Structural analysis of the KGD sequence loop of barbourin, an α(IIb)β3-specific disintegrin

Journal of Computer-Aided Molecular Design

Volumn 14, Issue 4, 2000, Pages 317-327

  Minoux, Hervé ^a   Chipot, Christophe ^a   Brown, David ^a   Maigret, Bernard ^a  

^a UNIVERSITÉ DE LORRAINE   (France)

Author keywords

Cation interactions; Integrin; KGD; Molecular dynamics

Indexed keywords

AMINO ACIDS; BIOACTIVITY;

ARG GLY ASPS; CATION-Π INTERACTIONS; DISINTEGRINS; HOMOLOGY MODELING; INTEGRINS; KGD; PLATELET AGGREGATION; RECOGNITION SITE; SMALL PROTEINS; THREE DIMENSIONAL MODELLING;

MOLECULAR DYNAMICS;

AMINO ACID; ARGINYLGLYCYLASPARTIC ACID; ASPARTIC ACID; BARBOURIN; DISINTEGRIN; ECHISTATIN; FIBRINOGEN; GLYCINE; KISTRIN; LYSINE; TRYPTOPHAN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 0034007914     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008182011731     Document Type: Article

References (50)

1. Seymour, J.L., Henzel, W.J., Nevins, B., Stults, J.T. and Lazarus, R.A., J. Biol. Chem., 265 (1990) 10143.
2. Huang, T.F., Peng, H.C., Peng, I.S., Teng, C.M. and Ouyang, C., Arch. Biochem. Biophys., 298 (1992) 13.
3. Gould, R.J., Polokoff, M.A., Friedman, P.A., Huang, T.F., Holt, J.C., Cook, J.J. and Niewiarowski, S., Proc. Soc. Exp. Biol. Med., 195 (1990) 168.
4. Cox, D., Aoki, T., Seki, J., Motoyama, Y. and Yoshida, K., Med. Res. Rev., 14 (1994) 195.
5. Hynes, R.O., Cell, 69 (1992) 11.
6. Phillips, D.R., Charo, I.F. and Scarborough, R.M., Cell, 65 (1991) 359.
7. Pierschbacher, M.D. and Ruoslahti, E., Proc. Natl. Acad. Sci. USA, 81 (1984) 5985.
8. Pierschbacher, M.D. and Ruoslahti, E., Nature 309 (1984) 5963.
9. Lazarus, R.A. and McDowell, R.S., Curr. Opin. Biotechnol., 4 (1993) 438.
10. Scarborough, R.M., Rose, J.W., Hsu, M.A., Phillips, D.R., Fried, V.A., Campbell, A.M., Nannizzi, L. and Charo, I.F., J. Biol. Chem., 266 (1991) 9359.
11. Scarborough, R.M., Rose, J.W., Naughton, M.A., Phillips, D.R., Nannizzi, L., Arfsten, A., Campbell, A.M. and Charo, I.F., J. Biol. Chem., 268 (1993) 1058.
12. Scarborough, R.M., Naughton, M.A., Teng, W., Rose, J.W., Phillips, D.R., Nannizzi, L., Arfsten, A., Campbell, A.M. and Charo, I.F., J. Biol. Chem., 268 (1993) 1066.
13. Cheng, S., Craig, W.S., Mullen, D., Tschopp, J.F., Dixon, D. and Pierschbacher, M.D., J. Med. Chem., 37 (1994) 1
14. Muller, G., Gurrath, M. and Kessler, H., J. Comput.-Aided Mol. Design., 8 (1994) 709
15. Craig, W.S., Cheng, S., Mullen, D.G., Blevit, J. and Pierschbacher, M.D., Biopolymers, 37 (1995) 157
16. Tselepis, V.H., Green, L.J. and Humphries, M.J., J. Biol. Chem., 272 (1997) 21341
17. Phillips, D.R. and Scarborough, R.M., Am. J. Cardiol., 80 (1997) 11B.
18. Oshikawa, K. and Terada, S., J. Biochem., 125 (1999) 31
19. Pearson, W.R. and Lipman, D.J., Proc. Natl. Acad. Sci. USA, 85 (1988) 2444.
20. Pearson, W.R., Methods Enzymol., 183 (1990) 63.
21. Abola, E.E., Bernstein, P.C., Bryant, S.H., Koetzle, T.F. and Weng, J., In Allen, F.H., Bergerhoff, G. and Sievers, R. (Eds), Protein Data Bank, in Crystallographic Databases-Information Content, Software Systems, Scientific Applications, Data Commission of the International Union of Crystallography, Bonn/Cambridge/Chester, 1987, pp. 107-132.
22. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer Jr., E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
23. Senn, H. and Klaus, W., J. Mol. Biol., 232 (1993) 907.
24. Klaus, W., Broger, C., Gerber, P. and Senn, H., J. Mol. Biol., 232 (1993) 897.
25. Dauber-Osguthorpe, P., Roberts, V.A., Osguthorpe, D.J., Wolff, J., Genest, M. and Hagler, A.T., Proteins, 4 (1988) 31.
26. Homology, Molecular Simulations Inc., San Diego, CA, 1997.
27. Saudek, V., Atkinson, R.A. and Pelton, J.T., Biochemistry, 30 (1991) 7369.
28. Atkinson, R.A., Saudek, V. and Pelton, J.T., Int. J. Pept. Protein. Res., 43 (1994) 563.
29. Adler, M., Lazarus, R.A., Dennis, M.S. and Wagner, G., Science, 253 (1991) 445.
30. OH = 0.96 Å, HOH = 104.5° (with the usual notations).
31. Ewald, P., Ann. Phys., 64 (1921) 253.
32. Brown, D., Minoux, H. and Maigret, B., Comput. Phys. Commun., 103 (1997) 170.
33. Brown, D. The gmq User Manual, 1998; available at: http://www.lctn.u-nancy.fr/Chercheurs/David.Brown
34. Brown, D., Clarke, J.H.R., Okuda, M. and Yamazaki, T., Comput. Phys. Commun., 83 (1994) 1; ibid Erratum Comput. Phys. Commun., 86 (1995) 312.
35. Frish, M.J., Trucks, G.W., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Keith, T., Peterson, G.A., Montgomery, J.A., Raghavachari, K., Al-Laham, M.A., Zakrzewski, V.G., Ortiz, J.V., Foresman, J.B., Peng, C.Y., Ayala, P.Y., Chen, W., Wong, M.W., Andres, J.L., Replogle, E.S., Gomperts, R., Martin, R.L., Fox, D.J., Binkley, J.S., Defrees, D.J., Baker, J., Stewart, J.P., Head-Gordon, M., Gonzales, C. and Pople, J.A., Gaussian 94. Gaussian Inc., Pittsburgh, PA, 1995.
36. Minoux, H., Brown, D., Chipot, C. and Maigret, B., unpublished results.
37. Greenspoon, N., Hershkoviz, R., Alon, R., Varon, D., Shenkman, B., Marx, G., Federman, S., Kapustina, G. and Lider, O., Biochemistry, 32 (1993) 1001.
38. Minoux, H., Moitessier, N., Chapleur, Y. and Maigret, B., J. Comput.-Aided Mol. Design, 12 (1998) 533.
39. Hartman, G.D., Egbertson, M.S., Halczenko, W., Laswell, W.L., Duggan, M.E., Smith, R.L., Naylor, A.M., Manno, P.D., Lynch, R.J., Zhang, G., Chang, C.T.-C. and Gould, R.J., J. Med. Chem., 35 (1992) 4640.
40. Alig, L., Edenhofer, A., Hadvary, P., Hurzeler, M., Knopp, D., Muller, M., Steiner, B., Trzeciak, A. and Weller, T.J., J. Med. Chem., 35 (1992) 4393.
41. Cox, D., Aoki, T., Seki, J., Motoyama, Y. and Yoshida, K., Thromb. Haemostas., 69 (1993) 706.
42. Marcinkiewicz, C., Vijay-Kumar, S., McLane, M.A. and Niewiarowski, S., Blood, 90 (1997) 1565.
43. Zablocki, J.A., Miyano, M., Garland, R.B., Pireh, D., Schretzman, L., Rao, S.N., Lindmark, R.J., Panzer-Knodle, S.G., Nicholson, N.S., Taite, B.B., Salyers, A.K., King, L.W., Campion, J.G. and Feigen, L.P., J. Med. Chem., 36 (1993) 1811.
44. Chipot, C., Maigret, B., Pearlman, D.A. and Kollman, P.A., J. Am. Chem. Soc., 118 (1996) 2998.
45. Minoux, H. and Chipot, C., J. Am. Chem. Soc., 121 (1999) 10366.
46. Loftus, J.C., Smith, J.W. and Ginsberg, M.H., J. Biol. Chem., 269 (1994) 25235.
47. Rahman, S., Lu, X., Kakkar, V.V. and Authi, K.S., Biochem. J., 312 (1995) 223.
48. Farrell, D.H., Thiagarajan, P., Chung, D.W. and Davie, E.W., Proc. Natl. Acad. Sci. USA, 89 (1992) 10729.
49. Liu, Q., Matsueda, G., Brown, E. and Frojmovic, M., Biochim. Biophys. Acta, 1343 (1997) 316.
50. Smith, J.W., Ruggeri, Z.M., Kunicki, T.J. and Cheresh, D.A., J. Biol. Chem., 265 (1990) 12267.