Investigation of the binding of a carbohydrate-mimetic peptide to its complementary anticarbohydrate antibody by STD-NMR spectroscopy and molecular-dynamics simulations

Chemistry - A European Journal

Volumn 17, Issue 41, 2011, Pages 11446-11455

  Szczepina, Monica G ^a   Bleile, Dustin W ^b   Pinto, B Mario ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b Zymeworks Inc   (Canada)

Author keywords

carbohydrates; molecular dynamics; peptides; Shigella flexneri Y; simulated annealing

Indexed keywords

ANTI-CARBOHYDRATE ANTIBODIES; ATOMIC POSITIONS; BINDING MODES; BOUND LIGANDS; CONFORMATIONAL EXCHANGE; CONFORMATIONAL FLEXIBILITY; EXCHANGE EFFECTS; EXPERIMENTAL DATA; MATRIX ANALYSIS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR DYNAMICS TRAJECTORIES; O-POLYSACCHARIDE; PENTASACCHARIDES; PEPTIDE EPITOPES; R FACTOR; RECEPTOR-LIGAND COMPLEX; RIGOROUS ANALYSIS; SATURATION TRANSFER; SATURATION-TRANSFER DIFFERENCES; SHIGELLA FLEXNERI; SOLUTION CONFORMATIONS;

ANTIBODIES; ANTIGENS; BINDING ENERGY; BIOMIMETICS; CARBOHYDRATES; COMPLEXATION; CONFORMATIONS; DYNAMICS; LIGANDS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDES; PROTONS; X RAY CRYSTALLOGRAPHY;

SIMULATED ANNEALING;

ANTIBODY; LIGAND; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; KINETICS; METABOLISM; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN BINDING; SHIGELLA FLEXNERI; X RAY CRYSTALLOGRAPHY;

ANTIBODIES; CRYSTALLOGRAPHY, X-RAY; KINETICS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN BINDING; SHIGELLA FLEXNERI;

EID: 80053218365     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.201100222     Document Type: Article

References (43)

1. T. L. Hale, in Topley and Wilson's Microbiology and Microbial Infections, Vol 3, 9 th ed., (Eds.: W. J. Hansler, M. Shuman,), Hodder Arnold, London, 1998, p. 479.
2. K. L. Kotloff, J. P. Winickoff, B. Ivanoff, J. D. Clemens, D. L. Swerdlow, P. J. Sansonetti, G. K. Adak, M. M. Levine, Bull. W. H. O. 1999, 77, 651-666.
3. D. R. Bundle, M. A. J. Gidney, S. Josephson, H. P. Wessel, ACS Symp. Ser. 1983, 231, 49-63
4. N. I. Carlin, M. A. Gidney, A. A. Lindberg, D. R. Bundle, J. Immunol. 1986, 137, 2361-2366
5. L. Kenne, B. Lindberg, K. Petersson, E. Katzenellenbogen, E. Romanowska, Eur. J. Biochem. 1977, 76, 327-330
6. L. Kenne, B. Lindberg, K. Petersson, E. Katzenellenbogen, E. Romanowska, Eur. J. Biochem. 1978, 91, 279-284
7. L. Kenne, B. Lindberg, K. Petersson, E. Romanowska, Carbohydr. Res. 1977, 56, 363-370.
8. R. B. Hossany, M. A. Johnson, A. A. Eniade, B. M. Pinto, Bioorg. Med. Chem. 2004, 12, 3743-3754.
9. M. A. Johnson, B. M. Pinto, Aust. J. Chem. 2002, 55, 13-25
10. B. Monzavi-Karbassi, G. Cunto-Amesty, P. Luo, T. Kieber-Emmons, Trends Biotechnol. 2002, 20, 207-214.
11. S. Borrelli, R. B. Hossany, B. M. Pinto, Clin. Vaccine Immunol. 2008, 15, 1106-1114.
12. S. L. Harris, L. Craig, J. S. Mehroke, M. Rashed, M. B. Zwick, K. Kenar, E. J. Toone, N. Greenspan, F. I. Auzanneau, J. R. Marino-Albernas, B. M. Pinto, J. K. Scott, Proc. Natl. Acad. Sci. USA 1997, 94, 2454-2459.
13. N. K. Vyas, M. N. Vyas, M. C. Chervenak, D. R. Bundle, B. M. Pinto, F. A. Quiocho, Proc. Natl. Acad. Sci. USA 2003, 100, 15023-15028.
14. N. K. Vyas, M. N. Vyas, M. C. Chervenak, M. A. Johnson, B. M. Pinto, D. R. Bundle, F. A. Quiocho, Biochemistry 2002, 41, 13575-13586.
15. M. A. Johnson, B. M. Pinto, Top. Curr. Chem. 2008, 273, 55-116.
16. M. A. Johnson, B. M. Pinto, Bioorg. Med. Chem. 2004, 12, 295-300.
17. V. Jayalakshmi, T. Biet, T. Peters, N. R. Krishna, J. Am. Chem. Soc. 2004, 126, 8610-8611.
18. V. Jayalakshmi, T. Biet, T. Peters, N. R. Krishna, J. Am. Chem. Soc. 2005, 127, 7261-7261.
19. V. Jayalakshmi, N. R. Krishna, J. Magn. Reson. 2002, 155, 106-118.
20. V. Jayalakshmi, N. R. Krishna, J. Magn. Reson. 2004, 168, 36-45.
21. V. Jayalakshmi, N. R. Krishna, J. Am. Chem. Soc. 2005, 127, 14080-14084
22. N. R. Krishna, V. Jayalakshmi, Prog. Nucl. Magn. Reson. Spectrosc. 2006, 49, 1-25.
23. N. R. Krishna, D. G. Agresti, J. D. Glickson, R. Walter, Biophys. J. 1978, 24, 791-814.
24. X. Wen, Y. Yuan, D. A. Kuntz, D. R. Rose, B. M. Pinto, Biochemistry 2005, 44, 6729-6737.
25. Y. Yuan, X. Wen, D. A. R. Sanders, B. M. Pinto, Biochemistry 2005, 44, 14080-14089
26. A. Bhunia, V. Jayalakshmi, A. J. Benie, O. Schuster, S. Kelm, N. R. Krishna, T. Peters, Carbohydr. Res. 2004, 339, 259-267.
27. Y. Yuan, D. W. Bleile, X. Wen, D. A. R. Sanders, K. Itoh, H. W. Liu, B. M. Pinto, J. Am. Chem. Soc. 2008, 130, 3157-3168.
28. T. D. W. Claridge, Tetrahedron Org. Chem. Ser. 1999, 19, 283.
29. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Proteins Struct. Funct. Bioinf. 2006, 65, 712-725.
30. H. C. Andersen, J. Comput. Phys. 1983, 52, 24-34.
31. S. Miyamoto, P. A. Kollman, J. Comput. Chem. 1992, 13, 952-962.
32. H. J. C. Berendsen, J. P. M. Postma, W. F. Vangunsteren, A. Dinola, J. R. Haak, J. Chem. Phys. 1984, 81, 3684-3690.
33. D. S. Wishart, B. D. Sykes, F. M. Richards, Biochemistry 1992, 31, 1647-1651.
34. D. S. Wishart, B. D. Sykes, J. Biomol. NMR 1994, 4, 171-180.
35. S. Schwarzinger, G. J. A. Kroon, T. R. Foss, P. E. Wright, H. J. Dyson, J. Biomol. NMR 2000, 18, 43-48.
36. G. M. Clore, A. M. Gronenborn, J. Magn. Reson. 1982, 48, 402-417
37. G. M. Clore, A. M. Gronenborn, J. Magn. Reson. 1983, 53, 423-442
38. J. P. Albrand, B. Birdsall, J. Feeney, G. C. K. Roberts, A. S. V. Burgen, Int. J. Biol. Macromol. 1979, 1, 37-41
39. P. Balaram, A. A. Bothner-By, E. Breslow, J. Am. Chem. Soc. 1972, 94, 4017-4018
40. P. Balaram, A. A. Bothner-By, J. Dadok, J. Am. Chem. Soc. 1972, 94, 4015-4017.
41. M. Mayer, T. L. James, J. Am. Chem. Soc. 2004, 126, 4453-4460.
42. J. Kuriyan, G. A. Petsko, R. M. Levy, M. Karplus, J. Mol. Biol. 1986, 190, 227-254.
43. P. G. Alotto, C. Eranda, B. Brandstatter, G. Furnstratt, C. Magele, G. Molinari, M. Nervi, K. Preis, M. Repetto, K. R. Richter, IEEE Trans. Magn. 1998, 34, 3674-3684.