Quantitative structure-function and structure-stability relationships of purposely modified proteins

Protein Engineering

Volumn 11, Issue 1, 1998, Pages 21-30

  Damborský, Jiří ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

Author keywords

AAindex; Haloalkane dehalogenase; Multivariate statistics; Phage T4 lysozyme; Point mutants; Prediction; Subtilisin; Tryptophan synthase

Indexed keywords

PROTEIN; SUBTILISIN; TRYPTOPHAN SYNTHASE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACTERIOPHAGE T4; DATA ANALYSIS; DATA BASE; GENETIC ENGINEERING; MOLECULAR MODEL; MULTIVARIATE ANALYSIS; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN STABILITY; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION;

EID: 0031888694     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/11.1.21     Document Type: Article

References (56)

1. Alber, T., Dao-pin, S., Wilson, K., Wozniak, J.A., Cook, S.P. and Matthews, B.W. (1987) Nature, 330, 41-46.
2. Argos, P. and Palau, J. (1982) Int. J. Peptide Protein Res., 19, 380-393.
3. Asami, T., Kishida, M., Mabuchi, T., Kim, B.T., Ichinose, K. and Yoshida, S. (1995) J. Plant Physiol., 145, 39-44.
4. Atkins, W.M. and Sligar, S.G. (1991) Curr. Opin. Struct. Biol. 1, 611-616.
5. Baroni, M., Costantino, G., Cruciani, G., Riganelli, D., Valigi, R. and Clementi, S. (1993) Quant. Struct. Act. Relat., 12, 9-20.
6. Bigelow, C.C. (1967) J. Theor. Biol., 16. 187-211.
7. Branden. C. and Tooze, J. (eds) (1991) Introduction to Protein Structure. Garland Publishing, New York.
8. Bull, H.B. and Breese, K. (1974) Arch. Biochem. Biophys., 161, 665-670.
9. Charton, M. and Charton, B.I. (1982) J. Theor. Biol., 99, 629-644.
10. Chothia, C. (1975) Nature, 254, 304-308.
11. Cid, H., Bunster, M., Canales, M. and Gazitua, F. (1992) Protein Engng., 5, 373-375.
12. Damborský, J. (1997) Quant. Struct. Act. Relat., 16, 126-135.
13. Damborský, J., Kuty, M., Nemec, M. and Koca, J. (1997) J. Chem. Inf. Comp. Sci., 37, 562-568.
14. Degli Esposti, M., Crimi, M. and Venturoli, G., (1990) Eur. J. Biochem., 190, 207-219.
15. Estell, D.A., Graycar, T.P. and Wells, J.A. (1985) J. Biol. Chem., 260, 6518-6521.
16. Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V. (1988) Int. J. Peptide Protein Res., 32, 269-278.
17. Fersht, A.R. (1987) In Oxender, D.L. and Fox, C.F. (eds), Protein Engineering. Alan R. Liss, New York, pp. 221-224.
18. Feshrt, A.R., Leatherbarrow, R.J. and Wells, T.N.C. (1987) Biochemistry, 26, 6030-6038.
19. Fersht, A.R. and Serrano, L. (1993) Curr. Opin. Struct. Biol., 3, 75-83.
20. Gerlt, J.A. (1994) Curr. Opin. Struct. Biol., 4, 593-600.
21. Goldsack, D.E. and Chalifoux, R.C. (1973) J. Theor. Biol., 39, 645-651.
22. Grantham, R. (1974) Science, 185, 862-864.
23. Jones, D.D. (1975) J. Theor. Biol., 50, 167-183.
24. Karplus, P.A. and Schultz, G.E. (1985) Naturwissenschaften, 72, 212-213.
25. Krigbaum, W.R. and Komoriya, A. (1979) Biochim. Biophys. Acta, 576, 204-228.
26. Krigbaum, W.R. and Rubin, B.H. (1971) Biochim. Biophys. Acta, 229, 368-383.
27. Kubinyi, H. (1990) J. Cancer Res. Clin. Oncol., 116, 529-537.
28. Kubinyi, H. (1994) Quant. Struct. Act. Rel., 13, 285-294.
29. Levitt, M. (1976) J. Mol. Biol., 104, 59-107.
30. Manavalan, P. and Ponnuswamy, P.K. (1978) Nature, 275, 673-674.
31. Miyazawa, S. and Jernigan, R.L. (1985) Macromolecules, 18, 534-552.
32. Nakai, K., Kidera, A. and Kanehisa, M. (1988) Protein Engng., 2, 93-100.
33. Nemeskosa, S. and Cserhati, T. (1995) J. Appl. Bacteriol., 79, 483-491.
34. Nirmalakhandan, N. and Speece, R.E. (1988) Environ. Sci. Technol., 22, 606-615.
35. Norinder, U., Karlsson, B.G., Sjolin, L., Pascher, T. and Bonander, N. (1996) Quant. Struct. Act. Relat., 15, 475-479.
36. Nozaki, Y. and Tanford, C. (1971) J. Biol. Chem., 246, 2211-2217.
37. Oobatake, M. and Ooi, T. (1977) J. Theor. Biol. 67, 567-584.
38. Oxender, D.L. and Fox, C.F. (eds) (1987) Protein Engineering. Alan R. Liss, New York.
39. Peijnenburg, W.J.G.M. and Damborský, J. (eds) (1996) Biodegradability Prediction. Kluwer Academic Publishers, Dordrecht.
40. Rackovsky, S. and Scheraga, H.A. (1977) Proc. Natl Acad. Sci. USA, 74, 5248-5251.
41. Salt, D.W., Yildiz, N., Livingstone, D.J. and Tinsley, C.J. (1992) Pestic. Sci., 36, 161-170.
42. Schanstra, J.P., Ridder, I.S., Heimeriks, G.J., Rink, R., Poelarends, G.J., Kalk, K.H., Dijkstra, B.W. and Janssen, D.B. (1996) Biochemistry, 35, 13186-13195.
43. Sneath, P.H.A. (1966) J. Theor. Biol., 12, 157-195.
44. So, S.S. and Karplus, M. (1996) J. Med. Chem., 39, 5246-5256.
45. Sweet, M.R. and Eisenberg, D. (1983) J. Mol. Biol., 171, 479-488.
46. Tomii, K. and Kanehisa, M. (1996) Protein Engng., 9, 27-36.
47. Topham, C.M., Srinivasan, N. and Blundell, T.L. (1997) Protein Engng., 10, 7-21.
48. Tumer, L., Choplin, F., Dugard, P., Hermens, J., Jaeckh, R., Marsmann, M. and Roberts, D. (1987) Toxicol. In Vitro, 1, 143-171.
49. Vasquez, M., Nemethy, G. and Scheraga, H.A. (1983) Macromolecules, 16, 1043-1049.
50. Weber, A.L. and Lacey, J.C. (1978) J. Mol. Evol., 11, 199-210.
51. Wells, J.A., Powers, D.B., Bott, R.R. et al. (1987) In Oxender, D.L. and Fox, C.F. (eds), Protein Engineering. Alan R. Liss, New York, pp. 279-287.
52. Wold, S. (1991) Quant. Struct. Act. Relat., 10, 191-193.
53. Wold, S., Johansson, E. and Cocchi, M. (1993) In Kubinyi, H. (ed.) 3D QSAR in Drug Design: Theory, Methods and Application. ESCOM, Leiden, pp. 523-550.
54. Wold, S., (1995) In van de Waterbeemd, H. (ed.) Chemometric Methods in Molecular Design. VCH, Weinheim, pp. 195-218.
55. Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. (1987) Proc. Natl Acad. Sci. USA, 84, 4441-4444.
56. Zimmerman, J.M., Eliezer, N. and Simha, R. (1968) J. Theor. Biol., 21, 170-201.