Conformational variants of the ternary complex of C5a, C5aR1, and G-protein

References

• Campbell, A. P., & Smrcka, A. V. (2018). Targeting G protein-coupled receptor signalling by blocking G proteins. Nature Reviews. Drug Discovery, 17(11), 789–803. https://doi.org/10.1038/nrd.2018.135
   PubMed Web of Science ®Google Scholar
• Costa-Neto, C. M., Parreiras-e-Silva, L. T., & Bouvier, M. (2016). A pluridimensional view of biased agonism. Molecular Pharmacology, 90(5), 587–595. https://doi.org/10.1124/mol.116.105940
   PubMed Web of Science ®Google Scholar
• Crilly, S. E., & Puthenveedu, M. A. (2021). Compartmentalized GPCR signalling from intracellular membranes. The Journal of Membrane Biology, 254(3), 259–271. https://doi.org/10.1007/s00232-020-00158-7
   PubMed Web of Science ®Google Scholar
• Das, A., Behera, L. M., & Rana, S. (2021). Interaction of human C5a with the major peptide fragments of C5aR1: Direct evidence in support of “two-site” binding paradigm. ACS Omega, 6(35), 22876–22887. https://doi.org/10.1021/acsomega.1c03400
   PubMed Web of Science ®Google Scholar
• Das, A., Ghosh, M., Gupta, P. K., & Rana, S. (2023). Neutraligands of C5a can potentially occlude the interaction of C5a with the complement receptors C5aR1 and C5aR2. Journal of Cellular Biochemistry, 124(2), 266–281. https://doi.org/10.1002/jcb.30360
   PubMed Web of Science ®Google Scholar
• Das, A., Gupta, P. K., & Rana, S. (2022). C5aR2 receptor: The genomic twin of the flamboyant C5aR1. Journal of Cellular Biochemistry, 123(11), 1841–1856. https://doi.org/10.1002/jcb.30320
   PubMed Web of Science ®Google Scholar
• Das, A., & Rana, S. (2021). The role of human C5a as a non-genomic target in corticosteroid therapy for management of severe COVID19. Computational Biology and Chemistry, 92, 107482. https://doi.org/10.1016/j.compbiolchem.2021.107482
   PubMed Web of Science ®Google Scholar
• Ding, P., Xu, Y., Li, L., Lv, X., Li, L., Chen, J., Zhou, D., Wang, X., Wang, Q., Zhang, W., Liao, T., Ji, Q. H., Lei, Q. Y., & Hu, W. (2022). Intracellular complement C5a/C5aR1 stabilizes β-catenin to promote colorectal tumorigenesis. Cell Reports, 39(9), 110851. https://doi.org/10.1016/j.celrep.2022.110851
   PubMed Web of Science ®Google Scholar
• Eichel, K., Jullié, D., Barsi-Rhyne, B., Latorraca, N. R., Masureel, M., Sibarita, J.-B., Dror, R. O., & von Zastrow, M. (2018). Catalytic activation of β-arrestin by GPCRs. Nature, 557(7705), 381–386. https://doi.org/10.1038/s41586-018-0079-1
   PubMed Web of Science ®Google Scholar
• Feng, Y., Zhao, C., Deng, Y., Wang, H., Ma, L., Liu, S., Tian, X., Wang, B., Bin, Y., Chen, P., Yan, W., Fu, P., & Shao, Z. (2023). Mechanism of activation and biased signalling in complement receptor C5aR1. Cell Research, 33(4), 312–324. https://doi.org/10.1038/s41422-023-00779-2
   PubMed Web of Science ®Google Scholar
• Ghosh, M., & Rana, S. (2023). The anaphylatoxin C5a: Structure, function, signalling, physiology, disease, and therapeutics. International Immunopharmacology, 118, 110081. https://doi.org/10.1016/j.intimp.2023.110081
   PubMed Web of Science ®Google Scholar
• Ghosh, M., Shadangi, S., & Rana, S. (2023). Rational design of antibody-like peptides for targeting the human complement fragment protein C5a. Proteins. https://doi.org/10.1002/prot.26637
   Web of Science ®Google Scholar
• Gupta, P. K., Das, A., Singh, A., & Rana, S. (2023). Ternary model structural complex of C5a, C5aR2, and β-arrestin1. Journal of Biomolecular Structure & Dynamics, 1–17. https://doi.org/10.1080/07391102.2023.2239927
   Web of Science ®Google Scholar
• Gurevich, V. V., & Gurevich, E. V. (2023). Dynamic nature of proteins is critically important for their function: GPCRs and signal transducers. Applied Magnetic Resonance, https://doi.org/10.1007/s00723-023-01561-8
   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. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Issuree, P. D., Pushparaj, P. N., Pervaiz, S., & Melendez, A. J. (2009). Resveratrol attenuates C5a-induced inflammatory responses in vitro and in vivo by inhibiting phospholipase D and sphingosine kinase activities. FASEB Journal, 23(8), 2412–2424. https://doi.org/10.1096/fj.09-130542
   PubMed Web of Science ®Google Scholar
• Jayne, D. R. W., Merkel, P. A., Schall, T. J., & Bekker, P. (2021). Avacopan for the treatment of ANCA-associated vasculitis. The New England Journal of Medicine, 384(7), 599–609. https://doi.org/10.1056/NEJMoa2023386
   PubMed Web of Science ®Google Scholar
• Kandt, C., Ash, W. L., & Tieleman, D. P. (2007). Setting up and running molecular dynamics simulations of membrane proteins. Methods (San Diego, Calif.), 41(4), 475–488. https://doi.org/10.1016/j.ymeth.2006.08.006
   PubMed Web of Science ®Google Scholar
• Kato, H. E., Zhang, Y., Hu, H., Suomivuori, C.-M., Kadji, F. M. N., Aoki, J., Krishna Kumar, K., Fonseca, R., Hilger, D., Huang, W., Latorraca, N. R., Inoue, A., Dror, R. O., Kobilka, B. K., & Skiniotis, G. (2019). Conformational transitions of a neurotensin receptor 1–Gi1 complex. Nature, 572(7767), 80–85. https://doi.org/10.1038/s41586-019-1337-6
   PubMed Web of Science ®Google Scholar
• Kim, Y., Hwang, S., Khalmuratova, R., Kang, S., Lee, M., Song, Y., Park, J.-W., Yu, J., Shin, H.-W., & Lee, Y. (2020). α-Helical cell-penetrating peptide-mediated nasal delivery of resveratrol for inhibition of epithelial-to-mesenchymal transition. Journal of Controlled Release, 317, 181–194. https://doi.org/10.1016/j.jconrel.2019.11.034
   PubMed Web of Science ®Google Scholar
• Koehl, A., Hu, H., Maeda, S., Zhang, Y., Qu, Q., Paggi, J. M., Latorraca, N. R., Hilger, D., Dawson, R., Matile, H., Schertler, G. F. X., Granier, S., Weis, W. I., Dror, R. O., Manglik, A., Skiniotis, G., & Kobilka, B. K. (2018). Structure of the µ-opioid receptor–Gi protein complex. Nature, 558(7711), 547–552. https://doi.org/10.1038/s41586-018-0219-7
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Consortium, O. S. D. D., & Lynn, A. (2014). g_mmpbsa A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lambright, D. G., Sondek, J., Bohm, A., Skiba, N. P., Hamm, H. E., & Sigler, P. B. (1996). The 2.0 Å crystal structure of a heterotrimeric G protein. Nature, 379(6563), 311–319. https://doi.org/10.1038/379311a0
   PubMed Web of Science ®Google Scholar
• Lamers, C., Ricklin, D., & Lambris, J. D. (2023). Complement-targeted therapeutics: An emerging field enabled by academic drug discovery. American Journal of Hematology, 98 Suppl 4(S4), S82–S89. https://doi.org/10.1002/ajh.26875
   PubMedGoogle Scholar
• Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England), 23(21), 2947–2948. https://doi.org/10.1093/bioinformatics/btm404
   PubMed Web of Science ®Google Scholar
• Latorraca, N. R., Venkatakrishnan, A. J., & Dror, R. O. (2017). GPCR dynamics: Structures in motion. Chemical Reviews, 117(1), 139–155. https://doi.org/10.1021/acs.chemrev.6b00177
   PubMed Web of Science ®Google Scholar
• Latorraca, N. R., Wang, J. K., Bauer, B., Townshend, R. J. L., Hollingsworth, S. A., Olivieri, J. E., Xu, H. E., Sommer, M. E., & Dror, R. O. (2018). Molecular mechanism of GPCR-mediated arrestin activation. Nature, 557(7705), 452–456. https://doi.org/10.1038/s41586-018-0077-3
   PubMed Web of Science ®Google Scholar
• Lefkowitz, R. J., & Shenoy, S. K. (2005). Transduction of receptor signals by ß-arrestins. Science (New York, N.Y.), 308(5721), 512–517. https://doi.org/10.1126/science.1109237
   PubMed Web of Science ®Google Scholar
• Li, R., Coulthard, L. G., Wu, M., Taylor, S. M., & Woodruff, T. M. (2013). C5L2: A controversial receptor of complement anaphylatoxin, C5a. FASEB Journal, 27(3), 855–864. https://doi.org/10.1096/fj.12-220509
   PubMed Web of Science ®Google Scholar
• Milligan, G., & Kostenis, E. (2006). Heterotrimeric G-proteins: A short history. British Journal of Pharmacology. 147 Suppl 1(Suppl 1), S46–S55. https://doi.org/10.1038/sj.bjp.0706405
   PubMedGoogle Scholar
• Mishra, R., Behera, L. M., & Rana, S. (2022). Binding of raloxifene to human complement fragment 5a ((h)C5a): A perspective on cytokine storm and COVID19. Journal of Biomolecular Structure & Dynamics, 40(3), 982–994. https://doi.org/10.1080/07391102.2020.1820381
   PubMed Web of Science ®Google Scholar
• Mishra, R., Das, A., & Rana, S. (2021). Resveratrol binding to human complement fragment 5a ((h)C5a) may modulate the C5aR signaling axes. Journal of Biomolecular Structure & Dynamics, 39(5), 1766–1780. https://doi.org/10.1080/07391102.2020.1738958
   PubMed Web of Science ®Google Scholar
• Mishra, R., & Rana, S. (2019). A rational search for discovering potential neutraligands of human complement fragment 5a ((h)C5a). Bioorganic & Medicinal Chemistry, 27(19), 115052. https://doi.org/10.1016/j.bmc.2019.115052
   PubMed Web of Science ®Google Scholar
• Moreira, I. S. (2014). Structural features of the G-protein/GPCR interactions. Biochimica et Biophysica Acta, 1840(1), 16–33. https://doi.org/10.1016/j.bbagen.2013.08.027
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Nguyen, A. H., & Lefkowitz, R. J. (2021). Signaling at the endosome: Cryo‐EM structure of a GPCR–G protein–beta‐arrestin megacomplex. The FEBS Journal, 288(8), 2562–2569. https://doi.org/10.1111/febs.15773
   PubMed Web of Science ®Google Scholar
• Orders, M. (2023). COVID-19 update: An EUA for Vilobelimab (Gohibic) for COVID-19. Med Lett Drugs Ther, 65(1677), 86–87.
   PubMed Web of Science ®Google Scholar
• Pandey, S., Kumari, P., Baidya, M., Kise, R., Cao, Y., Dwivedi-Agnihotri, H., Banerjee, R., Li, X. X., Cui, C. S., Lee, J. D., Kawakami, K., Maharana, J., Ranjan, A., Chaturvedi, M., Jhingan, G. D., Laporte, S. A., Woodruff, T. M., Inoue, A., & Shukla, A. K. (2021). Intrinsic bias at non-canonical, β-arrestin-coupled seven transmembrane receptors. Molecular Cell, 81(22), 4605–4621. e4611. https://doi.org/10.1016/j.molcel.2021.09.007
   PubMed Web of Science ®Google Scholar
• Pandey, S., Maharana, J., Li, X. X., Woodruff, T. M., & Shukla, A. K. (2020). Emerging insights into the structure and function of complement C5a receptors. Trends in Biochemical Sciences, 45(8), 693–705. https://doi.org/10.1016/j.tibs.2020.04.004
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Rana, S., & Sahoo, A. R. (2015). Model structures of inactive and peptide agonist bound C5aR: Insights into agonist binding, selectivity and activation. Biochemistry and Biophysics Reports, 1, 85–96. https://doi.org/10.1016/j.bbrep.2015.03.002
   PubMedGoogle Scholar
• Rana, S., Sahoo, A. R., & Majhi, B. K. (2016). Allosterism in human complement component 5a (hC5a): A damper of C5a receptor (C5aR) signaling. Journal of Biomolecular Structure & Dynamics, 34(6), 1201–1213. https://doi.org/10.1080/07391102.2015.1073634
   PubMed Web of Science ®Google Scholar
• Sahoo, A. R., Mishra, R., & Rana, S. (2018). The model structures of the complement component 5a receptor (C5aR) bound to the native and engineered hC5a. Scientific Reports, 8(1), 2955. https://doi.org/10.1038/s41598-018-21290-4
   PubMed Web of Science ®Google Scholar
• Sakari, M., Tran, M. T., Rossjohn, J., Pulliainen, A. T., Beddoe, T., & Littler, D. R. (2022). Crystal structures of pertussis toxin with NAD(+) and analogs provide structural insights into the mechanism of its cytosolic ADP-ribosylation activity. The Journal of Biological Chemistry, 298(5), 101892. https://doi.org/10.1016/j.jbc.2022.101892
   PubMed Web of Science ®Google Scholar
• Skokowa, J., Ali, S. R., Felda, O., Kumar, V., Konrad, S., Shushakova, N., Schmidt, R. E., Piekorz, R. P., Nürnberg, B., Spicher, K., Birnbaumer, L., Zwirner, J., Claassens, J. W. C., Verbeek, J. S., van Rooijen, N., Köhl, J., & Gessner, J. E. (2005). Macrophages induce the inflammatory response in the pulmonary Arthus reaction through Gαi2 activation that controls C5aR and Fc receptor cooperation. Journal of Immunology (Baltimore, Md.: 1950), 174(5), 3041–3050. https://doi.org/10.4049/jimmunol.174.5.3041
   PubMed Web of Science ®Google Scholar
• Szczepek, M., Beyrière, F., Hofmann, K. P., Elgeti, M., Kazmin, R., Rose, A., Bartl, F. J., von Stetten, D., Heck, M., Sommer, M. E., Hildebrand, P. W., & Scheerer, P. (2014). Crystal structure of a common GPCR-binding interface for G protein and arrestin. Nature Communications, 5(1), 4801. https://doi.org/10.1038/ncomms5801
   PubMedGoogle Scholar
• UniProt, C. (2023). UniProt: The universal protein knowledgebase in 2023. Nucleic Acids Research, 51(D1), D523–D531. https://doi.org/10.1093/nar/gkac1052
   PubMed Web of Science ®Google Scholar
• Wang, Y., Liu, W., Xu, Y., He, X., Yuan, Q., Luo, P., Fan, W., Zhu, J., Zhang, X., Cheng, X., Jiang, Y., Xu, H. E., & Zhuang, Y. (2023). Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins. Nature Chemical Biology, 19(11), 1351–1360. https://doi.org/10.1038/s41589-023-01339-w
   PubMed Web of Science ®Google Scholar
• West, R. E., Jr., Moss, J., Vaughan, M., Liu, T., & Liu, T. Y. (1985). Pertussis toxin-catalyzed ADP-ribosylation of transducin. Cysteine 347 is the ADP-ribose acceptor site. Journal of Biological Chemistry. 260(27), 14428–14430. https://doi.org/10.1016/S0021-9258(17)38585-X
   PubMed Web of Science ®Google Scholar
• Wingler, L. M., & Lefkowitz, R. J. (2020). Conformational basis of G protein-coupled receptor signaling versatility. Trends in Cell Biology, 30(9), 736–747. https://doi.org/10.1016/j.tcb.2020.06.002
   PubMed Web of Science ®Google Scholar
• Wisler, J. W., Rockman, H. A., & Lefkowitz, R. J. (2018). Biased G protein-coupled receptor signaling: Changing the paradigm of drug discovery. Circulation, 137(22), 2315–2317. https://doi.org/10.1161/circulationaha.117.028194
   PubMed Web of Science ®Google Scholar
• Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web server for predicting the binding affinity of protein–protein complexes. Bioinformatics (Oxford, England), 32(23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
   PubMed Web of Science ®Google Scholar
• Yuan, D., Liu, Z., Kaindl, J., Maeda, S., Zhao, J., Sun, X., Xu, J., Gmeiner, P., Wang, H.-W., & Kobilka, B. K. (2020). Activation of the α2B adrenoceptor by the sedative sympatholytic dexmedetomidine. Nature Chemical Biology, 16(5), 507–512. https://doi.org/10.1038/s41589-020-0492-2
   PubMed Web of Science ®Google Scholar
• Zhuang, Y., Liu, H., Edward Zhou, X., Kumar Verma, R., de Waal, P. W., Jang, W., Xu, T.-H., Wang, L., Meng, X., Zhao, G., Kang, Y., Melcher, K., Fan, H., Lambert, N. A., Eric Xu, H., & Zhang, C. (2020). Structure of formylpeptide receptor 2-Gi complex reveals insights into ligand recognition and signaling. Nature Communications, 11(1), 885. https://doi.org/10.1038/s41467-020-14728-9
   PubMed Web of Science ®Google Scholar