Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics

Structure

Volumn 7, Issue 6, 1999, Pages 663-670

  Stigler, Rolf Dietrich ^a   Hoffmann, Berit ^a   Abagyan, Ruben ^b   Schneider Mergener, Jens ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Flexible docking; ICM; Monoclonal antibody; Peptide epitope analogues

Indexed keywords

ANTIBODY; CHOLERA TOXIN; EPITOPE;

ARTICLE; CONFORMATIONAL TRANSITION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; X RAY ANALYSIS;

EID: 0033152106     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80087-2     Document Type: Article

References (31)

1. Kuntz, I.D., Shoichet, B.K. & Meng, E.C. (1994). Structure-based molecular design. Acc. Chem. Res. 27, 117-123.
2. Verlinde, C.L.M.J. & Hol, W.G.J. (1994). Structure-based drug design: Progress, results, and challenges. Structure 2, 577-587.
3. Moult, J., Hubbard, T., Bryant, S.H., Fidelis, K. & Pedersen, J.T. (1997). Critical assessment of methods of protein structure prediction (CASP): Round II. Proteins supplement 1, 2-6.
4. Frenkel, D., et al., & Westhead, D.R. (1995). PRO_LIGAND: An approach to de novo molecular design. 4. Application to the design of peptides. J. Comput. Aided Mol. Des. 9, 213-225.
5. Rosenfeld, R., Vajda, S. & DeLisi, C. (1995). Flexible docking and design. Annu. Rev. Biophys. Biomol. Struct. 24, 677-700.
6. Desmet, J., Wilson, I.A., Joniau, M., De Maeyer, M. & Lasters, I. (1997). Computation of the binding of fully flexible peptides to proteins with flexible side chains. FASEB J. 11, 164-172.
7. Nakajima, N., Higo, J., Kidera, A. & Nakamura, H. (1997). Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation. Chem. Phys. Lett. 278, 297-301.
8. Zhou, Y. & Abagyan, R.A. (1998). How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold. Des. 3, 513-522.
9. Abagyan, R., Totrov, M. & Kuznetsov, D. (1994). ICM - A new method for protein modelling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15, 488-506.
10. Levy, R., Assulin, O., Scherf, T., Levitt, M. & Anglister, J. (1989). Probing antibody diversity by 2D NMR: Comparison of amino acid sequences, predicted structures, and observed antibody-antigen interactions in complexes of two antipeptide antibodies. Biochemistry 28, 7168-7175.
11. Lockman, H. & Kaper, J.B. Nucleotide sequence analysis of the A2 and B subunits of Vibrio cholerae enterotoxin. (1983). J. Biol. Chem. 258, 13722-13726.
12. Shoham, M. Crystal structure of an anticholera toxin peptide complex at 2.3 Å. (1993). J. Mol. Biol. 232, 1169-1175.
13. Kramer, A., Stigler, R.D., Knaute, T., Hoffmann, B. & Schneider-Mergener J. (1998). Stepwise transformation of a cholera toxin and a p24 (HIV-1) epitope into D-peptide analogs. Prot. Eng. 11, 941-948.
14. Abagyan, R. & Totrov, M. (1994). Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235, 983-1002.
15. Zauhar, R.J. & Morgan, R.S. (1985). A new method for computing the macromolecular electric potential. J. Mol. Biol. 186, 815-820.
16. Totrov, M. & Abagyan, R. (1996). The contour buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 116, 138-143.
17. Momany, F.A., McGuire, R.F., Burgess, A.W. & Scheraga, H.A. (1975). Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79, 2361-2381.
18. Nemethy, G., et al., & Scheraga, H.A. (1992). Energy parameters in polypeplides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96, 6472-6484.
19. Friguet, B., Chaffotte, A.F., Djavadi-Ohaniance, L. & Goldberg, M.E. (1985). Measurement of the true affinity constant in solution of antigen-antibody complexes by enzyme-linked immunosorbent assay. J. Immunol. Methods 77, 305-319.
20. Wallace, A.C., Laskowski, R.A. & Thornton, J.M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Prof. Eng. 8, 127-134.
21. Sali, A. & Blundell, T.L. (1993). Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
22. Hsieh-Wilson, L.C., Schultz, P.G. & Stevens, R.C. (1996). Insights into antibody catalysis: Structure of an 2 oxygenation catalyst at 1.9 Å resolution. Proc. Natl Acad. Sci. USA 93, 5363-5367.
23. Arevalo, J.H., Stura, E.A., Taussig, M.J. & Wilson, I.A. (1993). Three-dimensional structure of an anti-steroid 2 Fab' and progesterone-Fab' complex. J. Mol. Biol. 231, 103-118.
24. 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.
25. Totrov, M. & Abagyan, R. (1994). Detailed ab-initio prediction of lysozyme-antibody complex with 1.6 Å accuracy. Nat. Struct. Biol. 1, 259-263.
26. Totrov, M., Abagyan, R. (1997). Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins supplement 1, 215-220.
27. Strynadka, N.C., et al., & James, M.N. (1996). Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to tem-1 β-lactamase. Nat. Struct. Biol. 3, 233-239.
28. Kramer, A. & Schneider-Mergener, J. (1998). Synthesis and screening of peptide libraries on continuous cellulose membrane supports. Methods Mol. Biol. 87, 25-39.
29. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N, Teller, A.H. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. Chem. Phys, 21, 1087-1092.
30. Kramer, A, Keitel, T., Winkler, K, Stöcklein, W., Höhne, W. & Schneider-Mergener, J. (1997). Molecular basis for the binding promiscuity of the anti-p24 (HIV-1) monoclonal antibody. Cell 91, 799-809.
31. Schultz, J., et al., & Oschkinat, H. (1998). Specific interactions between the syntropin PDZ domain and voltage-gated sodium channels. Nat. Struct. Biol. 5, 19-24.