Review Article

GPCR变构:从计算生物学的观点

卷 30, 期 40, 2023

发表于: 16 February, 2023

页: [4533 - 4553] 页: 21

弟呕挨: 10.2174/0929867330666230113125246

价格: $65

摘要

G蛋白偶联受体(gpcr)是细胞表面蛋白的一个大超家族,介导细胞信号传导并调节生理和病理过程的各个方面,因此是药物靶点的丰富来源。作为固有的变构蛋白,GPCRs的许多功能是通过变构调节的,即在远端位点结合的变构调节剂调节典型的正构位点的功能。然而,由于GPCR的高动态结构,目前只有少数GPCR变构配体被批准作为药物。幸运的是,计算生物学的快速发展为理解GPCR变构配体的机制提供了线索,这对发现新的治疗药物至关重要。在这里,我们全面概述了目前在计算生物学中与G蛋白偶联受体变构及其构象动力学相关的可用资源和方法。此外,还讨论了该领域目前的局限性和主要挑战。

关键词: 蛋白偶联受体,变构,变构调节剂,计算生物学,分子动力学模拟,构象动力学。

[1]
Katritch, V.; Cherezov, V.; Stevens, R.C. Structure-function of the G protein-coupled receptor superfamily. Annu. Rev. Pharmacol. Toxicol., 2013, 53(1), 531-556.
[http://dx.doi.org/10.1146/annurev-pharmtox-032112-135923] [PMID: 23140243]
[2]
Changeux, J.P.; Christopoulos, A. Allosteric modulation as a unifying mechanism for receptor function and regulation. Cell, 2016, 166(5), 1084-1102.
[http://dx.doi.org/10.1016/j.cell.2016.08.015] [PMID: 27565340]
[3]
Thal, D.M.; Glukhova, A.; Sexton, P.M.; Christopoulos, A. Structural insights into G-protein-coupled receptor allostery. Nature, 2018, 559(7712), 45-53.
[http://dx.doi.org/10.1038/s41586-018-0259-z] [PMID: 29973731]
[4]
Roth, B.L.; Kroeze, W.K. Integrated approaches for genome-wide interrogation of the druggable non-olfactory G protein-coupled receptor superfamily. J. Biol. Chem., 2015, 290(32), 19471-19477.
[http://dx.doi.org/10.1074/jbc.R115.654764] [PMID: 26100629]
[5]
Allen, J.A.; Roth, B.L. Strategies to discover unexpected targets for drugs active at G protein-coupled receptors. Annu. Rev. Pharmacol. Toxicol., 2011, 51(1), 117-144.
[http://dx.doi.org/10.1146/annurev-pharmtox-010510-100553] [PMID: 20868273]
[6]
Hauser, A.S.; Attwood, M.M.; Rask-Andersen, M.; Schiöth, H.B.; Gloriam, D.E. Trends in GPCR drug discovery: New agents, targets and indications. Nat. Rev. Drug Discov., 2017, 16(12), 829-842.
[http://dx.doi.org/10.1038/nrd.2017.178] [PMID: 29075003]
[7]
Singh, K.D.; Karnik, S.S. Current trends in GPCR allostery. J. Membr. Biol., 2021, 254(3), 293-300.
[http://dx.doi.org/10.1007/s00232-020-00167-6] [PMID: 33471142]
[8]
Krishnan, A.; Nijmeijer, S.; de Graaf, C.; Schiöth, H.B. Classification, nomenclature, and structural aspects of adhesion GPCRs. Handb. Exp. Pharmacol., 2016, 234, 15-41.
[http://dx.doi.org/10.1007/978-3-319-41523-9_2] [PMID: 27832482]
[9]
Hu, G.M.; Mai, T.L.; Chen, C.M. Visualizing the GPCR network: Classification and evolution. Sci. Rep., 2017, 7(1), 15495.
[http://dx.doi.org/10.1038/s41598-017-15707-9] [PMID: 29138525]
[10]
Traynelis, S.F.; Wollmuth, L.P.; McBain, C.J.; Menniti, F.S.; Vance, K.M.; Ogden, K.K.; Hansen, K.B.; Yuan, H.; Myers, S.J.; Dingledine, R. Glutamate receptor ion channels: Structure, regulation, and function. Pharmacol. Rev., 2010, 62(3), 405-496.
[http://dx.doi.org/10.1124/pr.109.002451] [PMID: 20716669]
[11]
Velazhahan, V.; Ma, N.; Pándy-Szekeres, G.; Kooistra, A.J.; Lee, Y.; Gloriam, D.E.; Vaidehi, N.; Tate, C.G. Structure of the class D GPCR Ste2 dimer coupled to two G proteins. Nature, 2021, 589(7840), 148-153.
[http://dx.doi.org/10.1038/s41586-020-2994-1] [PMID: 33268889]
[12]
Geng, H.; Jiang, R. cAMP receptor protein (CRP)-mediated resistance/tolerance in bacteria: Mechanism and utilization in biotechnology. Appl. Microbiol. Biotechnol., 2015, 99(11), 4533-4543.
[http://dx.doi.org/10.1007/s00253-015-6587-0] [PMID: 25913005]
[13]
Alfonso-Prieto, M.; Giorgetti, A.; Carloni, P. Multiscale simulations on human Frizzled and Taste2 GPCRs. Curr. Opin. Struct. Biol., 2019, 55, 8-16.
[http://dx.doi.org/10.1016/j.sbi.2019.02.009] [PMID: 30933747]
[14]
Wu, Y.; Tong, J.; Ding, K.; Zhou, Q.; Zhao, S. GPCR allosteric modulator discovery. Adv. Exp. Med. Biol., 2019, 1163, 225-251.
[http://dx.doi.org/10.1007/978-981-13-8719-7_10] [PMID: 31707706]
[15]
Zhao, L.H.; Ma, S.; Sutkeviciute, I.; Shen, D.D.; Zhou, X.E.; de Waal, P.W.; Li, C.Y.; Kang, Y.; Clark, L.J.; Jean-Alphonse, F.G.; White, A.D.; Yang, D.; Dai, A.; Cai, X.; Chen, J.; Li, C.; Jiang, Y.; Watanabe, T.; Gardella, T.J.; Melcher, K.; Wang, M.W.; Vilardaga, J.P.; Xu, H.E.; Zhang, Y. Structure and dynamics of the active human parathyroid hormone receptor-1. Science, 2019, 364(6436), 148-153.
[http://dx.doi.org/10.1126/science.aav7942] [PMID: 30975883]
[16]
Chun, L.; Zhang, W.; Liu, J. Structure and ligand recognition of class C GPCRs. Acta Pharmacol. Sin., 2012, 33(3), 312-323.
[http://dx.doi.org/10.1038/aps.2011.186] [PMID: 22286915]
[17]
Huang, P.; Zheng, S.; Wierbowski, B.M.; Kim, Y.; Nedelcu, D.; Aravena, L.; Liu, J.; Kruse, A.C.; Salic, A. Structural basis of smoothened activation in hedgehog signaling. Cell, 2018, 174(2), 312-324.e16.
[http://dx.doi.org/10.1016/j.cell.2018.04.029] [PMID: 29804838]
[18]
Latorraca, N.R.; Venkatakrishnan, A.J.; Dror, R.O. GPCR dynamics: Structures in motion. Chem. Rev., 2017, 117(1), 139-155.
[http://dx.doi.org/10.1021/acs.chemrev.6b00177] [PMID: 27622975]
[19]
Kobilka, B.K. G protein coupled receptor structure and activation. Biochim. Biophys. Acta Biomembr., 2007, 1768(4), 794-807.
[http://dx.doi.org/10.1016/j.bbamem.2006.10.021] [PMID: 17188232]
[20]
Zou, R.; Wang, X.; Li, S.; Chan, H.C.S.; Vogel, H.; Yuan, S. The role of metal ions in G protein coupled receptor signalling and drug discovery. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2022, 12(2), e1565.
[http://dx.doi.org/10.1002/wcms.1565]
[21]
Wang, J.; Miao, Y. Recent advances in computational studies of GPCR-G protein interactions. Adv. Protein Chem. Struct. Biol., 2019, 116, 397-419.
[http://dx.doi.org/10.1016/bs.apcsb.2018.11.011] [PMID: 31036298]
[22]
Mertz, B.; Struts, A.V.; Feller, S.E.; Brown, M.F. Molecular simulations and solid-state NMR investigate dynamical structure in rhodopsin activation. Biochim. Biophys. Acta Biomembr., 2012, 44, 1-7.
[http://dx.doi.org/10.1016/j.bbamem.2011.08.003] [PMID: 21851809]
[23]
He, X.; You, C.; Jiang, H.; Jiang, Y.; Xu, H.E.; Cheng, X. AlphaFold2 versus experimental structures: Evaluation on G protein-coupled receptors. Acta Pharmacol. Sin., 2022, 1818(2), 241-251.
[http://dx.doi.org/10.1038/s41401-022-00938-y] [PMID: 35778488]
[24]
Dror, R.O.; Green, H.F.; Valant, C.; Borhani, D.W.; Valcourt, J.R.; Pan, A.C.; Arlow, D.H.; Canals, M.; Lane, J.R.; Rahmani, R.; Baell, J.B.; Sexton, P.M.; Christopoulos, A.; Shaw, D.E. Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature, 2013, 503(7475), 295-299.
[http://dx.doi.org/10.1038/nature12595] [PMID: 24121438]
[25]
Hollingsworth, S.A.; Dror, R.O. Molecular dynamics simulation for all. Neuron, 2018, 99(6), 1129-1143.
[http://dx.doi.org/10.1016/j.neuron.2018.08.011] [PMID: 30236283]
[26]
Karplus, M.; McCammon, J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol., 2002, 9(9), 646-652.
[http://dx.doi.org/10.1038/nsb0902-646] [PMID: 12198485]
[27]
Horstman, D.A.; Brandon, S.; Wilson, A.L.; Guyer, C.A.; Cragoe, E.J., Jr; Limbird, L.E. An aspartate conserved among G-protein receptors confers allosteric regulation of alpha 2-adrenergic receptors by sodium. J. Biol. Chem., 1990, 265(35), 21590-21595.
[http://dx.doi.org/10.1016/S0021-9258(18)45781-X] [PMID: 2174879]
[28]
Tesmer, J.J.G. Hitchhiking on the heptahelical highway: Structure and function of 7TM receptor complexes. Nat. Rev. Mol. Cell Biol., 2016, 17(7), 439-450.
[http://dx.doi.org/10.1038/nrm.2016.36] [PMID: 27093944]
[29]
Pándy-Szekeres, G.; Esguerra, M.; Hauser, A.S.; Caroli, J.; Munk, C.; Pilger, S.; Keserű, G.M.; Kooistra, A.J.; Gloriam, D.E. The G protein database, GproteinDb. Nucleic Acids Res., 2022, 50(D1), D518-D525.
[http://dx.doi.org/10.1093/nar/gkab852] [PMID: 34570219]
[30]
Okuno, Y.; Yang, J.; Taneishi, K.; Yabuuchi, H.; Tsujimoto, G. GLIDA: GPCR-ligand database for chemical genomic drug discovery. Nucleic Acids Res., 2006, 34(90001), D673-D677.
[http://dx.doi.org/10.1093/nar/gkj028] [PMID: 16381956]
[31]
Rodríguez-Espigares, I.; Torrens-Fontanals, M.; Tiemann, J.K.S.; Aranda-García, D.; Ramírez-Anguita, J.M.; Stepniewski, T.M.; Worp, N.; Varela-Rial, A.; Morales-Pastor, A.; Medel-Lacruz, B.; Pándy-Szekeres, G.; Mayol, E.; Giorgino, T.; Carlsson, J.; Deupi, X.; Filipek, S.; Filizola, M.; Gómez-Tamayo, J.C.; Gonzalez, A.; Gutiérrez-de-Terán, H.; Jiménez-Rosés, M.; Jespers, W.; Kapla, J.; Khelashvili, G.; Kolb, P.; Latek, D.; Marti-Solano, M.; Matricon, P.; Matsoukas, M-T.; Miszta, P.; Olivella, M.; Perez-Benito, L.; Provasi, D.; Ríos, S.; R Torrecillas, I.; Sallander, J.; Sztyler, A.; Vasile, S.; Weinstein, H.; Zachariae, U.; Hildebrand, P.W.; De Fabritiis, G.; Sanz, F.; Gloriam, D.E.; Cordomi, A.; Guixà-González, R.; Selent, J. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat. Methods, 2020, 17(8), 777-787.
[http://dx.doi.org/10.1038/s41592-020-0884-y] [PMID: 32661425]
[32]
Huang, Z.; Zhu, L.; Cao, Y.; Wu, G.; Liu, X.; Chen, Y.; Wang, Q.; Shi, T.; Zhao, Y.; Wang, Y.; Li, W.; Li, Y.; Chen, H.; Chen, G.; Zhang, J. ASD: A comprehensive database of allosteric proteins and modulators. Nucleic Acids Res., 2011, 39, D663-D669.
[http://dx.doi.org/10.1093/nar/gkq1022] [PMID: 21051350]
[33]
Liu, W.; Chun, E.; Thompson, A.A.; Chubukov, P.; Xu, F.; Katritch, V.; Han, G.W.; Roth, C.B.; Heitman, L.H.; IJzerman, A.P.; Cherezov, V.; Stevens, R.C. Structural basis for allosteric regulation of GPCRs by sodium ions. Science, 2012, 337(6091), 232-236.
[http://dx.doi.org/10.1126/science.1219218] [PMID: 22798613]
[34]
Wu, F.; Yang, L.; Hang, K.; Laursen, M.; Wu, L.; Han, G.W.; Ren, Q.; Roed, N.K.; Lin, G.; Hanson, M.A.; Jiang, H.; Wang, M.W.; Reedtz-Runge, S.; Song, G.; Stevens, R.C. Full-length human GLP-1 receptor structure without orthosteric ligands. Nat. Commun., 2020, 11(1), 1272.
[http://dx.doi.org/10.1038/s41467-020-14934-5] [PMID: 32152292]
[35]
Wu, H.; Wang, C.; Gregory, K.J.; Han, G.W.; Cho, H.P.; Xia, Y.; Niswender, C.M.; Katritch, V.; Meiler, J.; Cherezov, V.; Conn, P.J.; Stevens, R.C. Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator. Science, 2014, 344(6179), 58-64.
[http://dx.doi.org/10.1126/science.1249489] [PMID: 24603153]
[36]
Wang, C.; Wu, H.; Evron, T.; Vardy, E.; Han, G.W.; Huang, X.P.; Hufeisen, S.J.; Mangano, T.J.; Urban, D.J.; Katritch, V.; Cherezov, V.; Caron, M.G.; Roth, B.L.; Stevens, R.C. Structural basis for smoothened receptor modulation and chemoresistance to anticancer drugs. Nat. Commun., 2014, 5(1), 4355.
[http://dx.doi.org/10.1038/ncomms5355] [PMID: 25008467]
[37]
Rose, P.W.; Prlić, A.; Altunkaya, A.; Bi, C.; Bradley, A.R.; Christie, C.H.; Costanzo, L.D.; Duarte, J.M.; Dutta, S.; Feng, Z.; Green, R.K.; Goodsell, D.S.; Hudson, B.; Kalro, T.; Lowe, R.; Peisach, E.; Randle, C.; Rose, A.S.; Shao, C.; Tao, Y.P.; Valasatava, Y.; Voigt, M.; Westbrook, J.D.; Woo, J.; Yang, H.; Young, J.Y.; Zardecki, C.; Berman, H.M.; Burley, S.K. The RCSB protein data bank: Integrative view of protein, gene and 3D structural information. Nucleic Acids Res., 2017, 45(D1), D271-D281.
[PMID: 27794042]
[38]
Kruse, A.C.; Ring, A.M.; Manglik, A.; Hu, J.; Hu, K.; Eitel, K.; Hübner, H.; Pardon, E.; Valant, C.; Sexton, P.M.; Christopoulos, A.; Felder, C.C.; Gmeiner, P.; Steyaert, J.; Weis, W.I.; Garcia, K.C.; Wess, J.; Kobilka, B.K. Activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature, 2013, 504(7478), 101-106.
[http://dx.doi.org/10.1038/nature12735] [PMID: 24256733]
[39]
Maeda, S.; Qu, Q.; Robertson, M.J.; Skiniotis, G.; Kobilka, B.K. Structures of the M1 and M2 muscarinic acetylcholine receptor/G-protein complexes. Science, 2019, 364(6440), 552-557.
[http://dx.doi.org/10.1126/science.aaw5188] [PMID: 31073061]
[40]
Staus, D.P.; Hu, H.; Robertson, M.J.; Kleinhenz, A.L.W.; Wingler, L.M.; Capel, W.D.; Latorraca, N.R.; Lefkowitz, R.J.; Skiniotis, G. Structure of the M2 muscarinic receptor–β-arrestin complex in a lipid nanodisc. Nature, 2020, 579(7798), 297-302.
[http://dx.doi.org/10.1038/s41586-020-1954-0] [PMID: 31945772]
[41]
Zheng, Y.; Qin, L.; Zacarías, N.V.O.; de Vries, H.; Han, G.W.; Gustavsson, M.; Dabros, M.; Zhao, C.; Cherney, R.J.; Carter, P.; Stamos, D.; Abagyan, R.; Cherezov, V.; Stevens, R.C.; IJzerman, A.P.; Heitman, L.H.; Tebben, A.; Kufareva, I.; Handel, T.M. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature, 2016, 540(7633), 458-461.
[http://dx.doi.org/10.1038/nature20605] [PMID: 27926736]
[42]
Jaeger, K.; Bruenle, S.; Weinert, T.; Guba, W.; Muehle, J.; Miyazaki, T.; Weber, M.; Furrer, A.; Haenggi, N.; Tetaz, T.; Huang, C.Y.; Mattle, D.; Vonach, J.M.; Gast, A.; Kuglstatter, A.; Rudolph, M.G.; Nogly, P.; Benz, J.; Dawson, R.J.P.; Standfuss, J. Structural basis for allosteric ligand recognition in the human CC chemokine receptor 7. Cell, 2019, 178(5), 1222-1230.e10.
[http://dx.doi.org/10.1016/j.cell.2019.07.028] [PMID: 31442409]
[43]
Oswald, C.; Rappas, M.; Kean, J.; Doré, A.S.; Errey, J.C.; Bennett, K.; Deflorian, F.; Christopher, J.A.; Jazayeri, A.; Mason, J.S.; Congreve, M.; Cooke, R.M.; Marshall, F.H. Intracellular allosteric antagonism of the CCR9 receptor. Nature, 2016, 540(7633), 462-465.
[http://dx.doi.org/10.1038/nature20606] [PMID: 27926729]
[44]
Sun, B.; Bachhawat, P.; Chu, M.L.H.; Wood, M.; Ceska, T.; Sands, Z.A.; Mercier, J.; Lebon, F.; Kobilka, T.S.; Kobilka, B.K. Crystal structure of the adenosine A2A receptor bound to an antagonist reveals a potential allosteric pocket. Proc. Natl. Acad. Sci. USA, 2017, 114(8), 2066-2071.
[http://dx.doi.org/10.1073/pnas.1621423114] [PMID: 28167788]
[45]
Liu, X.; Ahn, S.; Kahsai, A.W.; Meng, K.C.; Latorraca, N.R.; Pani, B.; Venkatakrishnan, A.J.; Masoudi, A.; Weis, W.I.; Dror, R.O.; Chen, X.; Lefkowitz, R.J.; Kobilka, B.K. Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure. Nature, 2017, 548(7668), 480-484.
[http://dx.doi.org/10.1038/nature23652] [PMID: 28813418]
[46]
Liu, X.; Kaindl, J.; Korczynska, M.; Stößel, A.; Dengler, D.; Stanek, M.; Hübner, H.; Clark, M.J.; Mahoney, J.; Matt, R.A.; Xu, X.; Hirata, K.; Shoichet, B.K.; Sunahara, R.K.; Kobilka, B.K.; Gmeiner, P. An allosteric modulator binds to a conformational hub in the β2 adrenergic receptor. Nat. Chem. Biol., 2020, 16(7), 749-755.
[http://dx.doi.org/10.1038/s41589-020-0549-2] [PMID: 32483378]
[47]
Wang, X.; Liu, D.; Shen, L.; Li, F.; Li, Y.; Yang, L.; Xu, T.; Tao, H.; Yao, D.; Wu, L.; Hirata, K.; Bohn, L.M.; Makriyannis, A.; Liu, X.; Hua, T.; Liu, Z.J.; Wang, J. A genetically encoded F-19 NMR probe reveals the allosteric modulation mechanism of cannabinoid receptor 1. J. Am. Chem. Soc., 2021, 143(40), 16320-16325.
[http://dx.doi.org/10.1021/jacs.1c06847] [PMID: 34596399]
[48]
Shao, Z.; Yan, W.; Chapman, K.; Ramesh, K.; Ferrell, A.J.; Yin, J.; Wang, X.; Xu, Q.; Rosenbaum, D.M. Structure of an allosteric modulator bound to the CB1 cannabinoid receptor. Nat. Chem. Biol., 2019, 15(12), 1199-1205.
[http://dx.doi.org/10.1038/s41589-019-0387-2] [PMID: 31659318]
[49]
Draper-Joyce, C.J.; Bhola, R.; Wang, J.; Bhattarai, A.; Nguyen, A.T.N.; Cowie-Kent, I.; O’Sullivan, K.; Chia, L.Y.; Venugopal, H.; Valant, C.; Thal, D.M.; Wootten, D.; Panel, N.; Carlsson, J.; Christie, M.J.; White, P.J.; Scammells, P.; May, L.T.; Sexton, P.M.; Danev, R.; Miao, Y.; Glukhova, A.; Imlach, W.L.; Christopoulos, A. Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia. Nature, 2021, 597(7877), 571-576.
[http://dx.doi.org/10.1038/s41586-021-03897-2] [PMID: 34497422]
[50]
Zhang, D.; Gao, Z.G.; Zhang, K.; Kiselev, E.; Crane, S.; Wang, J.; Paoletta, S.; Yi, C.; Ma, L.; Zhang, W.; Han, G.W.; Liu, H.; Cherezov, V.; Katritch, V.; Jiang, H.; Stevens, R.C.; Jacobson, K.A.; Zhao, Q.; Wu, B. Two disparate ligand-binding sites in the human P2Y1 receptor. Nature, 2015, 520(7547), 317-321.
[http://dx.doi.org/10.1038/nature14287] [PMID: 25822790]
[51]
Liu, H.; Kim, H.R.; Deepak, R.N.V.K.; Wang, L.; Chung, K.Y.; Fan, H.; Wei, Z.; Zhang, C. Orthosteric and allosteric action of the C5a receptor antagonists. Nat. Struct. Mol. Biol., 2018, 25(6), 472-481.
[http://dx.doi.org/10.1038/s41594-018-0067-z] [PMID: 29867214]
[52]
Robertson, N.; Rappas, M.; Doré, A.S.; Brown, J.; Bottegoni, G.; Koglin, M.; Cansfield, J.; Jazayeri, A.; Cooke, R.M.; Marshall, F.H. Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727. Nature, 2018, 553(7686), 111-114.
[http://dx.doi.org/10.1038/nature25025] [PMID: 29300009]
[53]
Liu, X.; Masoudi, A.; Kahsai, A.W.; Huang, L.Y.; Pani, B.; Staus, D.P.; Shim, P.J.; Hirata, K.; Simhal, R.K.; Schwalb, A.M.; Rambarat, P.K.; Ahn, S.; Lefkowitz, R.J.; Kobilka, B. Mechanism of β 2 AR regulation by an intracellular positive allosteric modulator. Science, 2019, 364(6447), 1283-1287.
[http://dx.doi.org/10.1126/science.aaw8981] [PMID: 31249059]
[54]
Srivastava, A.; Yano, J.; Hirozane, Y.; Kefala, G.; Gruswitz, F.; Snell, G.; Lane, W.; Ivetac, A.; Aertgeerts, K.; Nguyen, J.; Jennings, A.; Okada, K. High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875. Nature, 2014, 513(7516), 124-127.
[http://dx.doi.org/10.1038/nature13494] [PMID: 25043059]
[55]
Lu, J.; Byrne, N.; Wang, J.; Bricogne, G.; Brown, F.K.; Chobanian, H.R.; Colletti, S.L.; Di Salvo, J.; Thomas-Fowlkes, B.; Guo, Y.; Hall, D.L.; Hadix, J.; Hastings, N.B.; Hermes, J.D.; Ho, T.; Howard, A.D.; Josien, H.; Kornienko, M.; Lumb, K.J.; Miller, M.W.; Patel, S.B.; Pio, B.; Plummer, C.W.; Sherborne, B.S.; Sheth, P.; Souza, S.; Tummala, S.; Vonrhein, C.; Webb, M.; Allen, S.J.; Johnston, J.M.; Weinglass, A.B.; Sharma, S.; Soisson, S.M. Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40. Nat. Struct. Mol. Biol., 2017, 24(7), 570-577.
[http://dx.doi.org/10.1038/nsmb.3417] [PMID: 28581512]
[56]
Ho, J.D.; Chau, B.; Rodgers, L.; Lu, F.; Wilbur, K.L.; Otto, K.A.; Chen, Y.; Song, M.; Riley, J.P.; Yang, H.C.; Reynolds, N.A.; Kahl, S.D.; Lewis, A.P.; Groshong, C.; Madsen, R.E.; Conners, K.; Lineswala, J.P.; Gheyi, T.; Saflor, M.B.D.; Lee, M.R.; Benach, J.; Baker, K.A.; Montrose-Rafizadeh, C.; Genin, M.J.; Miller, A.R.; Hamdouchi, C. Structural basis for GPR40 allosteric agonism and incretin stimulation. Nat. Commun., 2018, 9(1), 1645.
[http://dx.doi.org/10.1038/s41467-017-01240-w] [PMID: 29695780]
[57]
Cheng, R.K.Y.; Fiez-Vandal, C.; Schlenker, O.; Edman, K.; Aggeler, B.; Brown, D.G.; Brown, G.A.; Cooke, R.M.; Dumelin, C.E.; Doré, A.S.; Geschwindner, S.; Grebner, C.; Hermansson, N.O.; Jazayeri, A.; Johansson, P.; Leong, L.; Prihandoko, R.; Rappas, M.; Soutter, H.; Snijder, A.; Sundström, L.; Tehan, B.; Thornton, P.; Troast, D.; Wiggin, G.; Zhukov, A.; Marshall, F.H.; Dekker, N. Structural insight into allosteric modulation of protease-activated receptor 2. Nature, 2017, 545(7652), 112-115.
[http://dx.doi.org/10.1038/nature22309] [PMID: 28445455]
[58]
Zhao, P.; Liang, Y.L.; Belousoff, M.J.; Deganutti, G.; Fletcher, M.M.; Willard, F.S.; Bell, M.G.; Christe, M.E.; Sloop, K.W.; Inoue, A.; Truong, T.T.; Clydesdale, L.; Furness, S.G.B.; Christopoulos, A.; Wang, M.W.; Miller, L.J.; Reynolds, C.A.; Danev, R.; Sexton, P.M.; Wootten, D. Activation of the GLP-1 receptor by a non-peptidic agonist. Nature, 2020, 577(7790), 432-436.
[http://dx.doi.org/10.1038/s41586-019-1902-z] [PMID: 31915381]
[59]
Cong, Z.; Chen, L.N.; Ma, H.; Zhou, Q.; Zou, X.; Ye, C.; Dai, A.; Liu, Q.; Huang, W.; Sun, X.; Wang, X.; Xu, P.; Zhao, L.; Xia, T.; Zhong, W.; Yang, D.; Eric Xu, H.; Zhang, Y.; Wang, M.W. Molecular insights into ago-allosteric modulation of the human glucagon-like peptide-1 receptor. Nat. Commun., 2021, 12(1), 3763.
[http://dx.doi.org/10.1038/s41467-021-24058-z] [PMID: 34145245]
[60]
Bueno, A.B.; Sun, B.; Willard, F.S.; Feng, D.; Ho, J.D.; Wainscott, D.B.; Showalter, A.D.; Vieth, M.; Chen, Q.; Stutsman, C.; Chau, B.; Ficorilli, J.; Agejas, F.J.; Cumming, G.R.; Jiménez, A.; Rojo, I.; Kobilka, T.S.; Kobilka, B.K.; Sloop, K.W. Structural insights into probe-dependent positive allosterism of the GLP-1 receptor. Nat. Chem. Biol., 2020, 16(10), 1105-1110.
[http://dx.doi.org/10.1038/s41589-020-0589-7] [PMID: 32690941]
[61]
Song, G.; Yang, D.; Wang, Y.; de Graaf, C.; Zhou, Q.; Jiang, S.; Liu, K.; Cai, X.; Dai, A.; Lin, G.; Liu, D.; Wu, F.; Wu, Y.; Zhao, S.; Ye, L.; Han, G.W.; Lau, J.; Wu, B.; Hanson, M.A.; Liu, Z.J.; Wang, M.W.; Stevens, R.C. Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators. Nature, 2017, 546(7657), 312-315.
[http://dx.doi.org/10.1038/nature22378] [PMID: 28514449]
[62]
Xu, Y.; Wang, Y.; Wang, Y.; Liu, K.; Peng, Y.; Yao, D.; Tao, H.; Liu, H.; Song, G. Mutagenesis facilitated crystallization of GLP-1R. IUCrJ, 2019, 6(6), 996-1006.
[http://dx.doi.org/10.1107/S2052252519013496] [PMID: 31709055]
[63]
Zhang, H.; Qiao, A.; Yang, D.; Yang, L.; Dai, A.; de Graaf, C.; Reedtz-Runge, S.; Dharmarajan, V.; Zhang, H.; Han, G.W.; Grant, T.D.; Sierra, R.G.; Weierstall, U.; Nelson, G.; Liu, W.; Wu, Y.; Ma, L.; Cai, X.; Lin, G.; Wu, X.; Geng, Z.; Dong, Y.; Song, G.; Griffin, P.R.; Lau, J.; Cherezov, V.; Yang, H.; Hanson, M.A.; Stevens, R.C.; Zhao, Q.; Jiang, H.; Wang, M.W.; Wu, B. Structure of the full-length glucagon class B G-protein-coupled receptor. Nature, 2017, 546(7657), 259-264.
[http://dx.doi.org/10.1038/nature22363] [PMID: 28514451]
[64]
Jazayeri, A.; Doré, A.S.; Lamb, D.; Krishnamurthy, H.; Southall, S.M.; Baig, A.H.; Bortolato, A.; Koglin, M.; Robertson, N.J.; Errey, J.C.; Andrews, S.P.; Teobald, I.; Brown, A.J.H.; Cooke, R.M.; Weir, M.; Marshall, F.H. Extra-helical binding site of a glucagon receptor antagonist. Nature, 2016, 533(7602), 274-277.
[http://dx.doi.org/10.1038/nature17414] [PMID: 27111510]
[65]
Hollenstein, K.; Kean, J.; Bortolato, A.; Cheng, R.K.Y.; Doré, A.S.; Jazayeri, A.; Cooke, R.M.; Weir, M.; Marshall, F.H. Structure of class B GPCR corticotropin-releasing factor receptor 1. Nature, 2013, 499(7459), 438-443.
[http://dx.doi.org/10.1038/nature12357] [PMID: 23863939]
[66]
Dore, A.S.; Bortolato, A.; Hollenstein, K.; Cheng, R.K.Y.; Read, R.J.; Marshall, F.H. Decoding corticotropin-releasing factor receptor type 1 crystal structures. Curr. Mol. Pharmacol., 2017, 10(4), 334-344.
[PMID: 28183242]
[67]
Gao, Y.; Robertson, M.J.; Rahman, S.N.; Seven, A.B.; Zhang, C.; Meyerowitz, J.G.; Panova, O.; Hannan, F.M.; Thakker, R.V.; Bräuner-Osborne, H.; Mathiesen, J.M.; Skiniotis, G. Asymmetric activation of the calcium-sensing receptor homodimer. Nature, 2021, 595(7867), 455-459.
[http://dx.doi.org/10.1038/s41586-021-03691-0] [PMID: 34194040]
[68]
Kim, Y.; Jeong, E.; Jeong, J.H.; Kim, Y.; Cho, Y. Structural basis for activation of the heterodimeric GABAB receptor. J. Mol. Biol., 2020, 432(22), 5966-5984.
[http://dx.doi.org/10.1016/j.jmb.2020.09.023] [PMID: 33058878]
[69]
Shaye, H.; Ishchenko, A.; Lam, J.H.; Han, G.W.; Xue, L.; Rondard, P.; Pin, J.P.; Katritch, V.; Gati, C.; Cherezov, V. Structural basis of the activation of a metabotropic GABA receptor. Nature, 2020, 584(7820), 298-303.
[http://dx.doi.org/10.1038/s41586-020-2408-4] [PMID: 32555460]
[70]
Weierstall, U.; James, D.; Wang, C.; White, T.A.; Wang, D.; Liu, W.; Spence, J.C.H.; Bruce Doak, R.; Nelson, G.; Fromme, P.; Fromme, R.; Grotjohann, I.; Kupitz, C.; Zatsepin, N.A.; Liu, H.; Basu, S.; Wacker, D.; Won Han, G.; Katritch, V.; Boutet, S.; Messerschmidt, M.; Williams, G.J.; Koglin, J.E.; Marvin Seibert, M.; Klinker, M.; Gati, C.; Shoeman, R.L.; Barty, A.; Chapman, H.N.; Kirian, R.A.; Beyerlein, K.R.; Stevens, R.C.; Li, D.; Shah, S.T.A.; Howe, N.; Caffrey, M.; Cherezov, V. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat. Commun., 2014, 5(1), 3309.
[http://dx.doi.org/10.1038/ncomms4309] [PMID: 24525480]
[71]
White, K.L.; Eddy, M.T.; Gao, Z.G.; Han, G.W.; Lian, T.; Deary, A.; Patel, N.; Jacobson, K.A.; Katritch, V.; Stevens, R.C. Structural connection between activation microswitch and allosteric sodium site in GPCR signaling. Structure, 2018, 26(2), 259-269.e5.
[http://dx.doi.org/10.1016/j.str.2017.12.013] [PMID: 29395784]
[72]
Ballesteros, J.A.; Weinstein, H. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods Neurosci., 1995, 25, 366-428.
[http://dx.doi.org/10.1016/S1043-9471(05)80049-7]
[73]
Wang, S.; Wacker, D.; Levit, A.; Che, T.; Betz, R.M.; McCorvy, J.D.; Venkatakrishnan, A.J.; Huang, X.P.; Dror, R.O.; Shoichet, B.K.; Roth, B.L. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science, 2017, 358(6361), 381-386.
[http://dx.doi.org/10.1126/science.aan5468] [PMID: 29051383]
[74]
Christopher, J.A.; Brown, J.; Doré, A.S.; Errey, J.C.; Koglin, M.; Marshall, F.H.; Myszka, D.G.; Rich, R.L.; Tate, C.G.; Tehan, B.; Warne, T.; Congreve, M. Biophysical fragment screening of the β1-adrenergic receptor: Identification of high affinity arylpiperazine leads using structure-based drug design. J. Med. Chem., 2013, 56(9), 3446-3455.
[http://dx.doi.org/10.1021/jm400140q] [PMID: 23517028]
[75]
Fenalti, G.; Giguere, P.M.; Katritch, V.; Huang, X.P.; Thompson, A.A.; Cherezov, V.; Roth, B.L.; Stevens, R.C. Molecular control of δ-opioid receptor signalling. Nature, 2014, 506(7487), 191-196.
[http://dx.doi.org/10.1038/nature12944] [PMID: 24413399]
[76]
Luginina, A.; Gusach, A.; Marin, E.; Mishin, A.; Brouillette, R.; Popov, P.; Shiriaeva, A.; Besserer-Offroy, É.; Longpré, J.M.; Lyapina, E.; Ishchenko, A.; Patel, N.; Polovinkin, V.; Safronova, N.; Bogorodskiy, A.; Edelweiss, E.; Hu, H.; Weierstall, U.; Liu, W.; Batyuk, A.; Gordeliy, V.; Han, G.W.; Sarret, P.; Katritch, V.; Borshchevskiy, V.; Cherezov, V. Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs. Sci. Adv., 2019, 5(10), eaax2518.
[http://dx.doi.org/10.1126/sciadv.aax2518] [PMID: 31633023]
[77]
Rappas, M.; Ali, A.A.E.; Bennett, K.A.; Brown, J.D.; Bucknell, S.J.; Congreve, M.; Cooke, R.M.; Cseke, G.; de Graaf, C.; Doré, A.S.; Errey, J.C.; Jazayeri, A.; Marshall, F.H.; Mason, J.S.; Mould, R.; Patel, J.C.; Tehan, B.G.; Weir, M.; Christopher, J.A. Comparison of orexin 1 and orexin 2 ligand binding modes using X-ray crystallography and computational analysis. J. Med. Chem., 2020, 63(4), 1528-1543.
[http://dx.doi.org/10.1021/acs.jmedchem.9b01787] [PMID: 31860301]
[78]
Schiffmann, A.; Gimpl, G. Sodium functions as a negative allosteric modulator of the oxytocin receptor. Biochim. Biophys. Acta Biomembr., 2018, 1860(6), 1301-1308.
[http://dx.doi.org/10.1016/j.bbamem.2018.03.003] [PMID: 29524392]
[79]
Michino, M.; Free, R.B.; Doyle, T.B.; Sibley, D.R.; Shi, L. Structural basis for Na+-sensitivity in dopamine D2 and D3 receptors. Chem. Commun. (Camb.), 2015, 51(41), 8618-8621.
[http://dx.doi.org/10.1039/C5CC02204E] [PMID: 25896577]
[80]
Chan, H.C.S.; Xu, Y.; Tan, L.; Vogel, H.; Cheng, J.; Wu, D.; Yuan, S. Enhancing the signaling of GPCRs via orthosteric ions. ACS Cent. Sci., 2020, 6(2), 274-282.
[http://dx.doi.org/10.1021/acscentsci.9b01247] [PMID: 32123746]
[81]
Ye, L.; Neale, C.; Sljoka, A.; Lyda, B.; Pichugin, D.; Tsuchimura, N.; Larda, S.T.; Pomès, R.; García, A.E.; Ernst, O.P.; Sunahara, R.K.; Prosser, R.S. Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations. Nat. Commun., 2018, 9(1), 1372.
[http://dx.doi.org/10.1038/s41467-018-03314-9] [PMID: 29636462]
[82]
Hu, X.; Provasi, D.; Ramsey, S.; Filizola, M. Mechanism of μ-opioid receptor-magnesium interaction and positive allosteric modulation. Biophys. J., 2020, 118(4), 909-921.
[http://dx.doi.org/10.1016/j.bpj.2019.10.007] [PMID: 31676132]
[83]
Waltenspühl, Y.; Schöppe, J.; Ehrenmann, J.; Kummer, L.; Plückthun, A. Crystal structure of the human oxytocin receptor. Sci. Adv., 2020, 6(29), eabb5419.
[http://dx.doi.org/10.1126/sciadv.abb5419] [PMID: 32832646]
[84]
Schetz, J.A.; Chu, A.; Sibley, D.R. Zinc modulates antagonist interactions with D2-like dopamine receptors through distinct molecular mechanisms. J. Pharmacol. Exp. Ther., 1999, 289(2), 956-964.
[PMID: 10215675]
[85]
White, A.D.; Fang, F.; Jean-Alphonse, F.G.; Clark, L.J.; An, H.J.; Liu, H.; Zhao, Y.; Reynolds, S.L.; Lee, S.; Xiao, K.; Sutkeviciute, I.; Vilardaga, J.P. Ca2+ allostery in PTH-receptor signaling. Proc. Natl. Acad. Sci. USA, 2019, 116(8), 3294-3299.
[http://dx.doi.org/10.1073/pnas.1814670116] [PMID: 30718391]
[86]
Cao, C.; Tan, Q.; Xu, C.; He, L.; Yang, L.; Zhou, Y.; Zhou, Y.; Qiao, A.; Lu, M.; Yi, C.; Han, G.W.; Wang, X.; Li, X.; Yang, H.; Rao, Z.; Jiang, H.; Zhao, Y.; Liu, J.; Stevens, R.C.; Zhao, Q.; Zhang, X.C.; Wu, B. Structural basis for signal recognition and transduction by platelet-activating-factor receptor. Nat. Struct. Mol. Biol., 2018, 25(6), 488-495.
[http://dx.doi.org/10.1038/s41594-018-0068-y] [PMID: 29808000]
[87]
Holst, B.; Elling, C.E.; Schwartz, T.W. Metal ion-mediated agonism and agonist enhancement in melanocortin MC1 and MC4 receptors. J. Biol. Chem., 2002, 277(49), 47662-47670.
[http://dx.doi.org/10.1074/jbc.M202103200] [PMID: 12244039]
[88]
Yu, J.; Gimenez, L.E.; Hernandez, C.C.; Wu, Y.; Wein, A.H.; Han, G.W.; McClary, K.; Mittal, S.R.; Burdsall, K.; Stauch, B.; Wu, L.; Stevens, S.N.; Peisley, A.; Williams, S.Y.; Chen, V.; Millhauser, G.L.; Zhao, S.; Cone, R.D.; Stevens, R.C. Determination of the melanocortin-4 receptor structure identifies Ca2+ as a cofactor for ligand binding. Science, 2020, 368(6489), 428-433.
[http://dx.doi.org/10.1126/science.aaz8995] [PMID: 32327598]
[89]
Israeli, H.; Degtjarik, O.; Fierro, F.; Chunilal, V.; Gill, A.K.; Roth, N.J.; Botta, J.; Prabahar, V.; Peleg, Y.; Chan, L.F.; Ben-Zvi, D.; McCormick, P.J.; Niv, M.Y.; Shalev-Benami, M. Structure reveals the activation mechanism of the MC4 receptor to initiate satiation signaling. Science, 2021, 372(6544), 808-814.
[http://dx.doi.org/10.1126/science.abf7958] [PMID: 33858992]
[90]
Li, M.; Li, M.; Guo, J. Molecular mechanism of Ca2+ in the allosteric regulation of human parathyroid hormone receptor-1. J. Chem. Inf. Model., 2022, 62, 5110-5119.
[http://dx.doi.org/10.1021/acs.jcim.1c00471] [PMID: 34464108]
[91]
Cournia, Z.; Allen, T.W.; Andricioaei, I.; Antonny, B.; Baum, D.; Brannigan, G.; Buchete, N.V.; Deckman, J.T.; Delemotte, L.; del Val, C.; Friedman, R.; Gkeka, P.; Hege, H.C.; Hénin, J.; Kasimova, M.A.; Kolocouris, A.; Klein, M.L.; Khalid, S.; Lemieux, M.J.; Lindow, N.; Roy, M.; Selent, J.; Tarek, M.; Tofoleanu, F.; Vanni, S.; Urban, S.; Wales, D.J.; Smith, J.C.; Bondar, A.N. Membrane protein structure, function, and dynamics: A perspective from experiments and theory. J. Membr. Biol., 2015, 248(4), 611-640.
[http://dx.doi.org/10.1007/s00232-015-9802-0] [PMID: 26063070]
[92]
Safdari, H.A.; Pandey, S.; Shukla, A.K.; Dutta, S. Illuminating GPCR signaling by cryo-EM. Trends Cell Biol., 2018, 28(8), 591-594.
[http://dx.doi.org/10.1016/j.tcb.2018.06.002] [PMID: 29945844]
[93]
Jisna, V.A.; Jayaraj, P.B. Protein structure prediction: Conventional and deep learning perspectives. Protein J., 2021, 40(4), 522-544.
[http://dx.doi.org/10.1007/s10930-021-10003-y] [PMID: 34050498]
[94]
Zhang, J.; Yang, J.; Jang, R.; Zhang, Y. GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome. Structure, 2015, 23(8), 1538-1549.
[http://dx.doi.org/10.1016/j.str.2015.06.007] [PMID: 26190572]
[95]
Bharathi; Roy, K.K. Structural basis for the binding of a selective inverse agonist AF64394 with the human G-protein coupled receptor 3 (GPR3). J. Biomol. Struct. Dyn., 2021. [Epub ahead of print]
[96]
Kashani-Amin, E.; Sakhteman, A.; Larijani, B.; Ebrahim-Habibi, A. Introducing a new model of sweet taste receptor, a class C G-protein coupled receptor (C GPCR). Cell Biochem. Biophys., 2019, 77(3), 227-243.
[http://dx.doi.org/10.1007/s12013-019-00872-7] [PMID: 31069640]
[97]
Chan, W.K.B.; Zhang, Y. Virtual screening of human class-A GPCRs using ligand profiles built on multiple ligand–receptor interactions. J. Mol. Biol., 2020, 432(17), 4872-4890.
[http://dx.doi.org/10.1016/j.jmb.2020.07.003] [PMID: 32652079]
[98]
Bender, B.J.; Marlow, B.; Meiler, J. Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs. PLOS Comput. Biol., 2020, 16(10), e1007597.
[http://dx.doi.org/10.1371/journal.pcbi.1007597] [PMID: 33112852]
[99]
Worth, C.L.; Kreuchwig, F.; Tiemann, J.K.S.; Kreuchwig, A.; Ritschel, M.; Kleinau, G.; Hildebrand, P.W.; Krause, G. GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors. Nucleic Acids Res., 2017, 45(W1), W408-W415.
[http://dx.doi.org/10.1093/nar/gkx399] [PMID: 28582569]
[100]
Tunyasuvunakool, K.; Adler, J.; Wu, Z.; Green, T.; Zielinski, M.; Žídek, A.; Bridgland, A.; Cowie, A.; Meyer, C.; Laydon, A.; Velankar, S.; Kleywegt, G.J.; Bateman, A.; Evans, R.; Pritzel, A.; Figurnov, M.; Ronneberger, O.; Bates, R.; Kohl, S.A.A.; Potapenko, A.; Ballard, A.J.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Clancy, E.; Reiman, D.; Petersen, S.; Senior, A.W.; Kavukcuoglu, K.; Birney, E.; Kohli, P.; Jumper, J.; Hassabis, D. Highly accurate protein structure prediction for the human proteome. Nature, 2021, 596(7873), 590-596.
[http://dx.doi.org/10.1038/s41586-021-03828-1] [PMID: 34293799]
[101]
Heo, L.; Feig, M. Multi state modeling of G protein coupled receptors at experimental accuracy. Proteins, 2022, 90(11), 1873-1885.
[http://dx.doi.org/10.1002/prot.26382] [PMID: 35510704]
[102]
Decherchi, S.; Cavalli, A. Thermodynamics and kinetics of drug-target binding by molecular simulation. Chem. Rev., 2020, 120(23), 12788-12833.
[http://dx.doi.org/10.1021/acs.chemrev.0c00534] [PMID: 33006893]
[103]
Jaakola, V.P.; Griffith, M.T.; Hanson, M.A.; Cherezov, V.; Chien, E.Y.T.; Lane, J.R.; IJzerman, A.P.; Stevens, R.C. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science, 2008, 322(5905), 1211-1217.
[http://dx.doi.org/10.1126/science.1164772] [PMID: 18832607]
[104]
Lebon, G.; Warne, T.; Edwards, P.C.; Bennett, K.; Langmead, C.J.; Leslie, A.G.W.; Tate, C.G. Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation. Nature, 2011, 474(7352), 521-525.
[http://dx.doi.org/10.1038/nature10136] [PMID: 21593763]
[105]
Carpenter, B.; Nehmé, R.; Warne, T.; Leslie, A.G.W.; Tate, C.G. Erratum: Structure of the adenosine A2A receptor bound to an engineered G protein. Nature, 2016, 538(7626), 542.
[http://dx.doi.org/10.1038/nature19803] [PMID: 27629518]
[106]
Yang, D.; Zhou, Q.; Labroska, V.; Qin, S.; Darbalaei, S.; Wu, Y.; Yuliantie, E.; Xie, L.; Tao, H.; Cheng, J.; Liu, Q.; Zhao, S.; Shui, W.; Jiang, Y.; Wang, M.W. G protein-coupled receptors: Structure and function-based drug discovery. Signal. Transduct. Target. Ther., 2021, 6(1), 7.
[http://dx.doi.org/10.1038/s41392-020-00435-w] [PMID: 33414387]
[107]
Kruse, A.C.; Hu, J.; Pan, A.C.; Arlow, D.H.; Rosenbaum, D.M.; Rosemond, E.; Green, H.F.; Liu, T.; Chae, P.S.; Dror, R.O.; Shaw, D.E.; Weis, W.I.; Wess, J.; Kobilka, B.K. Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature, 2012, 482(7386), 552-556.
[http://dx.doi.org/10.1038/nature10867] [PMID: 22358844]
[108]
Suomivuori, C.M.; Latorraca, N.R.; Wingler, L.M.; Eismann, S.; King, M.C.; Kleinhenz, A.L.W.; Skiba, M.A.; Staus, D.P.; Kruse, A.C.; Lefkowitz, R.J.; Dror, R.O. Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor. Science, 2020, 367(6480), 881-887.
[http://dx.doi.org/10.1126/science.aaz0326] [PMID: 32079767]
[109]
Li, M.; Bao, Y.; Xu, R.; La, H.; Guo, J. Critical extracellular Ca 2+ dependence of the binding between PTH1R and a G-protein peptide revealed by MD simulations. ACS Chem. Neurosci., 2022, 13(11), 1666-1674.
[http://dx.doi.org/10.1021/acschemneuro.2c00176] [PMID: 35543321]
[110]
Wootten, D.; Simms, J.; Miller, L.J.; Christopoulos, A.; Sexton, P.M. Polar transmembrane interactions drive formation of ligand-specific and signal pathway-biased family B G protein-coupled receptor conformations. Proc. Natl. Acad. Sci. USA, 2013, 110(13), 5211-5216.
[http://dx.doi.org/10.1073/pnas.1221585110] [PMID: 23479653]
[111]
Guo, J.; Zhou, H.X. Protein allostery and conformational dynamics. Chem. Rev., 2016, 116(11), 6503-6515.
[http://dx.doi.org/10.1021/acs.chemrev.5b00590] [PMID: 26876046]
[112]
Bernardi, R.C.; Melo, M.C.R.; Schulten, K. Enhanced sampling techniques in molecular dynamics simulations of biological systems. Biochim. Biophys. Acta, 2015, 1850(5), 872-877.
[http://dx.doi.org/10.1016/j.bbagen.2014.10.019] [PMID: 25450171]
[113]
Yang, Y.I.; Shao, Q.; Zhang, J.; Yang, L.; Gao, Y.Q. Enhanced sampling in molecular dynamics. J. Chem. Phys., 2019, 151(7), 070902.
[http://dx.doi.org/10.1063/1.5109531] [PMID: 31438687]
[114]
Ahmad, K.; Rizzi, A.; Capelli, R.; Mandelli, D.; Lyu, W.; Carloni, P. Enhanced-sampling simulations for the estimation of ligand binding kinetics: Current status and perspective. Front. Mol. Biosci., 2022, 9, 899805.
[http://dx.doi.org/10.3389/fmolb.2022.899805] [PMID: 35755817]
[115]
Harpole, T.J.; Delemotte, L. Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations. Biochim. Biophys. Acta Biomembr., 2018, 1860(4), 909-926.
[http://dx.doi.org/10.1016/j.bbamem.2017.10.033] [PMID: 29113819]
[116]
Bergonzo, C.; Campbell, A.J.; Walker, R.C.; Simmerling, C. A partial nudged elastic band implementation for use with large or explicitly solvated systems. Int. J. Quantum Chem., 2009, 109(15), 3781-3790.
[http://dx.doi.org/10.1002/qua.22405] [PMID: 20148191]
[117]
Hamelberg, D.; Mongan, J.; McCammon, J.A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J. Chem. Phys., 2004, 120(24), 11919-11929.
[http://dx.doi.org/10.1063/1.1755656] [PMID: 15268227]
[118]
Miao, Y.; Goldfeld, D.A.; Moo, E.V.; Sexton, P.M.; Christopoulos, A.; McCammon, J.A.; Valant, C. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. Proc. Natl. Acad. Sci. USA, 2016, 113(38), E5675-E5684.
[http://dx.doi.org/10.1073/pnas.1612353113] [PMID: 27601651]
[119]
Miao, Y.; Nichols, S.E.; Gasper, P.M.; Metzger, V.T.; McCammon, J.A. Activation and dynamic network of the M2 muscarinic receptor. Proc. Natl. Acad. Sci. USA, 2013, 110(27), 10982-10987.
[http://dx.doi.org/10.1073/pnas.1309755110] [PMID: 23781107]
[120]
Miao, Y.; Caliman, A.D.; McCammon, J.A. Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. Biophys. J., 2015, 108(7), 1796-1806.
[http://dx.doi.org/10.1016/j.bpj.2015.03.003] [PMID: 25863070]
[121]
Laio, A.; Parrinello, M. Escaping free-energy minima. Proc. Natl. Acad. Sci. USA, 2002, 99(20), 12562-12566.
[http://dx.doi.org/10.1073/pnas.202427399] [PMID: 12271136]
[122]
Lückmann, M.; Trauelsen, M.; Bentsen, M.A.; Nissen, T.A.D.; Martins, J.; Fallah, Z.; Nygaard, M.M.; Papaleo, E.; Lindorff-Larsen, K.; Schwartz, T.W.; Frimurer, T.M. Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1. Proc. Natl. Acad. Sci. USA, 2019, 116(14), 7123-7128.
[http://dx.doi.org/10.1073/pnas.1811066116] [PMID: 30872479]
[123]
Cong, X.; Zhang, X.; Liang, X.; He, X.; Tang, Y.; Zheng, X.; Lu, S.; Zhang, J.; Chen, T. Delineating the conformational landscape and intrinsic properties of the angiotensin II type 2 receptor using a computational study. Comput. Struct. Biotechnol. J., 2022, 20, 2268-2279.
[http://dx.doi.org/10.1016/j.csbj.2022.05.012] [PMID: 35615027]
[124]
Lu, S.; He, X.; Yang, Z.; Chai, Z.; Zhou, S.; Wang, J.; Rehman, A.U.; Ni, D.; Pu, J.; Sun, J.; Zhang, J. Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nat. Commun., 2021, 12(1), 4721.
[http://dx.doi.org/10.1038/s41467-021-25020-9] [PMID: 34354057]
[125]
Kästner, J. Umbrella sampling. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2011, 1(6), 932-942.
[http://dx.doi.org/10.1002/wcms.66]
[126]
Agostino, M.; Pohl, S.Ö.G. Activation barriers in Class F G protein-coupled receptors revealed by umbrella sampling simulations. Org. Biomol. Chem., 2020, 18(48), 9816-9825.
[http://dx.doi.org/10.1039/D0OB02175J] [PMID: 33290484]
[127]
Paila, Y.D.; Jindal, E.; Goswami, S.K.; Chattopadhyay, A. Cholesterol depletion enhances adrenergic signaling in cardiac myocytes. Biochim. Biophys. Acta Biomembr., 2011, 1808(1), 461-465.
[http://dx.doi.org/10.1016/j.bbamem.2010.09.006] [PMID: 20851100]
[128]
Soubias, O.; Gawrisch, K. The role of the lipid matrix for structure and function of the GPCR rhodopsin. Biochim. Biophys. Acta Biomembr., 2012, 1818(2), 234-240.
[http://dx.doi.org/10.1016/j.bbamem.2011.08.034] [PMID: 21924236]
[129]
Ansell, T.B.; Song, W.; Sansom, M.S.P. The glycosphingolipid GM3 modulates conformational dynamics of the glucagon receptor. Biophys. J., 2020, 119(2), 300-313.
[http://dx.doi.org/10.1016/j.bpj.2020.06.009] [PMID: 32610088]
[130]
Hanson, M.A.; Cherezov, V.; Griffith, M.T.; Roth, C.B.; Jaakola, V.P.; Chien, E.Y.T.; Velasquez, J.; Kuhn, P.; Stevens, R.C. A specific cholesterol binding site is established by the 2.8 A structure of the human β2-adrenergic receptor. Structure, 2008, 16(6), 897-905.
[http://dx.doi.org/10.1016/j.str.2008.05.001] [PMID: 18547522]
[131]
Prasanna, X.; Chattopadhyay, A.; Sengupta, D. Cholesterol modulates the dimer interface of the β-adrenergic receptor via cholesterol occupancy sites. Biophys. J., 2014, 106(6), 1290-1300.
[http://dx.doi.org/10.1016/j.bpj.2014.02.002] [PMID: 24655504]
[132]
Song, W.; Yen, H.Y.; Robinson, C.V.; Sansom, M.S.P. State-dependent lipid interactions with the A2a receptor revealed by MD simulations using in vivo-mimetic membranes. Structure, 2019, 27(2), 392-403.e3.
[http://dx.doi.org/10.1016/j.str.2018.10.024] [PMID: 30581046]
[133]
Wingler, L.M.; Elgeti, M.; Hilger, D.; Latorraca, N.R.; Lerch, M.T.; Staus, D.P.; Dror, R.O.; Kobilka, B.K.; Hubbell, W.L.; Lefkowitz, R.J. Angiotensin analogs with divergent bias stabilize distinct receptor conformations. Cell, 2019, 176(3), 468-478.e11.
[http://dx.doi.org/10.1016/j.cell.2018.12.005] [PMID: 30639099]
[134]
Yang, L.; Yang, D.; de Graaf, C.; Moeller, A.; West, G.M.; Dharmarajan, V.; Wang, C.; Siu, F.Y.; Song, G.; Reedtz-Runge, S.; Pascal, B.D.; Wu, B.; Potter, C.S.; Zhou, H.; Griffin, P.R.; Carragher, B.; Yang, H.; Wang, M.W.; Stevens, R.C.; Jiang, H. Conformational states of the full-length glucagon receptor. Nat. Commun., 2015, 6(1), 7859.
[http://dx.doi.org/10.1038/ncomms8859] [PMID: 26227798]
[135]
Zhang, J.; Bai, Q.; Pérez-Sánchez, H.; Shang, S.; An, X.; Yao, X. Investigation of ECD conformational transition mechanism of GLP-1R by molecular dynamics simulations and Markov state model. Phys. Chem. Chem. Phys., 2019, 21(16), 8470-8481.
[http://dx.doi.org/10.1039/C9CP00080A] [PMID: 30957116]
[136]
Torrens-Fontanals, M.; Stepniewski, T.M.; Aranda-García, D.; Morales-Pastor, A.; Medel-Lacruz, B.; Selent, J. How do molecular dynamics data complement static structural data of GPCRs. Int. J. Mol. Sci., 2020, 21(16), 5933.
[http://dx.doi.org/10.3390/ijms21165933] [PMID: 32824756]
[137]
Cao, S.; Montoya-Castillo, A.; Wang, W.; Markland, T.E.; Huang, X. On the advantages of exploiting memory in Markov state models for biomolecular dynamics. J. Chem. Phys., 2020, 153(1), 014105.
[http://dx.doi.org/10.1063/5.0010787] [PMID: 32640825]
[138]
Konovalov, K.A.; Unarta, I.C.; Cao, S.; Goonetilleke, E.C.; Huang, X. Markov state models to study the functional dynamics of proteins in the wake of machine learning. JACS Au, 2021, 1(9), 1330-1341.
[http://dx.doi.org/10.1021/jacsau.1c00254] [PMID: 34604842]
[139]
Schultze, S.; Grubmüller, H. Time-lagged independent component analysis of random walks and protein dynamics. J. Chem. Theory Comput., 2021, 17(9), 5766-5776.
[http://dx.doi.org/10.1021/acs.jctc.1c00273] [PMID: 34449229]
[140]
Kohlhoff, K.J.; Shukla, D.; Lawrenz, M.; Bowman, G.R.; Konerding, D.E.; Belov, D.; Altman, R.B.; Pande, V.S. Cloud-based simulations on google exacycle reveal ligand modulation of GPCR activation pathways. Nat. Chem., 2014, 6(1), 15-21.
[http://dx.doi.org/10.1038/nchem.1821] [PMID: 24345941]
[141]
Wang, Y.; Li, M.; Liang, W.; Shi, X.; Fan, J.; Kong, R.; Liu, Y.; Zhang, J.; Chen, T.; Lu, S. Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor. Comput. Struct. Biotechnol. J., 2022, 20, 628-639.
[http://dx.doi.org/10.1016/j.csbj.2022.01.015] [PMID: 35140883]
[142]
Taylor, B.C.; Lee, C.T.; Amaro, R.E. Structural basis for ligand modulation of the CCR2 conformational landscape. Proc. Natl. Acad. Sci. USA, 2019, 116(17), 8131-8136.
[http://dx.doi.org/10.1073/pnas.1814131116] [PMID: 30975755]
[143]
Wingler, L.M.; Lefkowitz, R.J. Conformational basis of G protein-coupled receptor signaling versatility. Trends Cell Biol., 2020, 30(9), 736-747.
[http://dx.doi.org/10.1016/j.tcb.2020.06.002] [PMID: 32622699]
[144]
Morales-Pastor, A.; Nerín-Fonz, F.; Aranda-García, D.; Dieguez-Eceolaza, M.; Medel-Lacruz, B.; Torrens-Fontanals, M.; Peralta-García, A.; Selent, J. In silico study of allosteric communication networks in GPCR signaling bias. Int. J. Mol. Sci., 2022, 23(14), 7809.
[http://dx.doi.org/10.3390/ijms23147809] [PMID: 35887157]
[145]
Eyal, E.; Lum, G.; Bahar, I. The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics, 2015, 31(9), 1487-1489.
[http://dx.doi.org/10.1093/bioinformatics/btu847] [PMID: 25568280]
[146]
Daily, M.D.; Upadhyaya, T.J.; Gray, J.J. Contact rearrangements form coupled networks from local motions in allosteric proteins. Proteins, 2008, 71(1), 455-466.
[http://dx.doi.org/10.1002/prot.21800] [PMID: 17957766]
[147]
Bhattacharya, S.; Vaidehi, N. Differences in allosteric communication pipelines in the inactive and active states of a GPCR. Biophys. J., 2014, 107(2), 422-434.
[http://dx.doi.org/10.1016/j.bpj.2014.06.015] [PMID: 25028884]
[148]
Bhattacharya, S.; Salomon-Ferrer, R.; Lee, S.; Vaidehi, N. Conserved mechanism of conformational stability and dynamics in G-protein-coupled receptors. J. Chem. Theory Comput., 2016, 12(11), 5575-5584.
[http://dx.doi.org/10.1021/acs.jctc.6b00618] [PMID: 27709935]
[149]
Ma, N.; Nivedha, A.K.; Vaidehi, N. Allosteric communication regulates ligand-specific GPCR activity. FEBS J., 2021, 288(8), 2502-2512.
[http://dx.doi.org/10.1111/febs.15826] [PMID: 33738925]
[150]
Atilgan, A.R.; Durell, S.R.; Jernigan, R.L.; Demirel, M.C.; Keskin, O.; Bahar, I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 2001, 80(1), 505-515.
[http://dx.doi.org/10.1016/S0006-3495(01)76033-X] [PMID: 11159421]
[151]
Isin, B.; Rader, A.J.; Dhiman, H.K.; Klein-Seetharaman, J.; Bahar, I. Predisposition of the dark state of rhodopsin to functional changes in structure. Proteins, 2006, 65(4), 970-983.
[http://dx.doi.org/10.1002/prot.21158] [PMID: 17009319]
[152]
Yanamala, N.; Tirupula, K.C.; Klein-Seetharaman, J. Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors. BMC Bioinformatics, 2008, 9(S1), S16.
[http://dx.doi.org/10.1186/1471-2105-9-S1-S16] [PMID: 18315847]
[153]
Clark, L.J.; Krieger, J.; White, A.D.; Bondarenko, V.; Lei, S.; Fang, F.; Lee, J.Y.; Doruker, P.; Böttke, T.; Jean-Alphonse, F.; Tang, P.; Gardella, T.J.; Xiao, K.; Sutkeviciute, I.; Coin, I.; Bahar, I.; Vilardaga, J.P. Allosteric interactions in the parathyroid hormone GPCR–arrestin complex formation. Nat. Chem. Biol., 2020, 16(10), 1096-1104.
[http://dx.doi.org/10.1038/s41589-020-0567-0] [PMID: 32632293]
[154]
Cong, Z.; Liang, Y.L.; Zhou, Q.; Darbalaei, S.; Zhao, F.; Feng, W.; Zhao, L.; Xu, H.E.; Yang, D.; Wang, M.W. Structural perspective of class B1 GPCR signaling. Trends Pharmacol. Sci., 2022, 43(4), 321-334.
[http://dx.doi.org/10.1016/j.tips.2022.01.002] [PMID: 35078643]
[155]
Liu, L.; Fan, Z.; Rovira, X.; Xue, L.; Roux, S.; Brabet, I.; Xin, M.; Pin, J.P.; Rondard, P.; Liu, J. Allosteric ligands control the activation of a class C GPCR heterodimer by acting at the transmembrane interface. eLife, 2021, 10, e70188.
[http://dx.doi.org/10.7554/eLife.70188] [PMID: 34866572]
[156]
Dror, R.O.; Jensen, M.Ø.; Borhani, D.W.; Shaw, D.E. Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J. Gen. Physiol., 2010, 135(6), 555-562.
[http://dx.doi.org/10.1085/jgp.200910373] [PMID: 20513757]

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