Designing the hydrophobic core of Thermus flavus malate dehydrogenase based on side-chain packing

Protein Engineering

Volumn 11, Issue 1, 1998, Pages 47-52

  Kono, Hidetoshi ^a,b   Nishiyama, Makoto ^a   Tanokura, Masaru ^a   Doi, Junta ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN TSUKUBA INSTITUTE   (Japan)

Author keywords

Hydrophobic core; Mutant stability; Side chain packing

Indexed keywords

GUANIDINE; MALATE DEHYDROGENASE;

ARTICLE; CIRCULAR DICHROISM; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ENGINEERING; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMOPHILIC BACTERIUM;

BACTERIA (MICROORGANISMS); THERMUS THERMOPHILUS;

EID: 0031887256     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/11.1.47     Document Type: Article

References (56)

1. Baldwin, E. and Matthews, B.W. (1994) Curr. Opin. Struct. Biol., 5, 396-402.
2. Baldwin, E., Xu, J., Hajiseyedjavadi, O., Baase, W.A. and Matthews, B.W. (1996) J. Mol. Biol., 259, 542-559.
3. Basch, P.A., Singh, U.C., Langridge, R. and Kollman, P.A. (1987) Science, 236, 564-568.
4. Buckle, A.M., Henrick, K. and Fersht, A.F. (1993) J. Mol. Biol., 234, 847-860.
5. Buckle, A.M., Cramer, P. and Fersht, A.F. (1996) Biochemistry, 35, 4298-4305.
6. Cardle, L. and Dufton, M.J. (1994) Protein Engng., 7, 1423-1431.
7. Chothia, C. (1974) Nature, 248, 338-339.
8. Dahiyat, B.I. and Mayo, S.L. (1996) Protein Sci., 5, 895-903.
9. Dang, L.X., Merz, K.M.,Jr and Kollman, P.A. (1989) J. Am. Chem. Soc., 111, 8505-8508.
10. Daopin, S., Alber, T., Baase, W.A., Wozniak, J.A. and Matthews, B.W. (1991) J. Mol. Biol., 221, 647-667.
11. DeFilippis, V., Sander, C. and Vriend, G. (1994) Protein Engng., 7, 1203-1208.
12. Desjarlasi, J.R. and Handel, T.M. (1995) Protein Sci., 4, 2006-2018.
13. Eijsink, V.G., Dijkstra, B.W., Vriend, G., van der Zee, J.R., Veltman, O.R., van der Vinne, B., van den Burg, B., Kempe, S. and Venema, G. (1992) Protein Engng., 5, 421-426.
14. Eriksson, A.E., Baase, W.A., Zhang, X.J., Heinz, D.W., Blaber, M., Baldwin, E.P. and Matthews, B.W. (1992) Science, 255, 178-183.
15. Fontana, A. (1991) Curr. Opin. Biotech., 2, 551-560.
16. Garvey, E.P. and Matthews, C.R. (1989) Biochemistry, 28, 2083-2093.
17. Hellinga, H.W. and Richards, F.M. (1994) Proc. Natl Acad. Sci., USA, 91, 5803-5807.
18. Herold, M. and Kirschner, K. (1990) Biochemistry, 29, 1907-1913.
19. Honda, N., Komeiji, Y., Uebayasi, M. and Yamato, I. (1996) Proteins: Struct. Funct. Genet., 26, 459-464.
20. Hurley, J.H., Baase, W.A. and Matthews, B.W. (1992) J. Mol. Biol.,224, 1143-1159.
21. Ishikawa, K., Nakamura, H., Morikawa, K. and Kanaya, S. (1993) Biochemistry, 32, 6171-6178.
22. Jackson, S.E., Moracci, M., elMasry, N., Johnson, C.M. and Fersht, A.R. (1993) Biochemistry, 32, 11259-11269.
23. Karpusas, M., Baase, W.A., Matsumura, M. and Matthews, B.W. (1989) Proc. Natl Acad. Sci., USA, 86, 8237-8241.
24. Kellis, J.T.J., Nyberg, K. and Fersht, A.R. (1989) Biochemistry, 28, 4914-4922.
25. Kelly, C.A., Nishiyama, M., Ohnishi, Y., Beppu, T. and Birktoft, J.J. (1993) Biochemistry, 32, 3913-3922.
26. Kim, K.S., Tao, F., Fuchs, J., Danishefsky, A.T., Housset, D., Wlodawer, A. and Woodward, C. (1993) Protein Sci., 2, 588-5896.
27. Kono, H. and Doi, J. (1994) Proteins: Struct. Funct. Genet., 19, 244-255.
28. Kono, H. and Doi, J. (1996) J. Comp. Chem., 17, 1667-1683.
29. Kraulis, P. (1991) J. Appt. Cryst., 24, 946-950.
30. Kunkel, T.A. (1985) Proc. Natl Acad. Sci. USA, 82, 488-492.
31. Lazar, G.A., Desjarlais, J.R. and Handel, T.M. (1997) Protein Sci., 6, 1167-1178.
32. Lee, C. (1994) J. Mol. Biol., 236, 918-939.
33. Lee, C. and Levitt, M. (1991) Nature, 352, 448-451.
34. Lim, W.A. and Sauer, R.T. (1991) J. Mol. Biol., 219, 359-376.
35. Lim, W.A. and Richards, F.M. (1994) Q. Rev. Biophys., 26, 423-498.
36. Lim, W.A., Farruggio, D.C. and Sauer, R.T. (1992) Biochemistry, 31, 423-498.
37. Messing, J. and Vieira, J. (1982) Gene, 19, 269-276.
38. Miller, S., Janin, J., Lesk, A.M. and Chothia, C. (1987) J. Mol. Biol., 196, 641-656.
39. Ooi, T., Oobatake, M., Memethy, G. and Scheraga, H.A. (1987) Proc. Natl Acad. Sci. USA, 84, 3086-3890.
40. Otzen, D.E., Rheinnecker, M. and Fersht, A.R. (1995) Biochemistry, 34, 13051-13058.
41. Pace, C.N. (1992) J. Mol. Biol., 226, 29-35.
42. Perrot, G., Cheng, B., Gibson, K.D., Vila, J., Palmer, K.A., Nayeem, A., Maigret, B. and Scheraga, H.A. (1992) J. Comp. Chem, 13, 1-11.
43. Ponder, J.W. and Richards, F.M. (1987) J. Mol. Biol., 193, 775-791.
44. Ponnuswamy, P.K. and Gromiha, M.M. (1994) J. Theor. Biol., 166, 63-74.
45. Sandberg, W.S. and Terwilliger, T.C. (1989) Science, 245, 54-57.
46. Sanger, F., Nicklen, N. and Coulson, A.R. (1977) Proc. Natl Acad. Sci. USA, 74, 5463-5467.
47. Serrano, L., Kellis, J.T.J., Cann, P., Matouschek, A. and Fersht, A.R. (1992) J. Mol. Biol., 224, 783-804.
48. Shortle, D. and Meeker, A.K. (1986) Proteins: Struct. Funct. Genet., 1, 81-89.
49. Shortle, D., Stites, W.E. and Meeker, A.K. (1990) Biochemistry, 29, 8033-8041.
50. Simonson, T. and Brünger, A.T. (1992) Biochemistry, 31, 8661-8674.
51. Sternberg, M.J.E. and Chickos, J.S. (1994) Protein Engng., 7, 149-155.
52. Tidor, B. and Karplus, M. (1991) Biochemistry, 30, 3127-3228.
53. Weiner, J.S., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S.,Jr. and Weiner, P. (1984) J. Am. Chem. Soc., 106, 765-784.
54. Wilson, C., Mace, J.E. and Agard, D.A. (1991) J. Mol. Biol.,220, 495-506.
55. Wynn, R. and Richards, F.M. (1993) Protein Sci., 2, 395-403.
56. Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y. (1987) Proc. Natl Acad. Sci. USA, 84, 4441-4444.