X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2′,3′-epoxypropyl β-glycoside of N-acetyllactosamine

Journal of Molecular Recognition

Volumn 16, Issue 2, 2003, Pages 72-82

  Muraki, Michiro ^a   Harata, Kazuaki ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Affinity labeling; Carbohydrate carbohydrate interaction; CH interaction; Galactose; Ligand recognition; Lysozyme; N acetylglucosamine; N acetyllactosamine; Protein carbohydrate interaction; X ray analysis

Indexed keywords

AFFINITY LABELS; AMINO SUGARS; ANIMALS; BINDING SITES; CARBOHYDRATE CONFORMATION; CHICKENS; CRYSTALLOGRAPHY, X-RAY; GLUCOSIDES; HUMANS; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; MURAMIDASE; MUTAGENESIS, SITE-DIRECTED; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 0038332160     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.611     Document Type: Article

References (29)

1. Bovin NV. 1996. Carbohydrate-carbohydrate interactions: a review. Biochemistry (Moscow), 61: 694-704.
2. Brünger AT. 1992. X-PLOR version 3.1, A system for X-ray crystallography and NMR. Yale University Press: New Haven, CT.
3. Chen L, Garret TPJ, Fincher GB, HøJ PB. 1995. A tetrad of ionizable amino acids is important for catalysis in Barley β-glucanases. J. Biol. Chem. 270: 8093-8101.
4. Ducruix A, Giegé R. 1992. Crystallization of Nucleic Acids and Proteins, a Practical Approach. IRL Press: New York.
5. x determinants. J. Biol. Chem. 264: 9476-9484.
6. Fraczkiewicz R, Brawn W. 1998. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comp. Chem. 19: 319-333.
7. Havukainen R, Törrönen A, Laitinen T, Rouvinen J. 1996. Covalent binding of three epoxyalkyl xylosides to the active site of endo-1, 4-xylanase II from Trichoderma reesei. Biochemistry 35: 9617-9624.
8. Keitel T, Simon O, Borris R, Heinemann U. 1993. Molecular and active-site structure of Bacillus 1, 3-1, 4-β-glucanase. Proc. Natl Acad. Sci. USA 90: 5287-5291.
9. Laskowski RA, Macarthur MW, Moss DS, Thornton JM. 1993. PROCHECK-A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26: 283-291.
10. Legler G. 1990. Glycoside hydrolases-Mechanistic information from studies with reversible and irreversible inhibitors. Adv. Carbohydr. Chem. Biochem. 48: 319-384.
11. London E. 2002. Insights into lipid raft structure and formation from experiments in membranes. Curr. Opin. Struct. Biol. 12: 480-486.
12. Luzzati V. 1952. Traitement statisque des erreurs dans la determination des structures cristallines. Acta Crystallogr. 5: 802-810.
13. Mo F, Jensen LH. 1987. The crystal structure of a β-(1→4) linked disaccharide, α-N, N-diacetylchitobiose monohydrate. Acta Crystallogr. B 34: 1562-1569.
14. Motoshima H, Mine S, Masumoto K, Abe Y, Iwashita H, Hashimoto Y, Chijiiwa Y, Ueda T, Imoto T. 1997. Analysis of the stabilization of hen lysozyme by helix macrodipole and charged side chain interaction. J. Biochem. 121: 1076-1081.
15. Muraki M. 2002. The importance of CH/π interactions to the function of carbohydrate binding proteins. Prot. Pept. Lett. 9: 195-209.
16. Muraki M, Harata K, Sugita N, Sato KI. 1996. Origin of carbohydrate recognition specificity of human lysozyme revealed by affinity labeling. Biochemistry 35: 13562-13567.
17. Muraki M, Harata K, Sugita N, Sato KI. 1998. X-ray structure of human lysozyme labeled with 2′,3′-epoxypropyl β-glycoside of Man-β1,4-GlcNAc. Structural change and recognition specificity at subsite B. Acta Crystallogr. D54: 834-843.
18. Muraki M, Harata K, Sugita N, Sato KI. 1999. Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand. Biochemistry 38: 540-548.
19. Muraki M, Harata K, Sugita N, Sato KI. 2000a. Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling. Biochemistry 39: 292-299.
20. Muraki M, Morii M, Harata K. 2000b. Chemically prepared hevein domains: effect of C-terminal truncation and the mutagenesis of aromatic residues on the affinity for chitin. Prot. Engnr. 13: 385-389.
21. Muraki M, Ishimura M, Harata K. 2002. Interactions of wheat-germ agglutinin with GlcNAcβ1,6Gal sequence. Biochim. Biophys. Acta Gen. Subj. 1569: 10-20.
22. Nishio M, Umezawa Y, Hirota M, Takeuchi Y. 1995. The CH/π interaction: significance in molecular recognition. Tetrahedron 51: 8665-8701.
23. Pérez S, Imberty A, Carver JP. 1994. Molecular modeling: an essential component in the structure determination of oligosaccharides and polysaccharides. Adv. Comput. Biol. 1: 147-202.
24. Pérez S, Mouhous-Riou N, E.Nifant'ev N, E.Tsvetkov Y, Bachet B, Imberty A. 1996. Crystal and molecular structure of a histo-blood group antigen involved in cell adhesion: the Lewis x trisaccharide. Glycobiology 6: 537-542.
25. Plapp BV. 1982. Application of affinity labeling for studying structure and function of enzymes. Meth. Enzymol. 87: 469-499.
26. Roussel A, Fontecillacamps JC, Cambillau C. 1990. Crystallize-A crystallographic symmetry display and handling subpackage in TOM/FRODO. J. Mol. Graph. 8: 86.
27. Thomas EW, McKelvy JF, Sharon N. 1969. Specific and irreversible inhibition of lysozyme by 2′,3′-epoxypropyl β-glycosides of N-acetyl-D-glucosamine oligomers. Nature 222: 485-486.
28. Varki A, Cummings R, Esko J, Freeze H, Hart G, Marth J. 1999. Essentials of Glycobiology. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
29. x group. Biochem. Biophys. Res. Commun. 180: 1214-1221.