (Aβ) induced oxidative stress and cognitive
impairment in normal and diabetic rats. Pharmacol. Biochem. Behav. 120, 65–72
(2014).
23.
Briyal, S., Nguyen, C., Leonard, M. & Gulati, A. Stimulation of endothelin B
receptors by IRL-1620 decreases the progression of Alzheimer’s disease.
Neuroscience 301, 1–11 (2015).
24.
Kim, R. et al. Phase 2 study of combination SPI-1620 with docetaxel as secondline advanced biliary tract cancer treatment. Br. J. Cancer 117, 189–194 (2017).
25.
Shihoya, W. et al. Activation mechanism of endothelin ET B receptor by
endothelin-1. Nature 537, 363–368 (2016).
26.
Shihoya, W. et al. X-ray structures of endothelin ETB receptor bound to clinical
antagonist bosentan and its analog. Nat. Struct. Mol. Biol. 24, 758–764 (2017).
27.
Kloog, Y. & Sokolovsky, M. Similarities in mode and sites of action of
72
sarafotoxins and endothelins. Trends Pharmacol. Sci. 10, 212–214 (1989).
28.
Bdolah, A., Wollberg, Z., Fleminger, G. & Kochva, E. SRTX-d, a new native
peptide of the endothelin/sarafotoxin family. FEBS Lett. 256, 1–3 (1989).
29.
Kochva, E., Bdolah, A. & Wollberg, Z. Sarafotoxins and endothelins: evolution,
structure and function. Toxicon 31, 541–568 (1993).
30.
Lauer-Fields, J. L. et al. Engineered sarafotoxins as tissue inhibitor of
metalloproteinases-like matrix metalloproteinase inhibitors. J. Biol. Chem. 282,
26948–26955 (2007).
31.
Serhan, C. N., Chiang, N. & Van Dyke, T. E. Resolving inflammation: dual antiinflammatory and pro-resolution lipid mediators. Nat. Rev. Immunol. 8, 349–361
(2008).
32.
Fukushima, N., Ishii, I., Contos, J. J. A., Weiner, J. A. & Chun, J.
Lysophospholipid Receptors. Annu. Rev. Pharmacol. Toxicol. 41, 34 (2001).
33.
Nojima, S. et al. Cryo-EM Structure of the Prostaglandin E Receptor EP4
Coupled to G Protein. Structure 1–9 (2020). doi:10.1016/j.str.2020.11.007
34.
Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nat.
Protoc. 4, 706–731 (2009).
35.
Taniguchi, R. et al. Structural insights into ligand recognition by the
lysophosphatidic acid receptor LPA 6. Nature 548, 356–360 (2017).
36.
Yamashita, K., Hirata, K. & Yamamoto, M. KAMO: towards automated data
processing for microcrystals. Acta Crystallogr. Sect. D Struct. Biol. 74, 441–449
(2018).
37.
Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr 66, 125–132 (2010).
38.
Foadi, J. et al. Clustering procedures for the optimal selection of data sets from
multiple crystals in macromolecular crystallography. Acta Crystallogr. Sect. D
Biol. Crystallogr. 69, 1617–1632 (2013).
39.
Ueno, G. et al. Remote access and automation of SPring-8 MX beamlines. AIP
Conf. Proc. 1741, 050021 (2016).
40.
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40,
658–674 (2007).
41.
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development
of Coot. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 486–501 (2010).
42.
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for
73
macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66,
(2010).
43.
Chen, V. B. et al. MolProbity: All-atom structure validation for macromolecular
crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 12–21 (2010).
44.
Inoue, A. et al. TGFα shedding assay: An accurate and versatile method for
detecting GPCR activation. Nat. Methods 9, 1021–1029 (2012).
45.
Dixon, A. S. et al. NanoLuc Complementation Reporter Optimized for Accurate
Measurement of Protein Interactions in Cells. ACS Chem. Biol. 11, 400–408
(2016).
46.
Vrecl, M., Jorgensen, R., Pogačnik, A. & Heding, A. Development of a BRET2
screening assay using β-arrestin 2 mutants. J. Biomol. Screen. 9, 322–333 (2004).
47.
Šali, A. & Blundell, T. L. Comparative Protein Modelling by Satisfaction of
Spatial Restraints. Journal of Molecular Biology 234, 779–815 (1993).
48.
Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem.
26, 1781–1802 (2005).
49.
Humphrey, W., Dalke, A. & Schulten, K. VMD: Visual Molecular Dynamics. J.
Mol. Graph. 14, 33–38 (1996).
50.
Best, R. B. et al. Optimization of the additive CHARMM all-atom protein force
field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2
Dihedral Angles. J. Chem. Theory Comput. 8, 3257–3273 (2012).
51.
Klauda, J. B. et al. Update of the CHARMM All-Atom Additive Force Field for
Lipids: Validation on Six Lipid Types. J. Phys. Chem. B 114, 7830–7843 (2010).
52.
Feller, S. E., Zhang, Y., Pastor, R. W. & Brooks, B. R. Constant pressure
molecular dynamics simulation: The Langevin piston method. J. Chem. Phys.
103, 4613–4621 (1995).
53.
Darden, T., York, D. & Pedersen, L. Particle mesh Ewald: An N·log(N) method
for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).
54.
Saeki, T., Ihara, M., Fukuroda, T., Yamagiwa, M. & Yano, M.
[Ala1,3,11,15]endothelin-1 analogs with ETB agonistic activity. Biochem.
Biophys. Res. Commun. 179, 286–292 (1991).
55.
Saeki, T., Ihara, M., Fukuroda, T. & Yano, M. Structure-activity relationship for
ETB agonism in truncated endothelin-1 analogs. Biochem. Int. 28, 305—312
(1992).
74
56.
Heyl, D. L. et al. Truncated analogues of endothelin and sarafotoxin are selective
for the ETB receptor subtype. Pept. Res. 6, 238—241 (1993).
57.
Lättig, J., Oksche, A., Beyermann, M., Rosenthal, W. & Krause, G. Structural
determinants for selective recognition of peptide ligands for endothelin receptor
subtypes ETA and ETB. J. Pept. Sci. 15, 479–491 (2009).
58.
Manglik, A. et al. Structural Insights into the Dynamic Process of β2-Adrenergic
Receptor Signaling. Cell 161, 1101–1111 (2015).
59.
Kruse, A. C. et al. Activation and allosteric modulation of a muscarinic
acetylcholine receptor. Nature 504, 101–106 (2013).
60.
Fenalti, G. et al. Molecular control of δ-opioid receptor signalling. Nature 506,
191–196 (2014).
61.
Holst, B. et al. A conserved aromatic lock for the tryptophan rotameric switch in
TM-VI of seven-transmembrane receptors. J. Biol. Chem. 285, 3973–3985
(2010).
62.
Eddy, M. T. et al. Allosteric Coupling of Drug Binding and Intracellular
Signaling in the A2A Adenosine Receptor. Cell 172, 68-80.e12 (2018).
63.
Warne, T. et al. The structural basis for agonist and partial agonist action on a
β1-adrenergic receptor. Nature 469, 241–244 (2011).
75
Original papers related to this thesis
(1)
Wataru Shihoya*, Tamaki Izume*, Asuka Inoue, Keitaro Yamashita, Francois
Marie Ngako Kadji, Kunio Hirata, Junken Aoki, Tomohiro Nishizawa and Osamu
Nureki
Crystal structures of human ETB receptor provide mechanistic insight into receptor
activation and partial activation
Nature communications 9 4711 (9 November 2018)
(2)
Tamaki Izume, Hirotake Miyauchi, Wataru Shihoya, Osamu Nureki
Crystal structure of human endothelin ETB receptor in complex with sarafotoxin
S6b
Biochemical and Biophysical Research Communications 23 July 2020 528-2 383388
76
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