Anti-idiotypic monobodies derived from a fibronectin scaffold

Biochemistry

Volumn 52, Issue 10, 2013, Pages 1802-1813

  Sullivan, Mark A ^a   Brooks, Lauren R ^a   Weidenborner, Philip ^a   Domm, William ^a   Mattiacio, Jonelle ^a   Xu, Qingfu ^b   Tiberio, Michael ^a   Wentworth, Timothy ^a   Kobie, James ^a   Bryk, Peter ^a   Zheng, Bo ^a   Murphy, Mary ^c   Sanz, Ignacio ^d   Dewhurst, Stephen ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

^b ROCHESTER GENERAL HOSPITAL   (United States)

^c Reichert Inc   (United States)

^d EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BROAD APPLICATION; COMPLEX STRUCTURE; CONFORMATIONAL EPITOPES; CONFORMATIONAL INTERACTION; ENVELOPE GLYCOPROTEINS; HUMAN FIBRONECTIN; MONOCLONAL ANTIBODIES (MABS); SEQUENCE HOMOLOGY;

DISEASES; EPITOPES; MONOCLONAL ANTIBODIES; PROTEINS;

SCAFFOLDS (BIOLOGY);

ANTIIDIOTYPIC ANTIBODY; EPITOPE; FIBRONECTIN; MOLECULAR SCAFFOLD; RITUXIMAB; VIRUS ENVELOPE PROTEIN; VIRUS GLYCOPROTEIN;

ARTICLE; CLONE; CONTROLLED STUDY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MUTAGENESIS; NONHUMAN; PEPTIDE LIBRARY; PRIORITY JOURNAL; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANTIBODIES, ANTI-IDIOTYPIC; ANTIBODIES, MONOCLONAL; BINDING, COMPETITIVE; BIOMIMETIC MATERIALS; FIBRONECTINS; HIV ANTIBODIES; HIV-1; HUMANS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PEPTIDE LIBRARY; PROTEIN CONFORMATION;

EID: 84874998080     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi3016668     Document Type: Article

References (55)

1. Goletz, S. 2002, Selection of large diversities of antiidiotypic antibody fragments by phage display J. Mol. Biol. 315 (5) 1087-1097
2. Simmons, D. P. 2008, Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures Proteins 71 (1) 119-130
3. Jiang, G. 2013, Evaluation of semi-homogeneous assay formats for dual-specificity antibodies J. Immunol. Methods 387 (1-2) 51-56
4. Tornetta, M. 2007, Isolation of human anti-idiotypic antibodies by phage display for clinical immune response assays J. Immunol. Methods 328 (1-2) 34-44
5. Scott, J. K. and Smith, G. P. (1990) Searching for peptide ligands with an epitope library Science 249 (4967) 386-390
6. Larralde, O. G. 2007, Identification of hepatitis A virus mimotopes by phage display, antigenicity and immunogenicity J. Virol. Methods 140 (1-2) 49-58
7. Houimel, M. and Dellagi, K. (2009) Peptide mimotopes of rabies virus glycoprotein with immunogenic activity Vaccine 27 (34) 4648-4655
8. Matthews, L. J., Davis, R., and Smith, G. P. (2002) Immunogenically fit subunit vaccine components via epitope discovery from natural peptide libraries J. Immunol. 169 (2) 837-846
9. Saphire, E. O. 2007, Structure of a high-affinity "mimotope" peptide bound to HIV-1-neutralizing antibody b12 explains its inability to elicit gp120 cross-reactive antibodies J. Mol. Biol. 369 (3) 696-709
10. Zwick, M. B. 2001, Identification and characterization of a peptide that specifically binds the human, broadly neutralizing anti-human immunodeficiency virus type 1 antibody b12 J. Virol. 75 (14) 6692-6699
11. McLafferty, M. A. 1993, M13 bacteriophage displaying disulfide- constrained microproteins Gene 128 (1) 29-36
12. O'Neil, K. T. 1992, Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library Proteins 14 (4) 509-515
13. Bonnycastle, L. L. 1996, Probing the basis of antibody reactivity with a panel of constrained peptide libraries displayed by filamentous phage J. Mol. Biol. 258 (5) 747-762
14. Koide, A. 1998, The fibronectin type III domain as a scaffold for novel binding proteins J. Mol. Biol. 284 (4) 1141-1151
15. Koide, A. and Koide, S. (2007) Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain Methods Mol. Biol. 352, 95-109
16. Richards, J. 2003, Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human αvβ3 integrin J. Mol. Biol. 326 (5) 1475-1488
17. Lipovsek, D. (2010) Adnectins: Engineered target-binding protein therapeutics Protein Eng., Des. Sel. 24 (1-2) 3-9
18. Zwick, M. B. 2003, Molecular features of the broadly neutralizing immunoglobulin G1 b12 required for recognition of human immunodeficiency virus type 1 gp120 J. Virol. 77 (10) 5863-5876
19. Kunkel, T. A., Roberts, J. D., and Zakour, R. A. (1987) Rapid and efficient site-specific mutagenesis without phenotypic selection Methods Enzymol. 154, 367-382
20. Tonikian, R. 2007, Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries Nat. Protoc. 2 (6) 1368-1386
21. Barbas, C. F., III 1992, Recombinant human Fab fragments neutralize human type 1 immunodeficiency virus in vitro Proc. Natl. Acad. Sci. U.S.A. 89 (19) 9339-9343
22. Burton, D. R. 1991, A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic seropositive individuals Proc. Natl. Acad. Sci. U.S.A. 88 (22) 10134-10137
23. Burton, D. R. 1994, Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody Science 266 (5187) 1024-1027
24. Roben, P. 1994, Recognition properties of a panel of human recombinant Fab fragments to the CD4 binding site of gp120 that show differing abilities to neutralize human immunodeficiency virus type 1 J. Virol. 68 (8) 4821-4828
25. Buchacher, A. 1994, Generation of human monoclonal antibodies against HIV-1 proteins; electrofusion and Epstein-Barr virus transformation for peripheral blood lymphocyte immortalization AIDS Res. Hum. Retroviruses 10 (4) 359-369
26. Purtscher, M. 1996, Restricted antigenic variability of the epitope recognized by the neutralizing gp41 antibody 2F5 AIDS 10 (6) 587-593
27. Purtscher, M. 1994, A broadly neutralizing human monoclonal antibody against gp41 of human immunodeficiency virus type 1 AIDS Res. Hum. Retroviruses 10 (12) 1651-1658
28. Stiegler, G. 2001, A potent cross-clade neutralizing human monoclonal antibody against a novel epitope on gp41 of human immunodeficiency virus type 1 AIDS Res. Hum. Retroviruses 17 (18) 1757-1765
29. Conley, A. J. 1994, Neutralization of primary human immunodeficiency virus type 1 isolates by the broadly reactive anti-V3 monoclonal antibody, 447-52D J. Virol. 68 (11) 6994-7000
30. Gorny, M. K. 1992, Neutralization of diverse human immunodeficiency virus type 1 variants by an anti-V3 human monoclonal antibody J. Virol. 66 (12) 7538-7542
31. Gorny, M. K. 1997, Human monoclonal antibodies to the V3 loop of HIV-1 with intra- and interclade cross-reactivity J. Immunol. 159 (10) 5114-5122
32. Gorny, M. K. 1993, Repertoire of neutralizing human monoclonal antibodies specific for the V3 domain of HIV-1 gp120 J. Immunol. 150 (2) 635-643
33. Nyambi, P. N. 1998, Mapping of epitopes exposed on intact human immunodeficiency virus type 1 (HIV-1) virions: A new strategy for studying the immunologic relatedness of HIV-1 J. Virol. 72 (11) 9384-9391
34. Zolla-Pazner, S. 1995, Serotyping of primary human immunodeficiency virus type 1 isolates from diverse geographic locations by flow cytometry J. Virol. 69 (6) 3807-3815
35. Nelson, J. D. 2007, An affinity-enhanced neutralizing antibody against the membrane-proximal external region of human immunodeficiency virus type 1 gp41 recognizes an epitope between those of 2F5 and 4E10 J. Virol. 81 (8) 4033-4043
36. Zwick, M. B. 2001, Broadly neutralizing antibodies targeted to the membrane-proximal external region of human immunodeficiency virus type 1 glycoprotein gp41 J. Virol. 75 (22) 10892-10905
37. Reff, M. E. 1994, Depletion of B cells in vivo by a chimeric mouse human monoclonal antibody to CD20 Blood 83 (2) 435-445
38. Megret, F. 1992, Use of recombinant fusion proteins and monoclonal antibodies to define linear and discontinuous antigenic sites on the dengue virus envelope glycoprotein Virology 187 (2) 480-491
39. Sui, J. 2009, Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses Nat. Struct. Mol. Biol. 16 (3) 265-273
40. Tiller, T. 2008, Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning J. Immunol. Methods 329 (1-2) 112-124
41. Weiss, G. A. 2000, Rapid mapping of protein functional epitopes by combinatorial alanine scanning Proc. Natl. Acad. Sci. U.S.A. 97 (16) 8950-8954
42. Mattiacio, J. 2011, Dense display of HIV-1 envelope spikes on the lambda phage scaffold does not result in the generation of improved antibody responses to HIV-1 Env Vaccine 29 (14) 2637-2647
43. Moos, P. J., Edes, K., and Fitzpatrick, F. A. (2000) Inactivation of wild-type p53 tumor suppressor by electrophilic prostaglandins Proc. Natl. Acad. Sci. U.S.A. 97 (16) 9215-9220
44. Sullivan, M. A. 2012, Anti-idiotypic monobodies for immune response profiling Methods 58 (1) 62-68
45. Zhou, T. 2007, Structural definition of a conserved neutralization epitope on HIV-1 gp120 Nature 445 (7129) 732-737
46. Li, Y. 2007, Broad HIV-1 neutralization mediated by CD4-binding site antibodies Nat. Med. 13 (9) 1032-1034
47. de la Cruz, V. F., Lal, A. A., and McCutchan, T. F. (1988) Immunogenicity and epitope mapping of foreign sequences via genetically engineered filamentous phage J. Biol. Chem. 263 (9) 4318-4322
48. Greenwood, J., Willis, A. E., and Perham, R. N. (1991) Multiple display of foreign peptides on a filamentous bacteriophage. Peptides from Plasmodium falciparum circumsporozoite protein as antigens J. Mol. Biol. 220 (4) 821-827
49. Parmley, S. F. and Smith, G. P. (1989) Filamentous fusion phage cloning vectors for the study of epitopes and design of vaccines Adv. Exp. Med. Biol. 251, 215-218
50. Correia, B. E. 2011, Computational protein design using flexible backbone remodeling and resurfacing: Case studies in structure-based antigen design J. Mol. Biol. 405 (1) 284-297
51. Correia, B. E. 2010, Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope Structure 18 (9) 1116-1126
52. Guenaga, J. 2011, Heterologous epitope-scaffold prime:boosting immuno-focuses B cell responses to the HIV-1 gp41 2F5 neutralization determinant PLoS One 6 (1) e16074
53. Ofek, G. 2010, Elicitation of structure-specific antibodies by epitope scaffolds Proc. Natl. Acad. Sci. U.S.A. 107 (42) 17880-17887
54. Azoitei, M. L. 2011, Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold Science 334 (6054) 373-376
55. Zhou, T. 2010, Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01 Science 329 (5993) 811-817