Binding regularities in complexes of transcription factors with operator dna: Homeodomain family

Journal of Biomolecular Structure and Dynamics

Volumn 26, Issue 6, 2009, Pages 687-700

  Chirgadze, Yu N ^a   Zheltukhin, E I ^b   Polozov, R V ^b   Sivozhelezov, V S ^c,d   Ivanov, V V ^e  

^a INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^b INSTITUTE OF THEORETICAL AND EXPERIMENTAL BIOPHYSICS   (Russian Federation)

^c INSTITUTE OF CELL BIOPHYSICS   (Russian Federation)

^d UNIVERSITY OF GENOA   (Italy)

^e JOINT INSTITUTE FOR NUCLEAR RESEARCH   (Russian Federation)

Author keywords

Binding interface; Homeodomain; Invariant contacts; Protein DNA recognition; Transcription factor; Variable contacts

Indexed keywords

ADENINE; ASPARAGINE; HOMEODOMAIN PROTEIN; TRANSCRIPTION FACTOR;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; DNA PROTEIN COMPLEX; HYDROGEN BOND; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN FAMILY; PROTEIN MOTIF; PROTEIN STRUCTURE;

EID: 67249105776     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2009.10507282     Document Type: Article

References (37)

1. Luscombe, N. M., Laskowski, R. A., and Thornton, J. M., 1997. Nucleic Acids Res, 25:4940–4945.
2. Luscombe, N. M., Laskowski, R. A., and Thornton, J. M., 2001. Nucleic Acids Res, 29:2860–2874.
3. Jones, S., Heyningen, P., Berman, H. M., and Thornton, J. M., 1999. J Mol Biol, 287:877–896.
4. Jones, S., Shanahan, H. P., Berman, H. M., and Thornton, J. M., 2003. Nucleic Acids Res, 31:7189–7198.
5. Shanahan, H. P., Garcia, M. A., Jones, S., and Thornton, J. M., 2004. Nucleic Acids Res, 32:4732–4741.
6. Tsuchiya, Y., Kinoshita, K., and Nakamura, H., 2004. Proteins, 55:885–894.
7. Liu, Z., Mao, F., Guo, J., Yan, B., Wang, P., Qu, Y., and Xu, Y., 2005. Nucleic Acids Res, 33:546–558.
8. Szilagyi, A., and Skolnick, J., 2006. J Mol Biol, 358:922–933.
9. Mandel-Gutfreund, Y., Schueler, O., and Margalit, H., 1995. J Mol Biol, 253:370–382.
10. Chirgadze, Y. N., and Tabolina, O. Y., 1996. Protein Eng, 9:745–754.
11. Chirgadze, Y. N., and Larionoiva, E. A., 1999. Protein Eng, 12:101–105.
12. Chirgadze, Y. N., and Larionoiva, E. A., 2001. Mol Biol (Moscow), 35:709–716.
13. Chirgadze, Y. N., and Larionoiva, E. A., 2003. Mol Biol (Moscow), 37:232–239.
14. Chirgadze, Y. N., and Larionoiva, E. A., 2005. Mol Biol (Moscow), 39:892–905.
15. Pabo, C. O., and Nekludova, L., 2000. J Mol Biol, 301:597–624.
16. Cappen, C., 2005. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 1. 1. Genetic Variation and Evolution., DOI:10.1002/047001153X.g101209 http://mrw.interscience.wiley.com/ggpb/articles/g101209/frame.html
17. Gehring, W. J., Qian, Y. Q., Billeter, M., Furukubo-Tokunaga, K., Schier, A. F., Resendez-Perez, D., Affolter, M., Otting, G., and Wüthrich, K., 1994. Cell, 78:211–223.
18. Ledneva, R. K., Alexseevskii, A. V., Vasiliev, S. A., Spirin, S. A., and Karyagina, A. S., 2001. Mol Biol (Moscow), 35:764–777.
19. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C., 1995. J Mol Biol, 247:536–540.
20. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E., 2000. Nucleic Acids Res, 28:235–242.
21. Fraenkel, E., Rould, M. A., Chambers, K. A., and Pabo, C. O., 1998. J Mol Biol, 284:351–361.
22. Clarke, N. D., Kissinger, C. R., Desjarlais, J., Gilliland, G. L., and Pabo, C. O., 1994. Protein Sci, 3:1779–1787.
23. Zhao, X., Huang, X. R., and Sun, C. C., 2006. J Struct Biol, 155:426–437.
24. Jacobson, E. M., Li, P., Leon-del-Rio, A., Rosenfeld, M. G., and Aggarwal, A. K., 1997. Genes Dev, 11:198–212.
25. Hovde, S., Abate-Shen, C., and Geiger, J. H., 2001. Biochemistry, 40:12013–12021.
26. Fraenkel, E., and Pabo, C. O., 1998. Nat Struct Biol, 5:692–697.
27. Wilson, D. S., Guenther, B., Desplan, C., and Kuriyan, J., 1995. Cell, 82:709–719.
28. Ohlendorf, D. H., and Matthew, J. B., 1985. Adv Biophys, 20:137–151.
29. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., and Demeny, T., 1992. Biophys J, 63:751–759.
30. Polozov, R. V., Montrel, M., Ivanov, V. V., Melnikov, Y., and Sivozhelezov, V. S., 2006. Biochemistry, 45:4481–4490.
31. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A., 2004. J Comput Chem, 25:1157–1174.
32. Netz, R. R., and Orland, H., 2003. Eur Phys J E Soft Matter, 11:301–311.
33. Felder, C. E., Prilusky, J., Silman, I., and Sussman, J. L., 2007. Nucleic Acids Res, 35:W512–W521.
34. Fogolari, F., Elcock, A. H., Esposito, G., Viglino, P., Briggs, J. M., and McCammon, J. A., 1997. J Mol Biol, 267:368–381.
35. Billeter, M., Qian, Y. Q., Otting, G., Müller, M., Gehring, W., and Wüthrich, K., 1993. J Mol Biol, 234:1084–1093.
36. Schwabe, J. W., 1997. Curr Opin Struct Biol, 7:126–134.
37. Suzuki, M., and Yagi, N., 1994. Proc Natl Acad Sci USA, 91:12357–12361.