Cluster analysis of amino acid indices for prediction of protein structure and function

Protein Engineering, Design and Selection

Volumn 2, Issue 2, 1988, Pages 93-100

  Nakai, Kenta ^a   Kidera, Akinori ^b   Kanehisa, Minoru ^a  

^a KYOTO UNIVERSITY   (Japan)

^b KYOTO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Amino acid index; Amino acid mutation data; Analysis; Cluster; Hydrophobicity scale

Indexed keywords

AMINO ACID; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; GENETICS; MUTATION; PROTEIN CONFORMATION; SOLUBILITY; STATISTICAL ANALYSIS;

AMINO ACIDS; DATA INTERPRETATION, STATISTICAL; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; PROTEINS; SOLUBILITY; SUPPORT, NON-U.S. GOV'T;

EID: 0024046665     PISSN: 17410126     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/2.2.93     Document Type: Article

References (87)

1. Beghin, F. and Dirkx, J. (1975) Arch. Int. Physiol. Biochem., 83, 167-168.
2. Bigelow, C.C. (1967) J. Theor. Biol., 16, 187-211.
3. Browne, C.A., Bennett, H.P.J. and Solomon, S. (1982) Anal. Biochem., 124, 201-208.
4. Bull, H.B. and Breese, K. (1974) Arch. Biochem. Biophys., 161, 665-670.
5. Burgess, A.W., Ponnuswamy, P.K. and Scheraga, H.A. (1974) hr. J. Chem., 12, 239-286.
6. Charton, M. (1981) J. Theor. Biol., 91, 115-123.
7. Charton, M. and Charton, B.I. (1982) J. Theor. Biol., 99, 629-64.
8. Chatfield, C. and Collins, A.J. (1984) Introduction to Multivariate Analysis. Chapman and Hall Ltd.
9. Chothia, C. (1975) Nature, 254, 304-308.
10. Chothia, C. (1976) J. Mol. Biol., 105, 1-14.
11. Chou, P.Y. and Fasman, G.D. (1978a) Annu. Rev. Biochem., 47, 251-275.
12. Chou, P.Y. and Fasman, G.D. (1978b) Adv. Enzymol., 47, 45-148.
13. Cohn, E.J. and Edsall, J.T. (1943) Protein, Amino Acid, and Peptides. Remhold, New York.
14. Comette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky J.A. and Delisi, C. (1987) J. Mol. Biol., 195, 659-685.
15. Crawford, J.L., Lipscomb, W.N. and Schellman, C.G. (1973) Proc. Natl. Acaa. Sci. USA, 70, 538-542.
16. Dawson, D.M. (1972) In Brock, D.J.H. and Mayo, O. (eds), The Biochemical Genetics of Man. Academic Press, New York, pp. 1-38.
17. Dayhoff, M.O. (ed.) (1972) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5.
18. Dayhoff, M.O. (ed.) (1978) Allas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, Suppl. 3.
19. Eisenberg, D. (1984) Annu. Rev. Biochem, 53, 595-623.
20. Eisenberg, D. and McLachlan, A.D. (1986) Nature, 319, 199-203.
21. Fasman, G.D. (ed.) Handbook of Biochemistry and Molecular Biology. CRC Press, Cleveland, OH, 3rd edn, Proteins Vol. 1.
22. Fauchere, J.-L. and Pliska, V. (1983) Eur. J. Med. Chem., 18, 369-375.
23. Finkelstein, A.V. and Ptitsyn, O.B. (1977) Biopolymers, 16, 497-524.
24. Gare U.P., Filliol, D. and Mandel, P. (1973) J. Chromatogr., 78, 381-391.
25. Goldsack, D.E. and Chalifoux, R.C. (1973) J. Theor. Biol, 39, 645-651.
26. Grantham, R. (1974) Science, 185, 862-864.
27. Guy, H.R. (1985) Biophys. J., 47, 61-70.
28. Hopp, T.P. and Woods, K.R. (1981) Proc. Natl. Acad Sci. USA, 78, 3824-3828.
29. Hutchens J.O. (1970) In Sober, H.A. (ed.), Handbook of Biochemistry. Chemical Rubber Co., Cleveland, OH, 2nd edn. pp. B60-B61.
30. Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga, H.A. (1980) Biopolymers, 19, 1183-1210.
31. Janin, J. (1979) Nature, 277 491-492.
32. Janin, J., Wodak, S., Levitt, M. and Maigret, B. (1978) J. Mol. Biol., 125, 357-386.
33. Jones, D.D. (1975) J. Theor. Biol., 50, 167-183.
34. Jukes, T.H., Holmquist, R. and Moise, H. (1975) Science, 189, 50-51.
35. Jungck, J.R. (1978) J. Mol. Evol., 11, 211-224.
36. Kanehisa, M. (1988) Prot. Eng., 2, 87-92.
37. Kanehisa, M.I. and Tsong, T.Y. (1980) Biopolymers, 19, 1617-1628.
38. Karplus, P.A. and Schulz, G.E. (1985) Naturwissenschaften, 72, 212-213.
39. Ktdera, A., Konishi, Y., Oka, M., Ooi, T. and Scheraga, H.A. (1985a) J. Protein Chem., 4, 23-55.
40. Kidera, A., Konishi, Y., Ooi, T. and Scheraga, H.A. (1985b) J. Protein Chem, 4, 265-297.
41. Klein, P., Kanehisa, M. and Delisi, C. (1984) Biodum. Biophys. Acta, 787, 221-226.
42. Krigbaum, W.R. and Komoriya, A. (1979) Biochem. Biophys. Acta, 576, 201-228.
43. Krigbaum, W.R. and Rubin, B.H. (1971) Biochem Biophys. Acta, 229, 368-383.
44. Kyte J. and Doolittle, R.F. (1982) J. Mol. Biol., 157, 105-132.
45. Lawson, E.Q., Sadler, A.J., Harmatz, D., Brandau, D.T., Micanovic, R. MacElroy, R.D. and Middaught, C.R. (1984) J. Biol. Chem, 259, 2910-2912.
46. Levitt, M. (1976) J. Mol. Biol., 104, 59-107.
47. Levitt, M. (1978) Biochemistry, 17, 4277-4285.
48. Lewis, P.N., Momany, F.A. and Scheraga, H.A. (1971) Proc. Natl. Acad. Sci. USA, 68, 2293-2297.
49. Lifson, S. and Sander, C. (1979) Nature, 282, 109-111.
50. Manavalan, P. and Ponnuswamy, P.K. (1978) Nature, 275, 673-674.
51. Maxfield, F.R. and Scheraga, H.A. (1976) Biochemistry, 15, 5138-5153.
52. McLachlan, A.D. (1972) J. Mol. Biol., 64, 417-437.
53. Meek, J.L. (1980) Proc. Natl. Acad. Sci. USA, 77, 1632-1636.
54. Meek, J.L. and Rossetti, Z.L. (1981) J. Chromatogr., 211, 15-28.
55. Meirovitch, H., Rackovsky, S. and Scheraga, H.A. (1980) Macromolecules, 13, 1398-1405.
56. Miyazawa, S. and Jemigan, R.L. (1985) Macromolecules, 18, 534-552.
57. Nagano, K. (1973) J. Mol. Biol., 75, 401-420.
58. Nishikawa, K. and Ooi, T. (1980) Int. J. Peptide Protein Res., 16, 19-32.
59. Nishikawa, K. and Ooi, T. (1986) J. Biochem., 100, 1043-1047.
60. Nozaki, Y. and Tanford, C. (1971) J. Biol Chem., 246, 2211-2217.
61. Oobatake, M. and Ooi, T. (1977) J. Theor. Biol., 61, 567-584.
62. Oobatake, M. and Ooi, T. (1988) J. Biol. Chem., submitted.
63. Parker J.M.R., Guo, D. and Hodges, R.S. (1986) Biochemistry, 25, 5425-5432.
64. Pliska, V., Schmidt, M. and Fauchere, J. L. (1981) J. Chromatogr., 216, 79-92.
65. Ponnuswamy, P.K., PrabhaklRan, M. and Manavalan, P. (1980) Biochem. Biophys. Acta, 623, 301-316.
66. Prabhakaran, M. and Ponnuswamy, P.K. (1982) Macromolecules, 15, 314-320.
67. Ptitsyn, O.B. and Finkelstein, A.V. (1983) Biopolymers, 22, 15-25.
68. Rackovsky, S. and Scheraga, H.A. (1977) Proc. Natl. Acad Sci. USA, 74, 5248-5251.
69. Rackovsky, S. and Scheraga, H.A. (1982) Macromolecules, 15, 1340-1346.
70. Robson, B. and Osguthorpe, D.J. (1979) J. Mol. Biol., 132, 19-51.
71. Robson, B. and Suzuki, E. (1976) J. Mol. Biol., 107, 327-356.
72. Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H. (1985) Science, 229, 834-838.
73. Sander, C. and Schulz, G.E. (1979) J. Mol. Evol., 13, 245-252.
74. Siegel, S. (1956) Nonparametric Statistics: For the Behavioral Sciences. McGraw-Hill, New York.
75. Sueki, M., Lee, S., Powers, S.P., Denton, J.B. Konishi, Y. and Scheraga, H.A. (1984) Macromolecules, 17, 148-155.
76. Sweet, R.M. and Eisenberg, D. (1983) J. Mol. Biol., 171, 479-488.
77. Tanaka, S. and Scheraga, H.A. (1977) Macromolecules, 10, 9-20.
78. Vasquez, M., Nemethy, G. and Scheraga, H.A. (1983) Macromolecules, 16, 1043-1049.
79. Veljkovic, V., Cosic, I., Dimitrijcvic, B. and Lalovic, D. (1985) IEEE Trans. Biomed. Engng., 32, 337-341.
80. Von Heijne, G. and Blomberg, C. (1979) Eur. J. Biochem., 91, 175-181.
81. Warme, P.K. and Morgan, R.S. (1978) J. Mol. Biol., 118, 289-304.
82. Weber, A.L. and Lacey J.C. Jr. (1978) J. Mol. Evol., 11, 199-210.
83. Wertz, D.H. and Scheraga, H.A. (1978) Macromolecules, 11, 9-15.
84. Woese, C.R. (1973) Natunvissenschaften, 60, 447-459.
85. Wolfenden, R., Andersson, L., Cullis, P.M. and Southgate, C.C.B. (1981) Biochemistry, 20, 849-855.
86. Yutani, K., Ogasihara, K., Tsujita, T. and Sugino, Y. (1987) Proc. Natl. Acad. Sci. USA, 84. 4441-4444.
87. Zimmerman J.M., Eliezer, N. and Simha, R. (1968) J. Theor. Biol, 21, 170-201.