Knowledge-based model building of the tertiary structures for lectin domains of the selectin family

Protein Journal

Volumn 15, Issue 2, 1996, Pages 161-168

  Chou, Kuo Chen ^a  

^a Pharmacia and Upjohn Inc ^*  (United States)

Author keywords

Convergence divergence duality; E selectin; ECEPP; Energy minimization; L selectin; P selectin

Indexed keywords

CARBOHYDRATE BINDING PROTEIN; ENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1; L SELECTIN; PADGEM PROTEIN;

AMINO ACID ANALYSIS; ARTICLE; DISULFIDE BOND; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; E-SELECTIN; L-SELECTIN; LECTINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; P-SELECTIN; PROTEIN STRUCTURE, TERTIARY; SELECTINS;

EID: 0029873999     PISSN: 15723887     EISSN: 18758355     Source Type: Journal    
DOI: 10.1007/BF01887396     Document Type: Article

References (34)

1. Bevilacqua, M. P. A. (1993). Endothelial-leukocyte adhesion molecules, Annu. Rev. Immunol. 11, 767-804.
2. Bevilacqua, M. P. A., Pober, J. S., Mendrick, D. L., Cotran, R. S., and Gimbrone, M. A., Jr. (1987). Identification of an inducible endothelial-leukocyte adhesion molecule, Proc. Natl. Acad. Sci. USA 84, 9238-9242.
3. Bevilacqua, M. P., Stenglin, S., Gimbrone, M. A., Jr., and Seed, B. (1989). Endothelial leukocyte adhesion molecule 1: An inducible receptor for neutrophils related to complement regulatory proteins and lectins, Science 243, 1160-1165.
4. Bonfanti, R., Furie, B., and Wagner, D. (1989). PADGEM (GMP140) is a component of Weibel-Palade bodies of human endothelial cells Blood 73, 1109-1112.
5. Butcher, E. C. (1991). Leukocyte-endothelial cell recognition: Three (or more) steps to specificity and diversity, Cell 67, 1033-1036.
6. Camerini, D., James, S. P., Stamenkovic, I., and Seed, B. (1989). Leu-8/TQl is the human equivalent of the Mel-14 lymph node homing receptor, Nature 342, 78-82.
7. Carlacci, L., Chou, K. C., and G. M. Maggiora (1991). A heuristic approach to predicting the tertiary structure of bovine somatotropin, Biochemistry 30, 4389-4398.
8. Chou, K. C. (1992). Energy-optimized structure of antifreeze protein and its binding mechanism, J. Mol. Biol. 223, 509-517.
9. Chou, K. C. (1995). The convergence-divergence duality in lectin domains of selectin family and its implications, FEBS Lett. 363, 123-126.
10. Chou, K. C., and Carlacci, L. (1991). Energetic approach to the folding of α/β barrels, Proteins Struct. Funct. Genet. 9, 280-295.
11. Chou, K. C. and Scheraga, H. A. (1982). Origin of the right-handed twist of β-sheets of poly(L-Val) chains, Proc. Natl. Acad. Sci. USA 79, 7047-7051.
12. Chou, K. C., Némethy, G., and Scheraga, H. A. (1984). Energy approach to the packing of α-helices, J. Am. Chem. Soc. 106, 3161-3170.
13. Chou, K. C, Némethy, G., Pottle, M., and Scheraga, H. A. (1989). Energy of stabilization of the right-handed βαβ crossover in proteins, J. Mol. Biol. 205, 241-249.
14. Drickamer, K. (1988). Two distinct classes of carbohydrate-recognition domains in animal lectins, J. Biol. Chem. 263, 9557-9560.
15. Drickamer, K., Dordal, M. S., and Reynolds, L. (1986). Mannose-binding proteins isolated from rat liver contain carbohydrate-recognition domains linked to collagenous tails-Complete primary structures and homology with pulmonary surfactant apoprotein, J. Biol. Chem. 261, 6878-6887.
16. Erbe, D. V., Wolitzky, B. A., Presta, L. G., Norton, C. R., Ramos, R. J., Burns, D. K., Rumberger, J. M., Rao, B. N. N., Foxall, C., Brandly, B. K., and Lasky, L. A. (1992). Identification of an E-selectin region critical for carbohydrate recognition and cell adhesion, J. Cell. Biol. 119, 215-227.
17. Gellatin, M., St. John, T. P., Siegelman, M., Reichert, R., Butcher, E. C., and Weissman, I. L. (1986). Lymphocyte homing reseptors, Cell 44, 673-680.
18. Gay, D. M. (1983). Subroutines for unconstrained minimization using a model/trust-region approach, Assoc. Comput. Mach. Trans. Math. Software 9, 503-524.
19. 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., and Burns, D. K. (1994). Insight into E-selectin/ligand interaction from the crystal structure and mutagenesis of the lec/EGF domains. Nature 367, 532-538.
20. Hollenbaugh, D., Bajorath, J., Stenkamp, R., and Aruffo, A. (1993). Interaction of P-selectin (CD62) and its cellular ligand: Analysis of critical residues. Biochemistry 32, 2960-2966.
21. IUPAC-IUB Commission on Biochemical Nomenclature (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains. Biochemistry 9, 3471-3479.
22. Johnston, G. L, Cook, R. G., and McEver, R. P. (1989). Cloning of GMP-140, a granule membrane protein of platelets and endothelium: Sequence similarity to proteins involved in cell adhesion and inflammation, Cell 56, 1033-1044.
23. Lasky, L. A. (1992). Selectins: Interpreters of cell-specific carbohydrate information during inflammation, Science 258, 964-969.
24. Lasky, L. A., Singer. M. S., Yednock, T. A., Dowbenko. D., Fennie, C., Rodriguez, H., Nguyen, T., Stachel, S., and Rosent, S. D. (1989). Cloning of a lymphocyte homing receptor reveals a lectin domain, Cell 56, 1045-1055.
25. Lasky, L. A., Singer, M. S., Dowbenko, D., Imai, Y. Henzel, W. J., Grimley, C., Fennie, C., Gillett, N., Watson, S. R., and Rosent, S. D. (1992). An endothelial ligand for L-selectin is a novel mucin-like molecule. Cell 69, 927-938.
26. Mills, A. (1993). Modelling the carbohydrate recognition domain of human E-selectin, FEBS Lett. 319, 5-11.
27. Momany, F. A., McGuire, R. F., Burgess, A. W., and Scheraga, H. A. (1975). Energy parameters in polypeptides. 7. Geo- metrical parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids, J. Phvs. Chem. 79, 2361-2381.
28. Nemethy, G., Pottle, M. S., and Scherage, H. A. (1983). Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids, J. Phys. Chem. 87, 1883-1887.
29. Siegelman, M. H., and Weissman, I. L. (1989). Human homologue of mouse lymph node homing receptor: Evolutionary conservation at tandem cell interaction domains, Proc. Natl. Acad. Sci. USA 86, 5562-5566.
30. Siegelman, M. H., van de Rijn, M., and Weissman, I. L. (1989). Mouse lymph node homing receptor cDNA clone encodes a glycoprotein revealing tandem interaction domains, Science 243,1165-1172.
31. Smith. R. F., and Smith, T. F. (1992). Pattern-induced multisequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng. 5, 35-41.
32. Vásquez, M., Némethy, G., and Scheraga, H. A. (1983). Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid, Macromolecules 16, 1043-1049.
33. Watson, S. R., Fennie, C, and Lasky, L. A. (1991). Neutrophil influx into an inflammatory site inhibited by a soluble homing receptor-IgG chimaera, Nature 349, 164-167.
34. Weis, W. L, Kahn, R., Fourme, R., Drickamer, K., and Hendrickson, W. A. (1991). Structure of the calciumdependent lectin domain from a rat manose-binding protein determined by MAD phasing, Science 254, 1608-1615.