A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes

Immunology

Volumn 143, Issue 1, 2014, Pages 13-20

  Davidson, Edgar ^a   Doranz, Benjamin J ^a  

^a Integral Molecular Inc   (United States)

Author keywords

Envelope; Epitope; G protein coupled receptor; High throughput; Mapping; Shotgun mutagenesis

Indexed keywords

ALANINE; B LYMPHOCYTE ANTIBODY; EPITOPE; G PROTEIN COUPLED RECEPTOR; MONOCLONAL ANTIBODY; VIRUS ENVELOPE PROTEIN;

ARTICLE; DENGUE VIRUS; EPITOPE MAPPING; HIGH THROUGHPUT SHOTGUN MUTAGENESIS; HUMAN; MOLECULAR CLONING; MUTAGENESIS; MUTANT; MUTATION; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN FOLDING;

ENVELOPE; EPITOPE; G PROTEIN-COUPLED RECEPTOR; HIGH-THROUGHPUT; MAPPING; SHOTGUN MUTAGENESIS;

ANTIBODIES, MONOCLONAL; B-LYMPHOCYTES; BINDING SITES, ANTIBODY; EPITOPE MAPPING; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MUTAGENESIS;

EID: 84904868707     PISSN: 00192805     EISSN: 13652567     Source Type: Journal    
DOI: 10.1111/imm.12323     Document Type: Article

References (45)

1. Cho HS, Mason K, Ramyar KX, Stanley AM, Gabelli SB, Denney DW Jr, Leahy DJ. Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab. Nature 2003; 421:756-60.
2. Franklin MC, Carey KD, Vajdos FF, Leahy DJ, de Vos AM, Sliwkowski MX. Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex. Cancer Cell 2004; 5:317-28.
3. Muller YA, Chen Y, Christinger HW, Li B, Cunningham BC, Lowman HB, de Vos AM. VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 Å resolution and mutational analysis of the interface. Structure 1998; 6:1153-67.
4. Fuh G, Wu P, Liang WC, Ultsch M, Lee CV, Moffat B, Wiesmann C. Structure-function studies of two synthetic anti-vascular endothelial growth factor Fabs and comparison with the Avastin Fab. J Biol Chem 2006; 281:6625-31.
5. Correia BE, Bates JT, Loomis RJ et al. Proof of principle for epitope-focused vaccine design. Nature 2014; 507:201-6.
6. Kulp DW, Schief WR. Advances in structure-based vaccine design. Curr Opin Virol 2013; 3:322-31.
7. Kirchenbaum GA, Ross TM. Eliciting broadly protective antibody responses against influenza. Curr Opin Immunol 2014; 28C:71-6.
8. Greenbaum JA, Andersen PH, Blythe M et al. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 2007; 20:75-82.
9. Crowe JE Jr. Recent advances in the study of human antibody responses to influenza virus using optimized human hybridoma approaches. Vaccine 2009; 27(Suppl. 6):G47-51.
10. Finn JA, Crowe JE Jr. Impact of new sequencing technologies on studies of the human B cell repertoire. Curr Opin Immunol 2013; 25:613-8.
11. Walker LM, Phogat SK, Chan-Hui PY et al. Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science 2009; 326:285-9.
12. Wu X, Yang ZY, Li Y et al. Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science 2010; 329:856-61.
13. Corti D, Langedijk JP, Hinz A et al. Analysis of memory B cell responses and isolation of novel monoclonal antibodies with neutralizing breadth from HIV-1-infected individuals. PLoS One 2010; 5:e8805.
14. Scheid JF, Mouquet H, Feldhahn N et al. Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature 2009; 458:636-40.
15. Zhou T, Georgiev I, Wu X et al. Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science 2010; 329:811-7.
16. Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998; 280:1-9.
17. Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999; 285:2177-98.
18. Cunningham BC, Wells JA. Comparison of a structural and a functional epitope. J Mol Biol 1993; 234:554-63.
19. Benjamin DC, Perdue SS. Site-directed mutagenesis in epitope mapping. Methods 1996; 9:508-15.
20. Rubinstein ND, Mayrose I, Halperin D, Yekutieli D, Gershoni JM, Pupko T. Computational characterization of B-cell epitopes. Mol Immunol 2008; 45:3477-89.
21. Ladner RC. Mapping the epitopes of antibodies. Biotechnol Genet Eng Rev 2007; 24:1-30.
22. Gershoni JM, Roitburd-Berman A, Siman-Tov DD, Tarnovitski Freund N, Weiss Y. Epitope mapping: the first step in developing epitope-based vaccines. BioDrugs 2007; 21:145-56.
23. Abbott WM, Damschroder MM, Lowe DC. Current approaches to fine mapping of antigen-antibody interactions. Immunology 2014; 142:526-35.
24. Kringelum JV, Nielsen M, Padkjaer SB, Lund O. Structural analysis of B-cell epitopes in antibody:protein complexes. Mol Immunol 2013; 53:24-34.
25. Paes C, Ingalls J, Kampani K et al. Atomic-level mapping of antibody epitopes on a GPCR. J Am Chem Soc 2009; 131:6952-4.
26. Jähnichen S, Blanchetot C, Maussang D et al. CXCR4 nanobodies (VHH-based single variable domains) potently inhibit chemotaxis and HIV-1 replication and mobilize stem cells. Proc Natl Acad Sci U S A 2010; 107:20565-70.
27. Greene TA, Alarcon S, Thomas A, Berdougo E, Doranz BJ, Breslin PA, Rucker JB. Probenecid inhibits the human bitter taste receptor TAS2R16 and suppresses bitter perception of salicin. PLoS One 2011; 6:e20123.
28. Berdougo E, Couto JR, Doranz BJ. Maximal Humanization of Monoclonal Abs. Genetic Engineering & Biotechnology News 2011; August:42.
29. Costin JM, Zaitseva E, Kahle KM et al. Mechanistic study of broadly neutralizing human monoclonal antibodies against dengue virus that target the fusion loop. J Virol 2013; 87:52-66.
30. Smith SA, de Alwis AR, Kose N et al. The potent and broadly neutralizing human dengue virus-specific monoclonal antibody 1C19 reveals a unique cross-reactive epitope on the bc loop of domain II of the envelope protein. MBio 2013; 4:e00873-13.
31. Edeling MA, Austin SK, Shrestha B et al. Potent Dengue virus neutralization by a low affinity therapeutic antibody requires bivalent engagement. PLOS Pathog 2014; 10:e1004072.
32. Sukupolvi-Petty S, Brien JD, Austin SK et al. Functional analysis of antibodies against Dengue virus type 4 reveals strain-dependent epitope exposure that impacts neutralization and protection. J Virol 2013; 87:8826-42.
33. Messer WB, de Alwis R, Yount BL et al. Dengue virus envelope protein domain I/II hinge determines long-lived serotype-specific dengue immunity. Proc Natl Acad Sci U S A 2014; 111:1939-44.
34. Mattia K, Puffer BA, Williams KL et al. Dengue reporter virus particles for measuring neutralizing antibodies against each of the four dengue serotypes. PLoS One 2011; 6:e27252.
35. Christian EA, Kahle KM, Mattia K-A et al. An atomic-level mechanism of Dengue virus envelope infectivity. Proc Natl Acad Sci U S A 2013; 110:18662-7.
36. de Alwis R, Smith SA, Olivarez NP et al. Identification of human neutralizing antibodies that bind to complex epitopes on dengue virions. Proc Natl Acad Sci U S A 2012; 109:7439-44.
37. Mancini N, Diotti RA, Perotti M et al. Hepatitis C virus (HCV) infection may elicit neutralizing antibodies targeting epitopes conserved in all viral genotypes. PLoS One 2009; 4:e8254.
38. Perotti M, Mancini N, Diotti RA et al. Identification of a broadly cross-reacting and neutralizing human monoclonal antibody directed against the hepatitis C virus E2 protein. J Virol 2008; 82:1047-52.
39. Kong L, Giang E, Robbins JB, Stanfield RL, Burton DR, Wilson IA, Law M. Structural basis of hepatitis C virus neutralization by broadly neutralizing antibody HCV1. Proc Natl Acad Sci U S A 2012; 109:9499-504.
40. Broering TJ, Garrity KA, Boatright NK et al. Identification and characterization of broadly neutralizing human monoclonal antibodies directed against the E2 envelope glycoprotein of hepatitis C virus. J Virol 2009; 83:12473-82.
41. Lok SM, Kostyuchenko V, Nybakken GE et al. Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins. Nat Struct Mol Biol 2008; 15:312-7.
42. Sukupolvi-Petty S, Austin SK, Purtha WE et al. Type- and subcomplex-specific neutralizing antibodies against domain III of dengue virus type 2 envelope protein recognize adjacent epitopes. J Virol 2007; 81:12816-26.
43. Crill WD, Chang GJ. Localization and characterization of flavivirus envelope glycoprotein cross-reactive epitopes. J Virol 2004; 78:13975-86.
44. Gromowski GD, Roehrig JT, Diamond MS, Lee JC, Pitcher TJ, Barrett AD. Mutations of an antibody binding energy hot spot on domain III of the dengue 2 envelope glycoprotein exploited for neutralization escape. Virology 2010; 407:237-46.
45. Vita R, Zarebski L, Greenbaum JA et al. The immune epitope database 2.0. Nucleic Acids Res 2010; 38:D854-62.