Engineered receptors for human cytomegalovirus that are orthogonal to normal human biology

English version

Autoři: Jihye Park ^aff001; Kevin Sean Gill ^aff001; Ali Asghar Aghajani ^aff001; Jeremiah Dallas Heredia ^aff001; Hannah Choi ^aff001; Adam Oberstein ^aff002; Erik Procko ^aff001
Působiště autorů: Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America ^aff001; Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois, United States of America ^aff002; Cancer Center at Illinois (CCIL), University of Illinois, Urbana, Illinois, United States of America ^aff003
Vyšlo v časopise: Engineered receptors for human cytomegalovirus that are orthogonal to normal human biology. PLoS Pathog 16(6): e32767. doi:10.1371/journal.ppat.1008647
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.ppat.1008647

Souhrn

A trimeric glycoprotein complex on the surface of human cytomegalovirus (HCMV) binds to platelet-derived growth factor (PDGF) receptor α (PDGFRα) to mediate host cell recognition and fusion of the viral and cellular membranes. Soluble PDGFRα potently neutralizes HCMV in tissue culture, and its potential use as an antiviral therapeutic has the benefit that any escape mutants will likely be attenuated. However, PDGFRα binds multiple PDGF ligands in the human body as part of developmental programs in embryogenesis and continuing through adulthood. Any therapies with soluble receptor therefore come with serious efficacy and safety concerns, especially for the treatment of congenital HCMV. Soluble virus receptors that are orthogonal to human biology might resolve these concerns. This engineering problem is solved by deep mutational scanning on the D2-D3 domains of PDGFRα to identify variants that maintain interactions with the HCMV glycoprotein trimer in the presence of competing PDGF ligands. Competition by PDGFs is conformation-dependent, whereas HCMV trimer binding is independent of proper D2-D3 conformation, and many mutations at the receptor-PDGF interface are suitable for functionally separating trimer from PDGF interactions. Purified soluble PDGFRα carrying a targeted mutation succeeded in displaying wild type affinity for HCMV trimer with a simultaneous loss of PDGF binding, and neutralizes trimer-only and trimer/pentamer-expressing HCMV strains infecting fibroblasts or epithelial cells. Overall, this work makes important progress in the realization of soluble HCMV receptors for clinical application.

Klíčová slova:

Cell binding – Cytomegalovirus infection – Flow cytometry – Human cytomegalovirus – Mutagenesis – Nonsense mutation – Signal processing – Substitution mutation

Zdroje

1. Cannon MJ, Schmid DS, Hyde TB. Review of cytomegalovirus seroprevalence and demographic characteristics associated with infection. Rev Med Virol. 2010;20: 202–213. doi: 10.1002/rmv.655 20564615

2. Staras SAS, Dollard SC, Radford KW, Flanders WD, Pass RF, Cannon MJ. Seroprevalence of cytomegalovirus infection in the United States, 1988–1994. Clin Infect Dis. 2006;43: 1143–1151. doi: 10.1086/508173 17029132

3. Emery VC. Investigation of CMV disease in immunocompromised patients. J Clin Pathol. 2001;54: 84–88. doi: 10.1136/jcp.54.2.84 11215290

4. Cobbs CS, Harkins L, Samanta M, Gillespie GY, Bharara S, King PH, et al. Human cytomegalovirus infection and expression in human malignant glioma. Cancer Res. 2002;62: 3347–3350. 12067971

5. Mitchell DA, Xie W, Schmittling R, Learn C, Friedman A, McLendon RE, et al. Sensitive detection of human cytomegalovirus in tumors and peripheral blood of patients diagnosed with glioblastoma. Neuro-oncology. 2008;10: 10–18. doi: 10.1215/15228517-2007-035 17951512

6. Scheurer ME, Bondy ML, Aldape KD, Albrecht T, El-Zein R. Detection of human cytomegalovirus in different histological types of gliomas. Acta Neuropathol. 2008;116: 79–86. doi: 10.1007/s00401-008-0359-1 18351367

7. Michaelis M, Doerr HW, Cinatl J. The story of human cytomegalovirus and cancer: increasing evidence and open questions. Neoplasia. 2009;11: 1–9. doi: 10.1593/neo.81178 19107226

8. Lawler SE. Cytomegalovirus and glioblastoma; controversies and opportunities. J Neurooncol. 2015;123: 465–471. doi: 10.1007/s11060-015-1734-0 25682092

9. Cannon MJ, Davis KF. Washing our hands of the congenital cytomegalovirus disease epidemic. BMC Public Health. 4 ed. 2005;5: 70. doi: 10.1186/1471-2458-5-70 15967030

10. Dollard SC, Grosse SD, Ross DS. New estimates of the prevalence of neurological and sensory sequelae and mortality associated with congenital cytomegalovirus infection. Rev Med Virol. 2007;17: 355–363. doi: 10.1002/rmv.544 17542052

11. Kenneson A, Cannon MJ. Review and meta-analysis of the epidemiology of congenital cytomegalovirus (CMV) infection. Rev Med Virol. 2007;17: 253–276. doi: 10.1002/rmv.535 17579921

12. Grosse SD, Ross DS, Dollard SC. Congenital cytomegalovirus (CMV) infection as a cause of permanent bilateral hearing loss: a quantitative assessment. J Clin Virol. 2008;41: 57–62. doi: 10.1016/j.jcv.2007.09.004 17959414

13. Suzuki Y, Toribe Y, Mogami Y, Yanagihara K, Nishikawa M. Epilepsy in patients with congenital cytomegalovirus infection. Brain Dev. 2008;30: 420–424. doi: 10.1016/j.braindev.2007.12.004 18215482

14. Zhang X-W, Li F, Yu X-W, Shi X-W, Shi J, Zhang J-P. Physical and intellectual development in children with asymptomatic congenital cytomegalovirus infection: a longitudinal cohort study in Qinba mountain area, China. J Clin Virol. 2007;40: 180–185. doi: 10.1016/j.jcv.2007.08.018 17919973

15. Gentile I, Zappulo E, Riccio MP, Binda S, Bubba L, Pellegrinelli L, et al. Prevalence of Congenital Cytomegalovirus Infection Assessed Through Viral Genome Detection in Dried Blood Spots in Children with Autism Spectrum Disorders. In Vivo. 2017;31: 467–473. doi: 10.21873/invivo.11085 28438881

16. Staras SAS, Flanders WD, Dollard SC, Pass RF, McGowan JE, Cannon MJ. Cytomegalovirus seroprevalence and childhood sources of infection: A population-based study among pre-adolescents in the United States. J Clin Virol. 2008;43: 266–271. doi: 10.1016/j.jcv.2008.07.012 18778968

17. Lanzieri TM, Kruszon-Moran D, Amin MM, Bialek SR, Cannon MJ, Carroll MD, et al. Seroprevalence of cytomegalovirus among children 1 to 5 years of age in the United States from the National Health and Nutrition Examination Survey of 2011 to 2012. Hodinka RL, editor. Clin Vaccine Immunol. American Society for Microbiology; 2015;22: 245–247. doi: 10.1128/CVI.00697-14 25520150

18. Dupont L, Reeves MB. Cytomegalovirus latency and reactivation: recent insights into an age old problem. Rev Med Virol. 2016;26: 75–89. doi: 10.1002/rmv.1862 26572645

19. Ross SA, Arora N, Novak Z, Fowler KB, Britt WJ, Boppana SB. Cytomegalovirus reinfections in healthy seroimmune women. J Infect Dis. 2010;201: 386–389. doi: 10.1086/649903 20039807

20. Lurain NS, Chou S. Antiviral drug resistance of human cytomegalovirus. Clin Microbiol Rev. American Society for Microbiology Journals; 2010;23: 689–712. doi: 10.1128/CMR.00009-10 20930070

21. American College of Obstetricians and Gynecologists. Practice bulletin no. 151: Cytomegalovirus, parvovirus B19, varicella zoster, and toxoplasmosis in pregnancy. Obstetrics and gynecology. 2015. pp. 1510–1525. doi: 10.1097/01.AOG.0000466430.19823.53

22. Gerna G, Kabanova A, Lilleri D. Human Cytomegalovirus Cell Tropism and Host Cell Receptors. Vaccines (Basel). 2019;7: 70. doi: 10.3390/vaccines7030070 31336680

23. Hahn G, Revello MG, Patrone M, Percivalle E, Campanini G, Sarasini A, et al. Human cytomegalovirus UL131-128 genes are indispensable for virus growth in endothelial cells and virus transfer to leukocytes. J Virol. American Society for Microbiology Journals; 2004;78: 10023–10033. doi: 10.1128/JVI.78.18.10023–10033.2004

24. Wang D, Shenk T. Human cytomegalovirus virion protein complex required for epithelial and endothelial cell tropism. Proc Natl Acad Sci USA. National Academy of Sciences; 2005;102: 18153–18158. doi: 10.1073/pnas.0509201102 16319222

25. Wang D, Shenk T. Human cytomegalovirus UL131 open reading frame is required for epithelial cell tropism. J Virol. American Society for Microbiology Journals; 2005;79: 10330–10338. doi: 10.1128/JVI.79.16.10330-10338.2005 16051825

26. Ryckman BJ, Chase MC, Johnson DC. HCMV gH/gL/UL128-131 interferes with virus entry into epithelial cells: evidence for cell type-specific receptors. Proc Natl Acad Sci USA. National Academy of Sciences; 2008;105: 14118–14123. doi: 10.1073/pnas.0804365105 18768787

27. Ryckman BJ, Rainish BL, Chase MC, Borton JA, Nelson JA, Jarvis MA, et al. Characterization of the human cytomegalovirus gH/gL/UL128-131 complex that mediates entry into epithelial and endothelial cells. J Virol. American Society for Microbiology Journals; 2008;82: 60–70. doi: 10.1128/JVI.01910-07 17942555

28. Adler B, Scrivano L, Ruzcics Z, Rupp B, Sinzger C, Koszinowski U. Role of human cytomegalovirus UL131A in cell type-specific virus entry and release. J Gen Virol. Microbiology Society; 2006;87: 2451–2460. doi: 10.1099/vir.0.81921-0 16894182

29. Martinez-Martin N, Marcandalli J, Huang CS, Arthur CP, Perotti M, Foglierini M, et al. An Unbiased Screen for Human Cytomegalovirus Identifies Neuropilin-2 as a Central Viral Receptor. Cell. 2018;174: 1158–1171.e19. doi: 10.1016/j.cell.2018.06.028 30057110

30. E X, Meraner P, Lu P, Perreira JM, Aker AM, McDougall WM, et al. OR14I1 is a receptor for the human cytomegalovirus pentameric complex and defines viral epithelial cell tropism. Proc Natl Acad Sci USA. National Academy of Sciences; 2019;116: 7043–7052. doi: 10.1073/pnas.1814850116 30894498

31. Huber MT, Compton T. The human cytomegalovirus UL74 gene encodes the third component of the glycoprotein H-glycoprotein L-containing envelope complex. J Virol. American Society for Microbiology (ASM); 1998;72: 8191–8197. 9733861

32. Huber MT, Compton T. Intracellular formation and processing of the heterotrimeric gH-gL-gO (gCIII) glycoprotein envelope complex of human cytomegalovirus. J Virol. American Society for Microbiology (ASM); 1999;73: 3886–3892. 10196283

33. Zhou M, Lanchy J-M, Ryckman BJ. Human Cytomegalovirus gH/gL/gO Promotes the Fusion Step of Entry into All Cell Types, whereas gH/gL/UL128-131 Broadens Virus Tropism through a Distinct Mechanism. Hutt-Fletcher L, editor. J Virol. American Society for Microbiology Journals; 2015;89: 8999–9009. doi: 10.1128/JVI.01325-15 26085146

34. Kabanova A, Marcandalli J, Zhou T, Bianchi S, Baxa U, Tsybovsky Y, et al. Platelet-derived growth factor-α receptor is the cellular receptor for human cytomegalovirus gHgLgO trimer. Nat Microbiol. 2016;1: 16082. doi: 10.1038/nmicrobiol.2016.82 27573107

35. Soroceanu L, Akhavan A, Cobbs CS. Platelet-derived growth factor-alpha receptor activation is required for human cytomegalovirus infection. Nature. 2008;455: 391–395. doi: 10.1038/nature07209 18701889

36. Wu Y, Prager A, Boos S, Resch M, Brizic I, Mach M, et al. Human cytomegalovirus glycoprotein complex gH/gL/gO uses PDGFR-α as a key for entry. Yurochko A, editor. PLoS Pathog. 2017;13: e1006281. doi: 10.1371/journal.ppat.1006281 28403202

37. Wu K, Oberstein A, Wang W, Shenk T. Role of PDGF receptor-α during human cytomegalovirus entry into fibroblasts. Proc Natl Acad Sci USA. National Academy of Sciences; 2018;115: E9889–E9898. doi: 10.1073/pnas.1806305115 30275317

38. Stegmann C, Hochdorfer D, Lieber D, Subramanian N, Stöhr D, Laib Sampaio K, et al. A derivative of platelet-derived growth factor receptor alpha binds to the trimer of human cytomegalovirus and inhibits entry into fibroblasts and endothelial cells. Yurochko A, editor. PLoS Pathog. 2017;13: e1006273. doi: 10.1371/journal.ppat.1006273 28403220

39. De Clercq E, Li G. Approved Antiviral Drugs over the Past 50 Years. Clin Microbiol Rev. American Society for Microbiology Journals; 2016;29: 695–747. doi: 10.1128/CMR.00102-15 27281742

40. Andrae J, Gallini R, Betsholtz C. Role of platelet-derived growth factors in physiology and medicine. Genes Dev. Cold Spring Harbor Lab; 2008;22: 1276–1312. doi: 10.1101/gad.1653708 18483217

41. Chen P-H, Chen X, He X. Platelet-derived growth factors and their receptors: structural and functional perspectives. Biochim Biophys Acta. 2013;1834: 2176–2186. doi: 10.1016/j.bbapap.2012.10.015 23137658

42. Fretto LJ, Snape AJ, Tomlinson JE, Seroogy JJ, Wolf DL, LaRochelle WJ, et al. Mechanism of platelet-derived growth factor (PDGF) AA, AB, and BB binding to alpha and beta PDGF receptor. J Biol Chem. 1993;268: 3625–3631. 7679113

43. Li X, Pontén A, Aase K, Karlsson L, Abramsson A, Uutela M, et al. PDGF-C is a new protease-activated ligand for the PDGF alpha-receptor. Nat Cell Biol. 2000;2: 302–309. doi: 10.1038/35010579 10806482

44. Shim AH-R, Liu H, Focia PJ, Chen X, Lin PC, He X. Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex. Proc Natl Acad Sci USA. National Academy of Sciences; 2010;107: 11307–11312. doi: 10.1073/pnas.1000806107 20534510

45. Chen P-H, Unger V, He X. Structure of Full-Length Human PDGFRβ Bound to Its Activating Ligand PDGF-B as Determined by Negative-Stain Electron Microscopy. J Mol Biol. 2015;427: 3921–3934. doi: 10.1016/j.jmb.2015.10.003 26463591

46. Fowler DM, Fields S. Deep mutational scanning: a new style of protein science. Nat Methods. Nature Publishing Group; 2014;11: 801–807. doi: 10.1038/nmeth.3027 25075907

47. Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, et al. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife. 2016;5: 1422. doi: 10.7554/eLife.20352 27805565

48. Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, et al. A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell. 2014;157: 1644–1656. doi: 10.1016/j.cell.2014.04.034 24949974

49. Wrenbeck EE, Azouz LR, Whitehead TA. Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded. Nat Commun. 2017;8: 15695. doi: 10.1038/ncomms15695 28585537

50. Park J, Selvam B, Sanematsu K, Shigemura N, Shukla D, Procko E. Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology; 2019;294: 4759–4774. doi: 10.1074/jbc.RA118.006173 30723160

51. Heredia JD, Park J, Brubaker RJ, Szymanski SK, Gill KS, Procko E. Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning. J Immunol. American Association of Immunologists; 2018;200: ji1800343–3839. doi: 10.4049/jimmunol.1800343 29678950

52. Heredia JD, Park J, Choi H, Gill KS, Procko E. Conformational Engineering of HIV-1 Env Based on Mutational Tolerance in the CD4 and PG16 Bound States. Kirchhoff F, editor. J Virol. American Society for Microbiology Journals; 2019;93: e00219–19. doi: 10.1128/JVI.00219-19 30894475

53. Sinzger C, Hahn G, Digel M, Katona R, Sampaio KL, Messerle M, et al. Cloning and sequencing of a highly productive, endotheliotropic virus strain derived from human cytomegalovirus TB40/E. J Gen Virol. Microbiology Society; 2008;89: 359–368. doi: 10.1099/vir.0.83286-0 18198366

54. Stegmann C, Rothemund F, Laib Sampaio K, Adler B, Sinzger C. The N Terminus of Human Cytomegalovirus Glycoprotein O Is Important for Binding to the Cellular Receptor PDGFRα. Sandri-Goldin RM, editor. J Virol. American Society for Microbiology Journals; 2019;93: 93. doi: 10.1128/JVI.00138-19 30894468

55. Pédelacq J-D, Cabantous S, Tran T, Terwilliger TC, Waldo GS. Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol. 2006;24: 79–88. doi: 10.1038/nbt1172 16369541

56. Ciferri C, Chandramouli S, Donnarumma D, Nikitin PA, Cianfrocco MA, Gerrein R, et al. Structural and biochemical studies of HCMV gH/gL/gO and Pentamer reveal mutually exclusive cell entry complexes. Proc Natl Acad Sci USA. National Academy of Sciences; 2015;112: 1767–1772. doi: 10.1073/pnas.1424818112 25624487

57. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. Oxford University Press; 2002;30: 207–210. doi: 10.1093/nar/30.1.207 11752295

58. Stanton RJ, Baluchova K, Dargan DJ, Cunningham C, Sheehy O, Seirafian S, et al. Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication. J Clin Invest. American Society for Clinical Investigation; 2010;120: 3191–3208. doi: 10.1172/JCI42955 20679731

59. Czajkowsky DM, Hu J, Shao Z, Pleass RJ. Fc-fusion proteins: new developments and future perspectives. EMBO Mol Med. 2012;4: 1015–1028. doi: 10.1002/emmm.201201379 22837174

60. Lu X, Nobrega RP, Lynaugh H, Jain T, Barlow K, Boland T, et al. Deamidation and isomerization liability analysis of 131 clinical-stage antibodies. MAbs. 2019;11: 45–57. doi: 10.1080/19420862.2018.1548233 30526254

61. Vidarsson G, Dekkers G, Rispens T. IgG subclasses and allotypes: from structure to effector functions. Front Immunol. Frontiers; 2014;5: 520. doi: 10.3389/fimmu.2014.00520 25368619

62. Roopenian DC, Christianson GJ, Sproule TJ, Brown AC, Akilesh S, Jung N, et al. The MHC class I-like IgG receptor controls perinatal IgG transport, IgG homeostasis, and fate of IgG-Fc-coupled drugs. J Immunol. American Association of Immunologists; 2003;170: 3528–3533. doi: 10.4049/jimmunol.170.7.3528 12646614

63. Li X, Zhao X, Fang Y, Jiang X, Duong T, Fan C, et al. Generation of destabilized green fluorescent protein as a transcription reporter. J Biol Chem. American Society for Biochemistry and Molecular Biology; 1998;273: 34970–34975. doi: 10.1074/jbc.273.52.34970 9857028

64. Reichhart E, Ingles-Prieto A, Tichy A-M, McKenzie C, Janovjak H. A Phytochrome Sensory Domain Permits Receptor Activation by Red Light. Angew Chem Int Ed Engl. 2016;55: 6339–6342. doi: 10.1002/anie.201601736 27101018

65. Yu D, Smith GA, Enquist LW, Shenk T. Construction of a self-excisable bacterial artificial chromosome containing the human cytomegalovirus genome and mutagenesis of the diploid TRL/IRL13 gene. J Virol. American Society for Microbiology Journals; 2002;76: 2316–2328. doi: 10.1128/jvi.76.5.2316–2328.2002

66. Vanarsdall AL, Chin AL, Liu J, Jardetzky TS, Mudd JO, Orloff SL, et al. HCMV trimer- and pentamer-specific antibodies synergize for virus neutralization but do not correlate with congenital transmission. Proc Natl Acad Sci USA. National Academy of Sciences; 2019;116: 3728–3733. doi: 10.1073/pnas.1814835116 30733288

67. Deen KC, McDougal JS, Inacker R, Folena-Wasserman G, Arthos J, Rosenberg J, et al. A soluble form of CD4 (T4) protein inhibits AIDS virus infection. Nature. 1988;331: 82–84. doi: 10.1038/331082a0 3257544

68. Fisher RA, Bertonis JM, Meier W, Johnson VA, Costopoulos DS, Liu T, et al. HIV infection is blocked in vitro by recombinant soluble CD4. Nature. 1988;331: 76–78. doi: 10.1038/331076a0 2829022

69. Marlin SD, Staunton DE, Springer TA, Stratowa C, Sommergruber W, Merluzzi VJ. A soluble form of intercellular adhesion molecule-1 inhibits rhinovirus infection. Nature. 1990;344: 70–72. doi: 10.1038/344070a0 1968231

70. Norkin LC. Virus receptors: implications for pathogenesis and the design of antiviral agents. Clin Microbiol Rev. American Society for Microbiology (ASM); 1995;8: 293–315. 7621403

71. Bialas KM, Tanaka T, Tran D, Varner V, Cisneros De La Rosa E, Chiuppesi F, et al. Maternal CD4+ T cells protect against severe congenital cytomegalovirus disease in a novel nonhuman primate model of placental cytomegalovirus transmission. Proc Natl Acad Sci USA. National Academy of Sciences; 2015;112: 13645–13650. doi: 10.1073/pnas.1511526112 26483473

72. Mocarski ES, Bonyhadi M, Salimi S, McCune JM, Kaneshima H. Human cytomegalovirus in a SCID-hu mouse: thymic epithelial cells are prominent targets of viral replication. Proc Natl Acad Sci USA. National Academy of Sciences; 1993;90: 104–108. doi: 10.1073/pnas.90.1.104 7678330

73. Smith MS, Goldman DC, Bailey AS, Pfaffle DL, Kreklywich CN, Spencer DB, et al. Granulocyte-colony stimulating factor reactivates human cytomegalovirus in a latently infected humanized mouse model. Cell Host Microbe. 2010;8: 284–291. doi: 10.1016/j.chom.2010.08.001 20833379

74. Crawford LB, Streblow DN, Hakki M, Nelson JA, Caposio P. Humanized mouse models of human cytomegalovirus infection. Curr Opin Virol. 2015;13: 86–92. doi: 10.1016/j.coviro.2015.06.006 26118890

75. Antoniades HN, Scher CD, Stiles CD. Purification of human platelet-derived growth factor. Proc Natl Acad Sci USA. National Academy of Sciences; 1979;76: 1809–1813. doi: 10.1073/pnas.76.4.1809 287022

76. Raines EW, Ross R. Purification of human platelet-derived growth factor. Meth Enzymol. Elsevier; 1985;109: 749–773. doi: 10.1016/0076-6879(85)09128-5 3990574

77. Petkova SB, Akilesh S, Sproule TJ, Christianson GJ, Khabbaz Al H, Brown AC, et al. Enhanced half-life of genetically engineered human IgG1 antibodies in a humanized FcRn mouse model: potential application in humorally mediated autoimmune disease. Int Immunol. 2006;18: 1759–1769. doi: 10.1093/intimm/dxl110 17077181

78. Roopenian DC, Christianson GJ, Proetzel G, Sproule TJ. Human FcRn Transgenic Mice for Pharmacokinetic Evaluation of Therapeutic Antibodies. Methods Mol Biol. New York, NY: Springer New York; 2016;1438: 103–114. doi: 10.1007/978-1-4939-3661-8_6_6 27150086

79. McShan AC, Devlin CA, Overall SA, Park J, Toor JS, Moschidi D, et al. Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. Proc Natl Acad Sci USA. National Academy of Sciences; 2019;116: 25602–25613. doi: 10.1073/pnas.1915562116 31796585

80. Wu NC, Xie J, Zheng T, Nycholat CM, Grande G, Paulson JC, et al. Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin. Cell Host Microbe. 2017;21: 742–753.e8. doi: 10.1016/j.chom.2017.05.011 28618270

81. Dingens AS, Haddox HK, Overbaugh J, Bloom JD. Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody. Cell Host Microbe. 2017;21: 777–787.e4. doi: 10.1016/j.chom.2017.05.003 28579254

82. Procko E. The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2. bioRxiv. 2020;: 2020.03.16.994236.

83. Zhu H, Shen Y, Shenk T. Human cytomegalovirus IE1 and IE2 proteins block apoptosis. J Virol. American Society for Microbiology (ASM); 1995;69: 7960–7970. 7494309

84. Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, et al. Computational design of a protein-based enzyme inhibitor. J Mol Biol. 2013;425: 3563–3575. doi: 10.1016/j.jmb.2013.06.035 23827138

85. Fowler DM, Araya CL, Gerard W, Fields S. Enrich: software for analysis of protein function by enrichment and depletion of variants. Bioinformatics. Oxford University Press; 2011;27: 3430–3431. doi: 10.1093/bioinformatics/btr577 22006916

86. Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Meth Enzymol. Elsevier; 2011;487: 545–574. doi: 10.1016/B978-0-12-381270-4.00019-6 21187238

87. Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011;414: 289–302. doi: 10.1016/j.jmb.2011.09.031 22001016

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