Structural modeling of the complex between an acetylcholine receptor- mimicking antibody and its snake toxin antigen

Proteins: Structure, Function and Genetics

Volumn 30, Issue 3, 1998, Pages 249-263

  Tenette Souaille, Catherine ^a   Smith, Jeremy C ^a  

^a CEA SACLAY   (France)

Author keywords

Antibody antigen complex; Protein docking; Snake toxin

Indexed keywords

ANTIBODY; ANTIGEN; CHOLINERGIC RECEPTOR; SNAKE VENOM;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; GEOMETRY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ANIMALS; ANTIBODIES; BINDING SITES; COBRA; ELECTROSTATICS; EPITOPE MAPPING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MUTAGENESIS; NEUROTOXINS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, CHOLINERGIC; SNAKE VENOMS;

SERPENTES;

EID: 0032519463     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980215)30:3<249::AID-PROT5>3.0.CO;2-F     Document Type: Article

References (48)

1. Zinn-Justin, S., Roumestand, C., Gilquin, B., Bontems, F., Menez, A., Toma, F. Three-dimensional solution of a curaremimetic toxin from Naja nigricollis venom: A proton NMR and molecular modeling study. Biochemistry 31:11335-11347, 1992.
2. Tenette C., Ducancel, F., Smith, J.C. Structural model of the anti-snake-toxin antibody, Mα2-3. Proteins Struct. Funct. Genet. 26:9-31, 1996.
3. Wodak S.J., Janin, J. Computer analysis of protein-protein interactions. J. Mol. Biol. 124:323-342, 1978.
4. Cherfils, J., Duquerroy, S., Janin, J. Protein-protein recognition analyzed by docking simulations. Proteins Struct. Funct. Genet. 11:271-280, 1991.
5. Kabat, E.A., Wu, T.T., Bilofsky, H., Reid-Milner, M., Perry, H. "Sequences of Proteins of Immunological Interest." Washington, DC: Public Health Service, NIH, 1991.
6. Berstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The protein data bank: A computer-based archival file for macromolecular structure. J. Mol. Biol. 112:535-542, 1977.
7. Bruccoleri, R.E., Karplus, M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26:137-168, 1987.
8. Moult, J., James, M.N.G. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins Struct. Funct. Genet. 1:146-163, 1986.
9. Fine, R.M., Wang, H., Shenkin, P.S., Yarmush, D.L., Levinthal, C. Predicting antibody hypervariable loop conformations. II. Minimization and molecular dynamics study of McPC603 from many randomly-generated loop conformations. Proteins Struct. Funct. Genet. 1:342-362, 1986.
10. Dudek, M.J., Scheraga, H.A. Protein structure prediction using a combination of sequence homology and global energy minimization. I. Global energy minimization of surface loops. J. Comp. Chem. 11:121-151, 1990.
11. Bruccoleri, R.E., Karplus, M. Conformational sampling using high-temperature molecular dynamics. Biopolymers 29:1847-1862, 1990.
12. Martin, A.C.R., Cheetham, J.C., Rees, A.R. Modeling antibody hypervariable loops: A combined algorithm. Proc. Natl. Acad. Sci. USA 86:9268-9272, 1989.
13. Cherfils, J., Janin, J. Protein docking algorithms: Simulating molecular recognition. Curr. Opin. Struct. Biol. 3:265-269, 1993.
14. Hart, T.N., Read, R.J. In "The Protein Folding Problem and Tertiary Structure Prediction." Merz, K., Jr., Le Grand, S. (eds.). Boston: Birkhauser, 1994:71-108.
15. Strynadka, N.C., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B.K., Kuntz, I.D., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., Zimmerman, F., Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M., James, M.N.G. Molecular docking algorithms successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase. Nature Struct. Biol. 3:234-239, 1996.
16. Jiang, F., Kim, S.-H. "Soft docking": Matching of molecular surface cubes. J. Mol. Biol. 219:79-102, 1991.
17. Shoichet, B.K., Kuntz, I.D. Protein docking and complementarity. J. Mol. Biol. 221:327-346, 1991.
18. Trémeau, O., Boulain, J.C., Couderc, J., Fromageot, P., Menez, A. A monoclonal antibody which recognizes the functional site of snake neurotoxins and which neutralizes all short-chain variants. FEBS Lett. 208:236-240, 1986.
19. Trémeau, O., Lemaire, C., Drevet, P., Pinkasfeld, S., Ducancel, F., Boulain, J.-C., Menez, A. Genetic engineering of snake toxins: The functional site of erabutoxin a, as delineated by site-directed mutagenesis, includes variant residues. J. Biol. Chem. 270:9362-9369, 1995.
20. Zinn-Justin, S., Roumestand, C., Drevet, P., Menez, A., Toma, F. Mapping of two "neutralizing" epitopes of a snake curaremimetic toxin by proton nuclear magnetic resonance spectroscopy. Biochemistry 32:6884-6891, 1993.
21. Ducancel, F., Mérienne, K., Fromen-Romano, C., Trémeau, O., Pillet, L., Drevet, P., Zinn-Justin, S., Boulain, J.-C., Ménez, A. Mimicry between receptors and antibodies: Identification of snake toxin determinants recognized by the acetylcholine receptor and an acetyylcholine receptor-mimicking monoclonal antibody. J. Biol. Chem. 271:31345-31353, 1996.
22. Janin, J., Chothia, C. The structure of protein-protein recognition. J. Biol. Chem. 265:16027-16030, 1990.
23. Padlan, E.A. On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands. Proteins Struct. Funct. Genet. 7:112-124, 1990.
24. Rini, J.M., Schulze-Gahmen, U., Wilson, I.A. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science 255:959-965, 1992.
25. Wilson, I.A., Stanfield, R.L. Antibody-antigen interactions: New structures and new conformational changes. Structure 4:857-867, 1994.
26. Bizebard, T., Gigant, B., Rigolet, P., Rasmussen, B., Diat, O., Bösecke, P., Wharton, S.A., Skehel, J.J., Knossow, M. Structure of influenza virus haemagglutinin complexed with a neutralizing antibody. Nature 376:92-94, 1995.
27. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4:187-217, 1983.
28. Zinn-Justin, S., Pillet, L., Ducancel, F., Thomas, A., Smith, J.C., Boulain, J.-C., Menez, A. Engineering of protein epitopes: A single deletion in a snake toxin generates full binding capacity to a previously unrecognized antibody. Protein Eng. 7:917-923, 1994.
29. De Vos, A.M., Ultisch, M., Kossiakof, A.A. Human growth hormone and extracellular domain of its receptor: Crystal structure of the complex. Science 255:306-312, 1992.
30. Cunningham, B.C., Wells, J.A. Comparison of a functional and structural epitope. J. Mol. Biol. 234:554-563, 1993.
31. Kam-Morgan, L.N.W., Smith-Gill, S.J., Taylor, M.G., Zhang, L., Wilson, C., Kirsch, J.F. High-resolution mapping of the HvHel-10 epitope of chicken lysozyme by site-directed mutagenesis. Proc. Natl. Acad. Sci. USA 90:3958-3962, 1993.
32. Prasad, L., Sharma, S., Vandonselaar, M., Quail, W.J., Lee, J.S., Waygood, E.B., Wilson, K.S., Dauter, Z., Delbaere, L.T.J. Evaluation of mutagenesis for epitope mapping: Structure of an antibody-antigen complex. J. Biol. Chem. 268:10705-10708,.
33. Novotný, J. Protein antigenicity: A thermodynamic approach. Mol. Immunol. 28:201-207, 1991.
34. Jin, L., Fendly, B.M., Wells, J.A. High resolution functional analysis of antibody-antigen interactions. J. Mol. Biol. 226:851-865, 1992.
35. Smith, A.L., Benjamin, D.C. The antigenic surface of Staphylococcal nuclease. II. Analysis of the N-1 epitope by site-directed mutagenesis. J. Immunol. 146:1259-1264, 1991.
36. Tulip W.R., Harley, V.R., Webster, R.G., Novotný, J. N9 neuraminidase complexes with the antibodies NC41 and NC10: Empirical free energy calculations capture specificity trends observed with mutant binding data. Biochemistry 33:7986-7997, 1994.
37. Kelley, R.F., O'Connell, M.P. Thermodynamic analysis of an antibody functional epitope. Biochemistry 32:6828-6835, 1993.
38. Novotny, J., Bruccoleri, R.E., Saul, F.A. On the attribution of binding energy in antigen-antibody complexes McPC603 and D1.3 and HyHEL-5. Biochemistry 28:4735-4749, 1989.
39. Wodak, S.J., Janin, J. Analytical approximation to the accessible surface area of proteins. Proc. Natl. Acad. Sci. USA 77:1736-1740, 1980.
40. Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
41. Levitt, M.A. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104:59-107, 1976.
42. Eisenberg, D., McLachlan, A.D. Solvation energy in protein folding and binding. Nature 319:199-203, 1986.
43. Sharp, K.A., Nicholls, A., Fine, R.F., Honig, B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252:106-109, 1991.
44. Sheriff, S., Silverton, E.W., Padlan, E.A., Cohen, G.H., Smith-Gill, S.J., Finzel, B.C., Davies, D.R. Three-dimensional structure of an antibody-antigen complex. Proc. Natl. Acad. Sci. USA 84:8075-8079, 1987.
45. Chothia, C., Lesk, A.M. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196:901-917, 1987.
46. Mian, I.S., Bradwell, A.R., Olson, A.J. Structure, function and properties of antibody binding sites. J. Mol. Biol. 217:133-151, 1991.
47. Mérienne, K., Germain, N., Zinn-Justin, S. Boulain, J.-C., Ducancel, F., Ménez, A. The functional architecture of an acetylcholine-mimicking antibody. J. Biol. Chem. (in press).
48. Quanta, Molecular Simulations Incorporated, Cambridge, United Kingdom.