Induced pocket to accommodate the cell attachment Arg-Gly-Asp motif in a neutralizing antibody against foot-and-mouth-disease virus

Journal of Molecular Biology

Volumn 256, Issue 2, 1996, Pages 364-376

  Verdaguer, Nuria ^a   Mateu, Mauricio G ^b   Bravo, Jerónimo ^a   Domingo, Esteban ^b   Fita, Ignasi ^a  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

Antigen antibody interactions; Arg Gly Asp motif; Foot and mouth disease virus; Induced fit; Viral epitope

Indexed keywords

IMMUNOGLOBULIN F(AB) FRAGMENT; MONOCLONAL ANTIBODY; NEUTRALIZING ANTIBODY; VIRUS ANTIBODY; VIRUS ANTIGEN;

AMINO ACID SEQUENCE; ANTIBODY STRUCTURE; ANTIGEN ANTIBODY COMPLEX; ARTICLE; COMPLEX FORMATION; FOOT AND MOUTH DISEASE VIRUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN QUATERNARY STRUCTURE; VIRUS ADSORPTION;

EID: 0029867609     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0092     Document Type: Article

References (58)

1. 3) inhibit binding and infection of foot-and-mouth disease virus to cultured cells. J. Virol. 69, 2664-2666.
2. Bittle, J. L., Houghten, R. A., Alexander, H., Shinnick, T. M., Sutcliffe, J. G., Lerner, R. A., Roulands, D. & Brown, F (1982). Protection against foot-and-mouth disease virus by inmunization with a chemically synthesized peptide predicted from the viral nucleotide sequence. Nature, 298, 30-33.
3. Brünger, A. T. (1992). XPLOR-manual, Version 3.0, Yale University, New Haven, CT, USA.
4. Brown, F. (1990). Picornaviruses. In Immunochemestry of Viruses, II (M. H. V. Van Regenmortel & A. R. Neuratn, eds), pp. 153-169, Elsevier, Amsterdam.
5. Cambillau, C. & Horjales, E. (1987). TOM: A FRODO subpackage for protein-ligand fitting with interactive energy minimization. J. Mol. Graphics, 5, 174-177.
6. Coloma, M. J., Hastings, A., Wims, L. A. & Morrison, S. L. (1992). Novel vectors for the expression of antibody molecules using variable regions generated by polymerase chain reaction. J. Immunol. Methods, 152, 89-104.
7. Connolly, M. L. (1983). Analytical molecular surface calculation. J. Appl. Crystallog. 16, 548-558.
8. Chothia, C., Lesk, A. M., Tramantano, A., Levitt, M., Smith-Gill, S. J., Air, G., Sheriff, S., Padlan, E. A., Davies, D., Tulip, W. R., Colman, P. M., Spinelli, S., Alzari, P. & Poljak, R. J. (1989). Conformation of immunoglobulin hypervariable regions. Nature, 342, 877-883.
9. Dimmock, N. J. (1993). Neutralization of animal viruses. Curr. Topics Microbiol. Immunol. 183.
10. Domingo, E., Mateu, M. G., Martinez, M. A., Dopazo, J., Moya, A. & Sobrino, F. (1990). Genetic variability and antigenic diversity of foot-and-mouth disease virus. In Applied Virology Research (Kurstak, E., Marusyk, R. G., Murphy, F. A. & Van Regenmortel, M. H. V., eds), vol. 3, pp. 223-266, Plenum Press, New York.
11. Duarte, E. A., Novella, I. S., Weaver, S. C., Domingo, E., Wain-Hobson, S., Clarke, D. K., Moya, A., Elena, S. F., de la Torre, V. C. & Holland, J. J. (1995). RNA virus quasispecies: significance for viral disease and epidemiology Infectious Agents Dis. 3, 201-214.
12. Fox, J., Parry, N., Barnett, P. V., McGinn, B., Rowlands, D. J. & Brown, F. (1989). The cell attachment site on foot-and-mouth disease virus includes the amino acid sequence RGD (arginine-glycine-aspartic acid). J. Gen. Virol. 70, 625-637.
13. Furey, W. (1993). PHASES Manual. VA Medical Center, Pittsburg, PA.
14. Ghiara, J. B., Stura, E. A., Stonfield, R. L., Profy, A. T. & Wilson, I. A. (1994). Crystal structure of the principal neutralization site of HIV-1. Science, 264, 82-85.
15. Hynes, R. O. (1992). Integrins: versatility modulation and signaling in cell adhesion. Cell, 69, 11-25.
16. Jones, E. Y., Harlos, K., Bottomley, M. J., Robinson, R. C., Driscoll, P. C., Edwards, R. M., Clements, J. M., Dudgeon, T. J. & Stuart, D. I. (1995). Crystal structure of an integrin-binding fragment of vascular cell adhesion molecule-1 at 1.8 Å resolution. Nature, 373, 539-544.
17. Jones, T. A. (1985). Interactive computer graphics: FRODO. Methods Enzymol. 115, 157-171.
18. Kabat, E. A., Wu, T. T., Reid-Miller, M., Perry, H. M. & Gottesman, K. S. (1987). Sequences of Proteins of Immunological Interest, 4th edit., National Institutes of Health, Bethesda, MD, USA.
19. Krezel, A. M., Wagner, G., Seymour-Ulmer, J. & Lazarus, R. A. (1994). Structure of the RGD protein decorsin: conserved motif and distinct function in leech proteins that affect blood clotting. Science, 264, 1944-1947.
20. Laskowski, R. A., MacArthur, M. W., Smith, D. K., Jones, D. T., Hutchinson, E. G., Morris, A. L., Naylor, D., Moss, D. & Thornton, J. M. (1994). PROCHECK Manual V.3.0, Oxford Molecular Ltd.
21. Lazarus, R. A. & McDowell, R. S. (1993). Structural and functional aspects of RGD-containing proteins antagonists of glycoprotein IIb-IIa. Curr. Opin. Struct. Biotechnol. 4, 438-445.
22. Lea, S., Hernández, J., Blakemore, W., Brocchi, E., Curry, S., Domingo, E., Fry, E., Abu-Ghazaleh, R., King, A., Newman, J., Stuart, D. & Mateu, M. G. (1994). The structure and antigenicity of a type C foot-and-mouth disease virus. Structure, 2, 123-139.
23. Leahy, D. J., Hendrickson, W. A., Aukhil, I. & Erickson, H. P. (1992). Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. Science, 258, 987-991.
24. Logan, D., Abu-Ghazaleh, R., Blakemore, W., Curry, S., Jackson, T., King, A., Lea, S., Lewis, R., Newan, J., Parry, N., Rowlands, D., Stuart, D. & Fry, E. (1993). Structure of a major immunogenic site on foot-and-mouth disease virus. Nature, 362, 566-568.
25. Mason, P. W., Rieder, E. & Baxt, B. (1994). RGD sequence of foot-and-mouth disease virus is essential for infecting cells via the natural receptor but can be bypassed by an antibody-dependent enhancement pathway Proc. Natl Acad. Sci. USA, 91, 1932-1936.
26. Mateu, M. G. (1995). Antibody recognition of picornavirus and escape from neutralization: a structural view. Virus Res. 38, 1-24.
27. Mateu, M. G., Rocha, E., Vicente, O., Vayreda, F., Navalpotro, C., Andreu, D., Pedroso, E., Giralt. E., Enjuanes, L. & Domingo, E. (1987). Reactivity with monoclonal antibodies of viruses from an episode of foot-and-mouth disease virus. Virus Res. 8, 261-274.
28. Mateu, M. G., Martinez, M. A., Rocha, E., Andreu, D., Parejo, J., Giralt, E., Sobrino, F. & Domingo, E. (1989). Implications of a quasispecies genome structure: effect of frequent, naturally occurring aminoacid substitutions on the antigenicity of foot-and-mouth disease virus. Proc. Natl Acad. Sci. USA, 86, 5883-5887.
29. Mateu, M. G., Martinez, M. A., Capucci, L., Andreu, D., Giralt, E., Sobrino, F., Brochi, E. & Domingo, E. (1990). A single amino acid substitution affects multiple overlapping epitopes in the major antigenic site of foot-and-mouth disease virus of serotype C. J. Gen. Virol. 71, 629-637.
30. Nicholls, A. Bharadwaj, R. & Honig, B. (1993). GRASP-Graphical representation and analysis of surface properties. Biophys. J. 64, A116.
31. Novella, I. S., Borrego, B., Mateu, M. G., Domingo, E., Giralt, E. & Andreu, D. (1993). Use of substituted and tandem-repeated peptides to probe the relevance of the highly conserved RGD tripeptide in the immune response against foot-and-mouth disease virus. FEBS Letters, 330, 253-259.
32. Pereira, H. G. (1981). Foot-and-mouth disease. In Virus Diseases of Food Animals (Gibbs, E. P. J., ed.), vol. 2. pp. 333-363, Academic Press, New York.
33. Pfaff, E., Mussgay, M., Bohm, H. O., Schultz, G. E. & Schaller, H. (1982). Antibodies against a preselected peptide recognize and neutralize foot-and-mouth disease virus. EMBO J. 1, 869-874.
34. Rini, J. M., Schulze-Gahmen, U. & Wilson, I. A. (1992). Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science, 255, 959-965.
35. Rossmann, M. G. (1972). The Molecular Replacement Method. Gordon and Breach, New York.
36. Ruoslathi, E. (1988). Fibronectin and its receptors. Annu. Rev. Biochem. 57, 375-413.
37. Sheriff, S., Silverton, E. W., Padlan, E. A., Cohen, G. H., Smith-Gill, S. J., Finzel, B. & Davies, D. R. (1987). The three dimensional structure of an antibody-antigen complex. Proc. Natl Acad. Sci. USA, 84, 8075-8079.
38. Smith, T. J., Olson, N. H., Cheng, R. H., Lin, H., Chase, E. S., Lee, W. M., Leippe, D. H., Mosser, A. G., Rueckert, R. R. & Baker, T. S. (1993a). Structure of a human rhinovirus complexed with fab fragments from a neutralizing antibody. J. Virol. 67, 1148-1158.
39. Smith, T. J., Olson, N. H., Cheng, R. H., Chase, E. S. & Baker, T. S. (1993b). Structure of a human rhinovirus-bivalently bound antibody complex - implications for viral neutralization and antibody flexibility Proc. Natl Acad. Sci. USA, 90, 7015-7018.
40. Smith, T. J., Olson, N. H., Chase, E. S., Che, A., Mosser, A. G., Rueckert, R. R. & Baker, T. S. (1995). Structural studies on the mechanism of antibody-mediated neutralization of human rhinovirus 14. Fourth International Symposium on positive strand RNA viruses, Utrecht.
41. Sobrino, F., Dávila, M., Ortín, J. & Domingo, E. (1983). Multiple genetic variants arise in the course of replication of foot-and-mouth disease virus in cell culture. Virology, 128, 310-318.
42. Stanfield, R. L., Fieser, T. M., Lerner, R. A. & Wilson, I. A. (1990). Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å. Science, 248, 712-719.
43. Stanfield, R. L., Takimoto-Kamimura, M., Rini, J. M., Profy, A. T. & Wilson, I. A. (1993). Major antigen-induced domain rearrangements in an antibody. Structure, 1, 83-93.
44. Stanfield, R. T. & Wilson, I. A. (1995). Protein-peptide interactions. Curr. Opin. Struct. Biol. 5, 103-113.
45. Strohmaier, K., Franze, R. & Adam, K. H. (1982). Location and characterization of the antigenic portion of the foot-and-mouth disease virus immunizing protein. J. Gen. Virol. 59, 295-306.
46. Tormo, J., Stadler, E., Skern, T., Auter, H., Kanzler, O., Betzel, C., Blaas, D. & Fita, I. (1992). Three dimensional structure of the Fab fragment of a neutralizing antibody to a human rhinovirus serotype 2. Protein Sci. 1, 1154-1161.
47. Tormo, J., Blaass, D., Parry, N. R., Rowlands, D., Stuart, D. & Fita, I. (1994). Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. EMBO J. 13, 2247-2256.
48. Tormo, J., Centeno, N. B., Fontana, E., Bubendorfer, T., Fita, I. & Blaas, D. (1995). Docking of a human rhinovirus neutralizing antibody onto the viral capsid. Proteins. In the press.
49. Tronrud, D. E. (1995). The TNT Refinement Package, Howard Hughes Medical Institute & University of Oregon. Eugene, OR 97403.
50. Tulip, W. R., Varghese, J. N., Webster, R. G., Laver, W. G. & Colman, J. (1992). Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex. J. Mol. Biol. 227, 149-159.
51. Verdaguer, N., Mateu, M. G., Bravo, J., Tormo, J., Giralt, E., Andreu, D., Domingo, E. & Fita, I. (1994). Crystallization and preliminary X-ray diffraction studies of a monoclonal antibody Fab fragment against foot-and-mouth disease virus and of its complex with the main antigenic site peptide. Proteins: Struct. Funct. Genet. 18, 201-203.
52. Verdaguer, N., Mateu, M. G., Andreu, D., Giralt, E., Domingo, E. & Fita, I. (1995). Structure of the major antigenic loop of foot-and-mouth disease virus complexed to a neutralizing antibody. Direct involvement of the Arg-Gly-Asp motif in the interaction. EMBO J. 14, 1690-1696.
53. Wang, G., Porta, C., Chen, Z., Baker, T. S. & Johnson, J. E. (1992). Identification of a Fab interaction footprint site on an icosahedral virus by crioelectron microscopy and X-ray crystallography. Nature, 355, 275-278.
54. Webster, D. M., Henry, A. H. & Rees, A. R. (1994). Antibody-antigen interactions. Curr. Opin. Struct. Biol. 4, 123-129.
55. Wien, M. W., Filman, D. J., Stura, E. A., Guillot, F. D., Crainic, R. & Hogle, J. M. (1995). Structure of the complex between the Fab fragment of a neutralizing antibody for type 1 poliovirus and its viral epitope. Nature Struct. Biol. 2, 234-243.
56. Wilson, I. A. & Stanfield, R. L. (1993). Antibody-antigen interactions. Curr. Opin. Struct. Biol. 3, 113-118.
57. Wilson, I. A. & Stanfield, R. L. (1994). Antibody-antigen interactions: new structures and new conformational changes. Curr. Opin. Struct. Biol. 4, 857-867.
58. Wistow, G., Turnell, B., Summers, L., Slingsby, C., Moss, D., Miller, L., Lindley, P. & Blundell, T. (1983). J. Mol. Biol. 170, 175-202.