Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition

Journal of Biomolecular Structure and Dynamics

Volumn 17, Issue 1, 1999, Pages 133-155

  Berezovsky, Igor N ^a   Namiot, Vladimir A ^b   Tumanyan, Vladimir G ^a   Esipova, Natalia G ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN;

ALGORITHM; ARTICLE; GEOMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; X RAY ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0032845660     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1999.10508347     Document Type: Article

References (72)

1. Drenth, J., Jansonius, N., Koekoek, R., Swen, H., and Wolthers, B., 1968. Nature, 218:929–932.
2. Porter, R. R., 1959. Biochem. J., 73:119–126.
3. Richardson, J. S., 1981. Adv. Protein Chem., 34:246–253.
4. Campbell, I. D., and Baron, M., 1991. Philos. Trans. R. Soc. Lond. (Biol.), 332:165–170.
5. Baron, M., and Campbell, I. D., 1991. Trends Biochem. Sci., 16:13–17.
6. Go, M., 1983. Proc. Nat. Acad., Sci. USA, 80:1964–1968.
7. Go, M., Nosaka, M., and Tomoda, S. H., 1993. In Methods in Protein Sequence Analysis Edited by:Imahori, K., and Sakiyama, F., 229–232. New York:Plenum Press.
8. Noguti, T., Sakakibara, H., and Go, M., 1993. PROTEINS:Structure, Function and Genetics, 16:357–363.
9. Yanagawa, H., Yoshida, K., Torigoe, C., Park, J.-S., Sata, K., Shirai, T., and Go, M., 1993. J. Biol. Chem., 268:5861–5865.
10. Yoshida, K., Shibata, T., Masai, J., Sata, K., Noguti, T., Go, M., and Yanagawa, H., 1993. Biochemistry, 32:2162–2166.
11. Patthy, L., 1994. Curr. Opin. Struct. Biol., 4:383–392.
12. Doolittle, R. F., 1995. Annu. Rev. Biochem., 64:287–314.
13. Bork, P., 1992. Curr. Opin. Struct. Biol., 2:413–412.
14. Wetlaufer, D. B., 1973. Proc. Nat. Acad. Sci. USA, 70:697–701.
15. Russell, D. B., 1994. Protein Engineering, 7:1407–1411.
16. Phillips, D. C., 1970. In British Biochemistry, Past and Present 11–28. London:Academic Press.
17. Nishikawa, K., and Ooi, T., 1972. J. Phys. Soc. Jp., 32:1338–1347.
18. Nishikawa, K., Ooi, T., Isogai, Y., and Saito, N., 1972. J. Phys. Soc. Jp., 32:1331–1337.
19. Ooi, T., and Nishikawa, K., 1973. In Conformation of Biological Molecules and Polymers Edited by:Bergmann, E., and Pullman, B., 173–187. New York:Academic Press.
20. Rao, S. T., and Rossmann, M. G., 1973. J. Mol. Biol., 76:241–256.
21. Chotia, C., 1975. Nature, 254:304–308.
22. Chotia, C., 1976. J. Mol. Biol., 105:1–14.
23. Rashin, A. A., 1981. Nature, 291:85–87.
24. Moult, J., and Unger, R., 1991. Biochemistry, 30:3816–3824.
25. Zehfus, M. H., and Rose, G. D., 1986. Biochemistry, 25:5759–5765.
26. Richards, F. M., 1977. Annu. Rev. Biophys. Bioeng., 6:151–176.
27. Wodak, S., and Janin, J., 1978. J. Mol. Biol., 124:323–342.
28. Lesk, A. M., and Rose, G. D., 1981. Proc. Nat. Acad. Sci. USA, 78:4304–4308.
29. Zehfus, M. H., 1993. PROTEINS:Structure, Function and Genetics, 16:293–300.
30. Zehfus, M. H., 1994. Protein Engineering, 7:335–340.
31. Zehfus, M. H., 1997. Protein Science, 6:1210–1219.
32. Janin, J., and Wodak, S., 1983. Prog. Biophys. Mol. Biol., 42:21–78.
33. Lee, B. K., and Richards, F. M., 1971. J. Mol. Biol., 55:379–400.
34. Chotia, C., 1974. Nature, 248:338–339.
35. Chotia, C., and Janin, J., 1975. Nature, 256:705–708.
36. Richmond, T. J., and Richards, F. M., 1978. J. Mol. Biol., 119:537–555.
37. Holm, L., and Sander, C., 1994. PROTEINS:Structure, Function and Genetics, 19:256–268.
38. Sander, C., 1981. In Structural Aspects of Recognition and Assembly in Biological Macromolecules. Edited by:Balaban, M., 183–195. Rehovot:Balaban ISS.
39. Rashin, A. A., 1976. Nature, 262:325–326.
40. Segawa, S., and Richards, F. M., 1988. Biopolymers, 27:23–40.
41. Nichols, W. L., Rose, G. D., Eyck, L. F.T., and Zimm, B. H., 1995. PROTEINS:Structure, Function and Genetics, 23:38–48.
42. Crippen, G. M., 1987. J. Mol. Biol., 126:315–332.
43. Rose, G. D., 1979. J. Mol. Biol., 134:447–470.
44. Siddiqui, A. S., and Barton, G. J., 1995. Protein Science, 4:872–884.
45. Islam, S. A., Luo, J., and Sternberg, M. J.E., 1995. Protein Engineering, 8:513–525.
46. Murzin, A., Brenner, S. E., Hubbard, T. J.P., and Chotia, C., 1995. J. Mol. Biol., 247:536–540.
47. Hubbard, T. J.P., Ailey, B., Brenner, S. E., Murzin, A. G., and Chotia, C., 1999. Nucleic Acids Res., 27:254–256.
48. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B., and Thornton, J. M., 1997. Structure, 5:1093–1108.
49. Orengo, C. A., Pearl, F. M.G., Bray, J. E., Todd, A. E., Martin, A. C., Lo Conte, L., and Thornton, J. M., 1999. Nucleic Acids Res., 27:275–279.
50. Prostasevich, I. I., Platonov, A. L., Pavlovsky, A. G., and Esipova, N. G., 1987. J. Biomol. Struct. Dyn., 4:885–893.
51. Dill, K. A., 1990. Biochemistry, 29:7133–7155.
52. Lazardis, T., Archontis, G., and Karplus, M., 1995. Adv. Prot. Chem., 47:231–306.
53. Baker, E. N., and Hubbard, R. E., 1984. Prog. Biophys. Mol. Biol., 44:97–179.
54. Stickle, D. F., Presta, L. G., Dill, K. A., and Rose, G. D., 1992. J. Miol. Biol., 226:1143–1159.
55. Derewenda, Z. S., Lee, L., and Derewenda, U., 1995. J. Mol. Biol., 252:248–262.
56. Barlow, D. J., and Thornton, J. M., 1983. J. Mol. Biol., 168:867–885.
57. Hendsch, Z. S., and Tidor, B., 1994. Protein Science, 3:211–226.
58. Horovitz, A., Serrano, L., Avron, B., Bycroft, M., and Fersht, A. R., 1990. J. Mol. Biol., 216:1031–1044.
59. Sali, D., Bycroft, M., and Fersht, A. R., 1991. J. Mol. Biol., 220:779–788.
60. Honig, B., and Yang, A. S., 1995. Adv. Prot. Chem., 46:27–58.
61. Makhatadze, G. I., and Privalov, P. L., 1995. Adv. Prot. Chem., 47:307–425.
62. Pace, C. N., Shirley, B. A., McNutt, M., and Gajiwala, K., 1996. FASEB J., 10:75–83.
63. Myers, J. K., and Pace, C. N., 1996. Biophysical J., 71:2033–2039.
64. Dunfield, L. G., Burgess, A. W., and Sheraga, H. A., 1978. J. Phys. Chem., 24:2609–2616.
65. Nemethy, G., Pottle, M. S., and Sheraga, H. A., 1983. J. Phys. Chem., 87:1883–1887.
66. Berezovskii, I. N., and Tumanyan, V. G., 1995. Biophysics (Biofizika, Moscow), 40:1181–1187.
67. Berezovskii, I. N., Esipova, N. G., and Tumanyan, V. G., 1997. Biophysics (Biofizika, Moscow), 42:557–565.
68. Berezovsky, I. N., Tumanyan, V. G., and Esipova, N. G., 1997. FEBS Letters, 418:43–46.
69. Jones, S., Stewart, M., Micjie, A., Swindells, M. B., Orengo, C., and Thornton, J. M., 1998. Protein Science, 7:233–242.
70. Barash, Yu. S., 1988. In Van der Waals Forces 29Moscow:Nauka.
71. Casimir, H. B.G., and Polder, D., 1948. Phys. Rev., 73:360–372.
72. Lifshits, E. M., and Pitaevsky, L. P., 1978. “ In Statistical Physics, Part 2. ”. In The Theory of Condensed Matter 370Moscow:Nauka.