Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: Application to HU protein from Bacillus stearothermophilus

Biopolymers

Volumn 39, Issue 5, 1996, Pages 691-707

  Van Geerestein Ujah, Elizabeth C ^a   Mariani, Matteo ^a,b   Vis, Hans ^a   Boelens, Rolf ^a   Kaptein, Robert ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UNIVERSITY OF GENOA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; GRAPH THEORY; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

BACILLUS STEAROTHERMOPHILUS; HETERONUCLEAR SINGLE QUANTUM CORRELATION SPECTRUM; NUCLEAR OVERHAUSER EFFECT SPECTROSCOPY; SECONDARY STRUCTURE ELEMENTS;

PROTEINS;

BACTERIAL PROTEIN;

ARTICLE; COMPUTER PROGRAM; GEOBACILLUS STEAROTHERMOPHILUS; MATHEMATICAL ANALYSIS; MOLECULAR RECOGNITION; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PROTEIN SECONDARY STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACILLUS STEAROTHERMOPHILUS; BACTERIAL PROTEINS; BIOPOLYMERS; CARBON ISOTOPES; DNA-BINDING PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; NITROGEN ISOTOPES; PROTEIN STRUCTURE, SECONDARY;

BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS;

EID: 0030297805     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0282(199611)39:5<691::aid-bip8>3.0.co;2-r     Document Type: Article

References (42)

1. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York.
2. Billeter, M., Basus, V. J. & Kuntz, I. D. (1988) J. Magn. Reson. 76, 400-415.
3. Cieslar, C., Clore, G. M. & Gronenborn, A. M. (1988) J. Magn. Reson. 80, 119-127.
4. Eads, C. D. & Kuntz, I. D. (1989) J. Magn. Reson. 82, 467-482.
5. Oschkinat, H., Holak, T. A. & Cieslar, C. (1991) Biopolymers 31, 699-712.
6. Kleywegt, G. J., Vuister, G. W., Padilla, A., Knegtel, R. M. A., Boelens, R. & Kaptein, R. (1993) J. Magn. Reson. B102, 166-176.
7. Meadows, R. P., Olejniczak, E. T. & Fesik, S. W. (1994) J. Biomol. NMR 4, 79-96.
8. Bartels, C., Xia, T., Billeter, M., Güntert, P. & Wüthrich, K. (1995) J. Biomol. NMR 6, 1-10.
9. Billeter, M., Braun, W. & Wüthrich, K. (1982) J. Mol. Biol. 155, 321-346.
10. Wand, A. J. & Nelson, S. J. (1991) Biophys. J. 59, 1101-1112.
11. Nelson, S. J., Schneider, D. M. & Wand, A. J. (1991) Biophys. J. 59, 1113-1122.
12. Artymiuk, P. J., Grindley, H. M., Mitchell, E. M., Rice, D. W., Ujah, E. C. & Willett, P. (1991) in Recent Advances In Chemical Information, Collier, H., Ed., Royal Society of Chemistry, Cambridge, pp. 91-106.
13. Rouvray, D. H., Ed. (1991) Computational Chemical Graph Theory, Nova, New York.
14. Artymiuk, P. J., Grindley, H. M., Poirrette, A. R., Rice, D. W., Ujah, E. C. & Willett, P. (1994) J. Chem. Inf. Comp. Sci. 34, 54-62.
15. Artymiuk, P. J., Grindley, H. M., MacKenzie, A. B., Rice, D. W., Ujah, E. C. & Willett, P. (1994b) in Molecular Similarity and Reactivity, Carbo, R., Ed., Kluwer, Dordrecht, in press.
16. Lipkus, A. H., Nieman, R. A. & Munk, M .E. (1993) J. Magn. Reson. 102, 24-28.
17. Xu, J., Gray, B. & Sanctuary, B. C. (1993) J. Chem. Inf. Comput. Sci. 33, 475-489.
18. Xu, J. & Sanctuary, B. C. (1993) J. Chem. Inf. Comput. Sci. 33, 490-500.
19. Xu, J., Strauss, S. K., Sanctuary, B. C. & Trimble, L. (1994) J. Magn. Reson. B103, 53-58.
20. van Geerestein-Ujah, E. C., Slijper, M., Boelens, R. & Kaptein, R. (1995) J. Biomol. NMR 6, 67-78.
21. Lau, H. (1989) Algorithms on Graphs. TAB Books, Blue Ridge Summit, PA.
22. Deo, N. (1975) Graph Theory with Applications to Engineering and Computer Science. Prentice-Hall, NJ.
23. Vis, H., Boelens, R., Mariani, M., Stroop, R., Vorgias, C. E., Wilson, K. S. & Kaptein, R. (1994) Biochemistry 33, 14858-14870.
24. Vis, H., Mariani, M., Vorgias, C. E., Wilson, K. S., Kaptein, R. & Boelens, R. (1995) J. Mol. Biol. 254, 692-703.
25. Drlica, K. & Rouviere-Yaniv, J. (1987) Microbiol. Rev. 51, 301-319.
26. Tanaka, I., Appelt, K., Dijk, J., White, S. W. & Wilson, K. S. (1984) Nature 310, 376-381.
27. White, S. W., Appelt, K., Wilson, K. S. & Tanaka, I. (1989) Proteins 5, 281-288.
28. Ikura, M., Kay, L. E. & Bax, A. (1990) Biochemistry 29, 4659-4667.
29. Bax, A. & Grzesiek, S. (1993) Acc. Chem. Res. 26, 131-138.
30. Clore, G. M. & Gronenborn, A. M. (1991) Progr. NMR Spectr. 23, 43-92.
31. Harary, F. (1972) Graph Theory, Addison-Wesley, Reading, MA.
32. Tarjan, R. E. (1977) ACS Symposium Series 46, 1-20.
33. Levi, G. (1972) Calcolo 9, 341-352.
34. Bron, C. & Kerbosch, J. (1973) Comm. ACM 16, 575-577.
35. Christofides, N., Mingozzi, A., Toth, P. & Sandi, S., Eds. (1979) Combinatorial Optimization, Wiley-Interscience, London and New York.
36. Gross, K. H. & Kalbitzer, H. R. (1988) J. Magn. Reson. 76, 87-99.
37. Wishart, D. S. & Sykes, B. D. (1994) J. Biomol. NMR 4, 171-180.
38. Wishart, D. S., Sykes, B. D. & Richards, F. M. (1991) J. Mol. Biol. 222, 311-333.
39. Levit, M. & Chothia, C. (1976) Nature 261, 552-558.
40. Orengo, C. A. & Thornton, J. (1994) Curr. Biol. 1, 105-120.
41. Kabsch, W. & Sander, C. (1983) Biopolymers 22, 2577-2637.
42. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.