Identification of preferred carbohydrate binding modes in xenoreactive antibodies by combining conformational filters and binding site maps

Glycobiology

Volumn 20, Issue 6, 2010, Pages 724-735

  Agostino, Mark ^a   Sandrin, Mauro S ^b   Thompson, Philip E ^a   Yuriev, Elizabeth ^a   Ramsland, Paul A ^b,c,d  

^a MONASH UNIVERSITY   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c BURNET INSTITUTE   (Australia)

^d MONASH UNIVERSITY   (Australia)

Author keywords

Antibody carbohydrate recognition; Binding mode prediction; Carbohydrate docking; Carbohydrate xenoantigens; Computational biology

Indexed keywords

CARBOHYDRATE; GALECTIN; MONOCLONAL ANTIBODY; MONOCLONAL ANTIBODY 12.15; MONOCLONAL ANTIBODY 15.101; MONOCLONAL ANTIBODY 22.121; MONOCLONAL ANTIBODY 24.7; MONOCLONAL ANTIBODY 6.13; MONOCLONAL ANTIBODY 8.17; N ACETYLGLUCOSAMINE; UNCLASSIFIED DRUG;

ANTIBODY SPECIFICITY; ANTIBODY TITER; ANTIGEN BINDING; ARTICLE; BINDING SITE; CARBOHYDRATE ANALYSIS; CARBOHYDRATE SYNTHESIS; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; EPITOPE MAPPING; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CARBOHYDRATE INTERACTION; PROTEIN CONFORMATION; XENOTRANSPLANTATION;

ANTIBODIES, MONOCLONAL; ANTIGEN-ANTIBODY REACTIONS; ANTIGENS; BINDING SITES; CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; CARBOHYDRATES; COMPUTATIONAL BIOLOGY;

EID: 77952842605     PISSN: 09596658     EISSN: 14602423     Source Type: Journal    
DOI: 10.1093/glycob/cwq022     Document Type: Article

References (37)

1. Agostino M, Jene C, Boyle T, Ramsland PA, Yuriev E. 2009. Molecular docking of carbohydrate ligands to antibodies: structural validation against crystal structures. J Chem Inf Model 49:2749-2760.
2. Agostino M, Sandrin MS, Thompson PE, Yuriev E, Ramsland PA. 2009. In silico analysis of antibody-carbohydrate interactions and its application to xenoreactive antibodies. Mol Immunol 47:233-246.
3. Almond A, Petersen BO, Duus JØ. 2004. Oligosaccharides implicated in recognition are predicted to have relatively ordered structures. Biochemistry 43:5853-5863.
4. Audette GF, Delbaere LTJ, Xiang J. 2003. Mapping protein:carbohydrate interactions. Curr Prot Pept Sci 4:11-20.
5. Azurmendi HF, Martin-Pastor M, Bush CA. 2002. Conformational studies of Lewis X and Lewis A trisaccharides using NMR residual dipolar couplings. Biopolymers 63:89-98.
6. Blanchard B, Nurisso A, Hollville E, Tetaud C, Wiels J, Pokorna M, Wimmerova M, Varrot A, Imberty A. 2008. Structural basis of the preferential binding for globo-series glycosphingolipids displayed by Pseudomonas aeruginosa lectin I. J Mol Biol 383:837-853.
7. Cooper DKC, Good AH, Koren E, Oriol R, Malcolm AJ, Ippolito RM, Neethling FA, Ye Y, Romano E, Zuhdi N. 1993. Identification of (-galactosyl and other carbohydrate epitopes that are bound by human anti-pig antibodies: relevance to discordant xenografting in man. Transpl Immunol 1:198-205.
8. Corzana F, Bettler E, Du Penhoat CH, Tyrtysh TV, Bovin NV, Imberty A. 2002. Solution structure of two xenoantigens: (Gal-LacNAc and (Gal-Lewis X. Glycobiology 12:241-250.
9. DeMarco ML, Woods RJ. 2008. Structural glycobiology: a game of snakes and ladders. Glycobiology 18:426-440.
10. Gabius H-J, Siebert H-C, André S, Jiménez-Barbero J, Rüdiger H. 2004. Chemical biology of the sugar code. Chem Bio Chem 5:740-764.
11. Grahn E, Askarieh G, Holmner A, Tateno H, Winter HC, Goldstein IJ, Krengel U. 2007. Crystal structure of the Marasmius oreades mushroom lectin in complex with a xenotransplantation epitope. J Mol Biol 369:710-721.
12. Greco A, Ho JG, Lin SJ, Palcic MM, Rupnik M, Ng KK. 2006. Carbohydrate recognition by Clostridium difficile toxin A. Nat Struct Mol Biol 13:460-461.
13. Imberty A, Mikros E, Koca J, Mollicone R, Oriol R, Perez S. 1995. Computer simulation of histo-blood group oligosaccharides: energy maps of all constituting disaccharides and potential energy surfaces of 14 ABH and Lewis carbohydrate antigens. Glycoconj J 12:331-349.
14. Kulkarni KA, Katiyar S, Surolia A, Vijayan M, Suguna K. 2007. Generation of blood group specificity: new insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin. Proteins 68:762-769.
15. Lefranc M-P, Pommié C, Manuel R, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G. 2003. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 27:55-77.
16. Lemieux RU. 1996. How water provides the impetus for molecular recognition in aqueous solution. Acc Chem Res 29:373-380.
17. Liebecq C. 1992. Biochemical nomenclature and related documents: a compendium 1992 (International Union of Biochemistry and Molecular Biology). London: Portland Press.
18. Lovell SC, Davis IW, Arendall BI, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. 2003. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50:437-450.
19. Lütteke T. 2009. Analysis and validation of carbohydrate three-dimensional structures. Acta Crystallogr D65:156-168.
20. Manallack DT, Hughes RA, Thompson PE. 2005. The next generation of phosphodiesterase inhibitors: structural clues to ligand and substrate selectivity of phosphodiesterases. J Med Chem 48:3449-3462.
21. Milland J, Yuriev E, Xing P-X, McKenzie IFC, Ramsland PA, Sandrin MS. 2007. Carbohydrate residues downstream of the terminal Galα(1,3)Gal epitope modulate the specificity of xenoreactive antibodies. Immunol Cell Biol 85:623-632.
22. Natchiar SK, Srinivas O, Mitra N, Surolia A, Jayaraman N, Vijayan M. 2006. Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin. Acta Crystallogr D62:1413-1421.
23. Ramsland PA, Farrugia W, Bradford TM, Hogarth PM, Scott AM. 2004. Structural convergence of antibody binding of carbohydrate determinants in Lewis Y tumor antigens. J Mol Biol 340:809-818.
24. Ramsland PA, Farrugia W, Yuriev E, Edmundson AB, Sandrin MS. 2003. Evidence for structurally conserved recognition of the major carbohydrate xenoantigen by natural antibodies. Cell Mol Biol 49:307-317.
25. Ramsland PA, Guddat LW, Edmundson AB, Raison RL. 1997. Diverse binding site structures revealed in homology models of polyreactive immunoglobulins. J Comp Aid Mol Des 11:453-461.
26. Sandrin MS, McKenzie IF. 1994. Galα(1, 3)Gal, the major xenoantigen(s) recognised in pigs by human natural antibodies. Immunol Rev 141:169-190.
27. Sandrin MS, Vaughan HA, Dabkowski PL, McKenzie IF. 1993. Anti-pig IgM antibodies in serum respond predominantly with Gal((1-3)Gal epitopes. Proc Nat Acad Sci USA 90:11391-11395.
28. Siebert H-C, André S, Asensio JL, Cañada FJ, Dong X, Espinosa JF, Frank M, Gilleron M, Kaltner H, Kozár T, et al. 2000. A new combined computational and NMR-spectroscopical strategy for the identification of additional conformational constraints of the bound ligand in an aprotic solvent. Chem Bio Chem 1:181-195.
29. Stanca-Kaposta EC, Gamblin DP, Screen J, Liu B, Snoek LC, Davis BG, Simons JP. 2007. Carbohydrate molecular recognition: a spectroscopic investigation of carbohydrate-aromatic interactions. Phys Chem Chem Phys 9:4444-4451.
30. Tempel W, Tschampel S, Woods RJ. 2002. The xenograft antigen bound to Griffonia simplicifolia lectin 1-B(4) X-ray crystal structure of the complex and molecular dynamics characterization of the binding site. J Biol Chem 277:6615-6621.
31. Vaughan HA, Oldenburg KR, Gallop MA, Atkin JD, McKenzie IFC, Sandrin MS. 1996. Recognition of an octapeptide sequence by multiple Gal((1, 3) Gal-binding proteins. Xenotransplantation 3:18-23.
32. Wallace AC, Laskowski RA, Thornton JM. 1995. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Prot Eng 8:127-134.
33. Walser PJ, Haebel PW, Kunzler M, Sargent D, Kues U, Aebi M, Ban N. 2004. Structure and functional analysis of the fungal galectin CGL2. Structure 12:689-702.
34. Winterburn PJ, Phelps CF. 1972. The significance of glycosylated proteins. Nature 236:147-151.
35. Yuriev E, Agostino M, Farrugia W, Christiansen D, Sandrin M, Ramsland P. 2009. Structural biology of carbohydrate xenoantigens. Expert Opin Biol Ther 9:1017-1029.
36. Yuriev E, Farrugia W, Scott AM, Ramsland PA. 2005. Three-dimensional structures of carbohydrate determinants of Lewis system antigens: implications for effective antibody targeting of cancer. Immunol Cell Biol 83:709-717.
37. Yuriev E, Sandrin MS, Ramsland PA. 2008. Antibody-ligand docking: insights into peptide-carbohydrate mimicry. Mol Sim 34:461-469.