Relationship between amino acid properties and protein stability: Buried mutations

Journal of Protein Chemistry

Volumn 18, Issue 5, 1999, Pages 565-578

  Gromiha, M Michael ^a   Oobatake, Motohisa ^a,b   Kono, Hidetoshi ^a   Uedaira, Hatsuho ^a   Sarai, Akinori ^a  

^a RIKEN TSUKUBA INSTITUTE   (Japan)

^b MEIJO UNIVERSITY   (Japan)

Author keywords

Amino acid properties; Multiple regression technique; Protein mutants; Protein stability; Secondary and tertiary structures; Unfolding free energy change

Indexed keywords

BARNASE; BETA LACTAMASE; CHYMOTRYPSIN; CYTOCHROME C; DIHYDROFOLATE REDUCTASE; LYSOZYME; NUCLEASE; PHOSPHOGLYCERATE KINASE; RIBONUCLEASE; SUBTILISIN; UBIQUITIN;

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; HYDROPHOBICITY; NONHUMAN; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACIDS; MUTATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 0032863182     PISSN: 02778033     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1020603401001     Document Type: Article

References (51)

1. Bash, P. A., Singh, U. C., Langridge, R., and Kollman, P. A. (1987), Science 236, 564-568.
2. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977). J. Mol. Biol. 112, 535-542.
3. Bhaskaran, R., and Ponnuswamy, P. K. (1984). Int. J. Pept. Protein Res. 24, 180-191.
4. Chothia, C. (1976). J. Mol. Biol. 105, 1-12.
5. Chou, P. Y., and Fasman, G. D. (1978). Adv. Enzymol. 47, 45-148.
6. Damborsky, J., Bohac, M., Prokop, M., Kuty, M., and Koca, J. (1998). Protein Eng. 11, 901-907.
7. Dill, K. A. (1990). Biochemistry 29, 7133-7155.
8. Eisenberg, D., Weiss, R. M., Terwilliger, T. C., and Wilcox, W. (1982). Faraday Symp. Chem. Soc. 17, 109-120.
9. Fauchere, J.- L., and Pliska, V. (1983). Eur. J. Med. Chem. 18, 369-375.
10. Gills, D., and Rooman, M. (1996). J. Mol. Biol. 257, 1112-1126.
11. Gills, D., and Rooman, M. (1997). J. Mol. Biol. 272, 276-290.
12. Grewal, P. S. (1987). Numerical Methods of Statistical Analysis, Sterling Publishers, New Delhi.
13. Gromiha, M. M., and Ponnuswamy, P. K. (1993). J. Theor. Biol. 165, 87-100.
14. Gromiha, M. M., and Ponnuswamy, P. K. (1995). Int. J. Pept. Protein Res. 45, 225-240.
15. Gromiha, M. M., and Selvaraj, S. (1997). J. Biol. Phys. 23, 151-162.
16. Gromiha, M. M., and Selvaraj, S. (1998). Protein Eng. 11, 249-251.
17. Gromiha, M. M., and Selvaraj, S. (1999). Biophys. Chem. 77, 49-68.
18. Gromiha, M. M., An, J., Kono, H., Oobatake, M., Uedaira, H., and Sarai, A. (1999a). Nucl. Acids Res. 27, 286-288.
19. Gromiha, M. M., Oobatake, M., Kono, H., Uedaira, H., and Sarai, A. (1999b). Protein Eng. (in press).
20. Iqbal, M., and Verrall, R. E. (1988). J. Biol. Chem. 263, 4159-4165.
21. Jones, D. D. (1975). J. Theor. Biol. 50, 167-183.
22. Lee, C. (1994). J. Mol. Biol. 236, 918-939.
23. Lee, C., and Levitt, M. (1991). Nature 352, 448-451.
24. Manavalan, P., and Ponnuswamy, P. K. (1978). Nature 275, 673-674.
25. Miyazawa, S., and Jernigan, R. L. (1994). Protein Eng. 7, 1209-1220.
26. Nozaki, Y., and Tanford, C. (1971). J. Biol. Chem. 246, 2211-2217.
27. Oobatake, M., and Ooi, T. (1977). J. Theor. Biol. 67, 567-584.
28. Oobatake, M., and Ooi, T. (1993). Prog. Biophys. Mol. Biol. 59, 237-284.
29. Pace, C. N. (1990). Trends Biochem. Sci. 15, 14-17.
30. Pace, C. N., Shirely, B. A., McNutt, M., and Gajiwala, K. (1996). FASEB J. 10, 75-83.
31. Pfeil, W. (1998). Protein Stability and Folding: A Collection of Thermodynamic Data, Springer-Verlag, Heidelberg, Germany.
32. Ponnuswamy, P. K. (1993). Prog. Biophys. Mol. Biol. 59, 57-103.
33. Ponnuswamy, P. K., and Gromiha, M. M. (1993). Int. J. Pept. Protein Res. 42, 326-341.
34. Ponnuswamy, P. K., and Gromiha, M. M. (1994). J. Theor. Biol. 166, 63-74.
35. Ponnuswamy, P. K., Prabhakaran, M., and Manavalan, P. (1980). Biochim. Biophys. Acta 623, 301-316.
36. Richmond, T. J., and Richards, F. M. (1978). J. Mol. Biol. 119, 537-555.
37. Rooman, M., and Gills, D. (1998). Eur. J. Biochem. 254, 135-143.
38. Rose, G. D., and Wolfenden, R. (1993). Annu. Rev. Biophys. Biomol. Struct. 22, 381-415.
39. Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H., and Zehfus, M. H. (1985). Science 229, 834-838.
40. Saito, M. (1995). J. Phys. Chem. 99, 17043-17048.
41. Sanders, D. H., Eng, R. J., and Murph, A. F. (1985). Statistics -A Fresh Approach, 3rd ed., McGraw-Hill, New York.
42. Selvaraj, S., and Gromiha, M. M. (1998). J. Protein Chem. 17, 691-697.
43. Sober, H. A. (1970). Handbook of Biochemistry, Selected Data for Molecular Biology, 2nd ed., Chemical Rubber co., Cleveland, Ohio.
44. Sugita, Y., and Kitao, A. (1998). Biophys. J. 75, 2178-2187.
45. Sweet, R. M., and Eisenberg, D. (1983). J. Mol. Biol. 171, 479-488.
46. Tidor, B., and Karplus, M. (1991). Biochemistry 30, 3217-3228.
47. Tomii, K., and Kanehisa, M. (1996). Protein Eng. 9, 27-36.
48. Topham, C. M., Srinivasan, N., and Blundell, T. L. (1997). Protein Eng. 10, 7-21.
49. van Gunsteren, W. F., and Mark, A. E. (1992). J. Mol. Biol. 227, 389-395.
50. Yutani, K., Ogasahara, K., Tsujita, T., and Sugino, Y. (1987). Proc. Natl. Acad. Sci. USA 84, 4441-4444.
51. Zimmerman, J. M., Eliezer, N., and Simha, R. (1968). J. Theor. Biol. 21, 170-201.