Selectin-ligand interactions revealed by molecular dynamics simulation in solution

Journal of Medicinal Chemistry

Volumn 40, Issue 3, 1997, Pages 362-369

  Tsujishita, Hideki ^a   Hiramatsu, Yasuyuki ^a   Kondo, Noriko ^a   Ohmoto, Hiroshi ^a   Kondo, Hirosato ^a   Kiso, Makoto ^b   Hasegawa, Akira ^b  

^a KANEBO LTD   (Japan)

^b GIFU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1; L SELECTIN;

ARTICLE; BINDING AFFINITY; CELL ADHESION; COMPUTER MODEL; COMPUTER SIMULATION; LIGAND BINDING; MOLECULAR INTERACTION; PROTEIN BINDING; STRUCTURE ANALYSIS;

CARBOHYDRATE SEQUENCE; COMPUTER SIMULATION; E-SELECTIN; GLYCOSPHINGOLIPIDS; LECTINS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; OLIGOSACCHARIDES; SULFATES;

EID: 0031044297     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9606103     Document Type: Article

References (38)

1. Springer, T. A. Traffic Signals for Lymphocyte Recirculation and Leukocyte Emigration: The Multiship Paradigm. Cell 1994, 76, 301-314.
2. Lasky, L. A. Selectins: Interpreters of Cell-Specific Carbohydrate Information During Inflammation. Science 1992, 258, 964-969.
3. Wada, Y.; Saito, T.; Matsuda, N.; Ohmoto, H.; Yoshino, K.; Ohashi, M.; Kondo, H.; Ishida, H.; Kiso, M.; Hasegawa, A. Studies on Selectin Blockers. 2. Novel Selectin Blocker as Potential Therapeutics for Inflammatory Disorders. J. Med. Chem. 1996, 39, 2055-2059.
4. Graves, B. J.; Crowther, R. L.; Chandran, C.; Rumberger, J. M.; Li, S.; Huang, K.-S.; Presky, D. H.; Familletti, P. C.; Wolitzky, B. A.; Burns, D. K. Insight into E-selectin/Ligand Interaction from the Crystal Structure and Mutagenesis of the Lec/EGF Domains. Nature 1994, 367, 532-538.
5. Weis, W. I.; Kahn, R.; Fourme, R.; Drickamer, K.; Hendrickson, W. A. Structure of the Calcium-Dependent Lectin Domain from a Rat Mannose-Binding Protein Determined by MAD Phasing. Science 1991, 254, 1608-1615.
6. Weis, W. I.; Drickamer, K.; Hendrickson, W. A. Structure of a C-Type Mannose-Binding Protein Complexed with an Oligosaccharide. Nature 1992, 360, 127-134.
7. Bajorath, J.; Hollenbaugh, D.; King, G.; Harte, W., Jr.; Eustice, D. C.; Darveau, R. P.; Aruffo, A. CD62/P-selectin Binding Sites for Myeloid Cells and Sulfatides Are Overlapping. Biochemistry 1994, 33, 1332-1339.
8. Blanck, O.; Iobst, S. T.; Gabel, C.; Drickmer, K. Introduction of Selectin-Like Binding Specificity into a Homologous Mannose-Binding Protein. J. Biol. Chem. 1996, 271, 7289-7292.
9. Brandley, B. K.; Kiso, M.; Abbas, S.; Nikrad, P.; Srivasatava, O.; Foxall, C.; Oda, Y.; Hasegawa, A. Structure-Function Studies on Selectin Carbohydrate Ligands. Modifications to Fucose, Sialic Acid and Sulphate as a Sialic Acid Replacement. Glycobiology 1993, 3, 633-639
10. Cooke, R. M.; Hale, R. S.; Lister, S. G.; Shah, G.; Weir, M. P. The Conformation of the Sialyl Lewis X Ligand Changes upon Binding to E-selectin. Biochemistry 1994, 33, 10591-10596.
11. DeFrees, S. A.; Gaeta, F. C.; Lin, Y.-C.; Ichikawa, Y.; Wong, C.-H. Ligand Recognition by E-selectin: Analysis of Conformation and Activity of Synthetic Monomeric and Bivalent Sialyl Lewis X Analogs. J. Am. Chem. Soc. 1993, 115, 7549-7550.
12. Erbe, D. V.; Watson, S. R.; Presta, L. G.; Wolitzky, B. A.; Foxall, C.; Brandley, B. K.; Lasky, L. A. P- and E-selectin Use Common Sites for Carbohydrate Ligand Recognition and Cell Adhesion. J. Cell. Biol. 1993, 120, 1227-1235.
13. Erbe, D. V.; Wolitzkey, B. A.; Presta, L. G.; Norton, C. R.; Ramos, R. J.; Burns, D. K.; Rumberger, J. M.; Rao, B. N. N.; Foxall, C.; Brandley, B. K.; Lasky, L. A. Identification of an E-selectin Region Critical for Carbohydrate Recognition and Cell Adhesion. J. Cell. Biol. 1992, 119, 215-227.
14. Hollenbaugh, D.; Aruffo, A.; Senter, P. D. Effects of Chemical Modification on the Binding Activities of P-selectin Mutants. Biochemistry 1995, 34, 5678-5684.
15. Hollenbaugh, D.; Bajorath, J.; Stenkamp, R.; Aruffo, A. Interaction of P-selectin (CD62) and Its Cellular Ligand: Analysis of Critical Residues. Biochemistry 1993, 32, 2960-2966.
16. Kogan, T. P.; Revelle, B. M.; Tapp, S.; Scott, D.; Beck, P. J. A Single Amino Acid Residue Can Determine the Ligand Specificity of E-selectin. J. Biol. Chem. 1995, 270, 14047-14055.
17. x Complex. Angew. Chem., Int. Ed. Engl. 1995, 34, 1841-1844.
18. Tyrrell, D.; James, P.; Rao, N.; Foxall, C.; Abbas, S.; Dasgupta, F.; Nashed, M.; Hasegawa, A.; Kiso, M.; Asa, D.; Kidd, J.; Brandley, B. K. Structural Requirements for the Carbohydrate Ligand of E-selectin. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 10372-10376.
19. Bruccoleri, R. E.; Karplus, M. Conformational Sampling Using High-Temperature Molecular Dynamics. Biopolymers 1990, 29, 1847-1862.
20. Pearlman, D. A.; Case, D. A.; Caldwell, G. L.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. (1991) AMBER 4.0, University Of California, San Francisco.
21. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
22. Woods, R. J.; Dwek, R. A.; Edge, C. J.; Fraser-Reid, B. Molecular Mechanical and Molecular Dynamical Simulations of Glycoproteins and Oligosaccharides. 1. GLYCAM_93 Parameter Development. J. Phys. Chem. 1995, 99, 3832-3846.
23. Hamaguchi, N.; Charifson, P.; Darden, T.; Xiao, L.; Padmanabhan, K.; Tulinsky, A.; Hiskey, R.; Pedersen, L. Molecular Dynamics Simulation of Bovine Prothrombin Fragment-1 in the Presence of Calcium Ions. Biochemistry 1992, 31, 8840-8848.
24. Maynard, A. T.; Eastman, M. A.; Darden, T.; Deerfield, D. W. I.; Hiskey, R. G.; Pedersen, L. Effect of Calcium (II) and Magnesium (II) Ions on the 18-23 γ-Carboxyglutamic Acid Containing Cyclic Peptide Loop of Bovine Prothrombin. An AMBER Molecular Mechanics Study. Int. J. Pept. Protein Res. 1988, 31, 137-149.
25. Huige, C. J. M.; Altona. C. Force Field Parameters for Sulfates and Sulfamates Based on Ab Initio Calculations: Extensions of AMBER and CHARMm Fields. J. Comput. Chem. 1995, 16, 56-79.
26. Ferrin, T. E.; Huang, C. C.; Jarvis, L. E.; Langridge, R. The MIDAS Display System. J. Mol. Graphics 1988, 6, 13-27.
27. Ichikawa, Y.; Lin, Y.-C.; Dumas, D. P.; Shen, G.-J.; Garcia-Juneeda, E.; Williams, M. A.; Bayer, R.; Ketcham, C.; Walker, L. E.; Paulson, J. C.; Wong, C.-H. Chemical-Enzymatic Synthesis and Conformational Analysis of Sialyl Lewis X and Derivatives. J. Am. Chem. Soc. 1992, 114, 9283-9298.
28. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984, 81, 3684-3690.
29. van Gunsteren, W. F.; Berendsen, H. J. C. Algorithms for Macromolecular Dynamics and Constraint Dynamics. Mol. Phys. 1977, 34, 1311-1327.
30. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926-935.
31. Richmond, T. J. Solvent Accessible Surface Area and Excluded Volume in Proteins. J. Mol. Biol. 1984, 178, 63-89.
32. Wesson, L.; Eisenberg, D. Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution. Protein Sci. 1992, 1, 227-235.
33. Bourne, Y.; van Tilbeurgh, H.; Cambillau, C. Protein-Carbohydrate Interactions. Curr. Opin. Struct. Biol. 1993, 3, 681-686.
34. Lawrence, M. B.; Springer, T. A. Leukocytes Roll on a Selectin at Physiologic Flow Rates: Distinction from and Prerequisite for Adhesion Through Integrins. Cell 1991, 65, 859-873.
35. Ushiyama, S.; Laue, T. M.; Moore, K. L.; Erickson, H. P.; McEver, R. P. Structural and Functional Characterization of Monomeric Soluble P-selectin and Comparison with Membrane P-selectin. J. Biol. Chem. 1993, 268, 15229-15237.
36. x Binding Interactions. Mutagenic Alteration of Ligand Binding Specificity. J. Biol. Chem. 1996, 271, 4289-4297.
37. Manning, D. D.; Bertozzi, C. R.; Pohl, N. L.; Rosen, S. D.; Kiessling, L. L. Selectin-Saccharide Interactions: Revealing Structure-Function Relationships with Chemical Synthesis. J. Org. Chem. 1995, 60, 6254-6255.
38. Nicolls, A.; Sharp, K. A.; Honig, B. Protein Folding and Association: Insights from the Interfacial and Thermodynamic Properties of Hydrocarbons. Proteins Struct. Funct. Genet. 1991, 11, 281-296.