Evaluation of methods for measuring amino acid hydrophobicities and interactions

Journal of Chromatography A

Volumn 1000, Issue 1-2, 2003, Pages 637-655

  Biswas, Kallol M ^a   DeVido, Daniel R ^a   Dorsey, John G ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Amino acids; Hydrophobicity; Reviews

Indexed keywords

AMINO ACIDS; HYDROPHOBICITY; PROTEINS;

BIOMOLECULES;

CHROMATOGRAPHIC ANALYSIS;

AMINO ACID;

AMINO ACID ANALYSIS; ANALYTIC METHOD; BIOCHEMISTRY; CHROMATOGRAPHY; HYDROPHOBICITY; MOLECULE; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW;

EID: 0038777517     PISSN: 00219673     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0021-9673(03)00182-1     Document Type: Review

References (100)

1. Burley S.K., Petsko G.A. FEBS Lett. 203:1986;139.
2. Burley S.K., Petsko G.A. Science. 229:1985;23.
3. Kauzmann W. Adv. Protein Chem. 14:1959;1.
4. Tanford C. J. Phys. Chem. 84:1962;4240.
5. Dill K.A. Biochemistry. 29:1990;7133.
6. Dill K.A. Science. 250:1990;297.
7. Southall N.T., Dill K.A., Haymet A.D.J. J. Phys. Chem. B. 106:2002;521.
8. Tanford C. The Hydrophobic Effect: Formation of Micelles and Biological Membranes. 1980;Wiley, New York.
9. Gill S.J., Nichols N.F., Wadso I. J. Chem. Thermodynamics. 8:1976;445.
10. Cole L.A., Dorsey J.G., Dill K.A. Anal. Chem. 64:1992;1324.
11. Honig B., Yang A.-S. Adv. Protein Chem. 46:1995;27.
12. Rose G.D., Gierasch L.M., Smith J.A. Adv. Protein Chem. 37:1985;1.
13. Hopp T.P. J. Immunol. Methods. 88:1986;1.
14. Cornette J.L., Cease B.K., Margalit H., Spouge J.L., Berzofsky J.A., DeLisi C. J. Mol. Biol. 195:1987;659.
15. Degli Espositi M., Crimi M., Venturoli G. Eur. J. Biochem. 190:1990;207.
16. Rodionov M.A., Galaktionov S.G. Mol. Biol. 36:1992;777.
17. Rose G.D., Wolfenden R. Annu. Rev. Biomol. Struct. 22:1993;381.
18. Nozaki Y., Tanford C. J. Biol. Chem. 246:1971;2211.
19. Yunger L.M., Cramer R.D.I. Mol. Pharm. 20:1981;602.
20. Fauchere J.L., Pliska V. Eur. J. Med. Chem. 18:1983;369.
21. Lawson E.Q., Sadler A.J., Harmatz D., Brandau D.T., Micanovic R., MacElroy R.D., Middaugh C.R. J. Biol. Chem. 259:1984;2910.
22. Damadoran S., Song K.B. J. Biol. Chem. 261:1986;7220.
23. Fendler J.H., Nome F., Nagyvary J. J. Mol. Evol. 6:1975;215.
24. Leodidas E.B., Hatton A.T. J. Phys. Chem. 94:1990;6411.
25. Wolfenden R., Andersson L., Cullis P.M., Southgate C.C.B. Biochemistry. 20:1981;849.
26. Sharp K.A., Nicholls A., Friedman R., Honig B. Biochemistry. 30:1991;9686.
27. Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. Science. 229:1985;834.
28. Radzicka A., Wolfenden R. Biochemistry. 27:1988;1663.
29. Rekker R.F. The Hydrophobic Fragmental Constant. 1977;Elsevier, New York.
30. Abraham D.J., Leo A.J. Proteins Struct. Funct. Genet. 2:1987;130.
31. Hansch C., Leo A.J. Substituent Constants for Correlation Analysis in Chemistry and Biology. 1979;1 Wiley, New York.
32. Black S.D., Mould D.R. Anal. Biochem. 193:1991;72.
33. Zaslavsky B.Y., Mestechkina N.M., Miheeva L.M., Rogozhin S.V. J. Chromatogr. 240:1982;21.
34. Ben-Naim A. Biopolymers. 29:1990;567.
35. Chothia C. J. Mol. Biol. 105:1976;1.
36. Roseman M.A. J. Mol. Biol. 200:1988;513.
37. Karplus P.A. Protein Sci. 6:1997;1302.
38. De Young L.R., Dill K.A. J. Phys. Chem. 94:1990;801.
39. Ben-Naim A. J. Chem. Phys. 107:1997;3698.
40. Lee B., Richards F.M. J. Mol. Biol. 55:1971;379.
41. Chothia C. Nature. 248:1974;338.
42. Meirovitch H., Rackovsky S., Scheraga H.A. Macromolecules. 13:1990;1398.
43. Wertz D.H., Scheraga H.A. Macromolecules. 11:1978;9.
44. Manavalan P., Ponnuswamy P.K. Nature. 275:1978;673.
45. Janin J. Science. 277:1979;491.
46. Guy H.R. Biophys. J. 47:1985;61.
47. Miller S., Janin J., Lesk A.M., Chothia C. J. Mol. Biol. 196:1987;641.
48. Kyte J., Doolittle R.F. J. Mol. Biol. 157:1982;105.
49. Eisenberg D., McLachlan A.D. Nature. 319:1986;199.
50. Matsumura M., Becktel W.J., Matthews B.W. Nature. 334:1988;406.
51. Hodges R.S., Shu B.-Y., Zhou N.E., Mant C.T. J. Chromatogr. A. 676:1994;3.
52. Aboderin A.A. Int. J. Biochem. 2:1971;537.
53. Pliska V., Schmidt M., Fauchere J.L. J. Chromatogr. 216:1981;79.
54. Gehas J., Wetlaufer D.B. J. Chromatogr. 511:1990;123.
55. Meek J.L. Proc. Natl. Acad. Sci. USA. 77:1980;1632.
56. Valko K., Bevan C., Reynolds D. Anal. Chem. 69:1997;2022.
57. Plass M., Valko K., Abraham M.H. J. Chromatogr. A. 803:1998;51-60.
58. Cohen K.A., Dolan J.W., Grillo S.A. J. Chromatogr. 316:1984;359.
59. Guo D., Mant C.T., Taneja A.K., Hodges R.S. J. Chromatogr. 359:1986;519.
60. Parker J.M.R., Guo D., Hodges R.S. Biochemistry. 25:1986;5425.
61. Jinno K., Tanigawa E. Chromatographia. 25:1988;613.
62. Sasagawa T., Okuyama T., Teller D.C. J. Chromatogr. 240:1982;329.
63. Mant C.T., Zhou N.E., Hodges R.S. J. Chromatogr. 476:1989;363.
64. Rothemund S., Krause E., Ehrlich A., Bienert M., Glusa E., Verhallen P. J. Chromatogr. 661:1994;77.
65. Wilce M.J.C., Aguilar M.I., Hearn M.T.W. Anal. Chem. 67:1995;1210.
66. DeVido D.R., Dorsey J.G., Chan H.S., Dill K.A. J. Phys. Chem. B. 102:1998;7272.
67. Yoshida T. J. Chromatogr A. 808:1998;105.
68. Silva M.F., Chipre L.F., Raba J., Luco J.M. Chromatographia. 53:2001;392.
69. Mant C.T., Hodges R.S. J. Chromatogr. A. 972:2002;45.
70. Mant C.T., Hodges R.S. J. Chromatogr. A. 972:2002;61.
71. Shortle D. J. Biol. Chem. 264:1989;5315.
72. Hecht M.H., Sturtevant J.M., Sauer R.T. Proc. Natl. Acad. Sci. USA. 81:1984;5685.
73. Yutani K., Ogasahara K., Tsujita T., Sugino Y. Proc. Natl. Acad. Sci. USA. 84:1987;4441.
74. Bowler B.E., May K., Zaragoza T., York P., Dong A. Biochemistry. 32:1993;183.
75. Takano K., Yutani K. Protein Eng. 14:2001;525.
76. Mendel D., Ellman J.A., Chang Z., Veenstra D.L., Kollman P.A., Schultz P.G. Science. 256:1992;1798.
77. Bull H.B., Breese K. Arch. Biochem. Biophys. 161:1974;665.
78. Makhatadze G.I., Privalov P.L. J. Mol. Biol. 213:1990;375.
79. Urry D.W., Luan C.H., Parker T.M., Gowda D.C., Prasad K.U., Reid M.C., Safavy A. J. Am. Chem. Soc. 113:1991;4346.
80. Luan C.H., Parker T.M., Gowda D.C., Urry D.W. Biopolymers. 32:1992;1251.
81. Baldwin R.L. Proc. Natl. Acad. Sci. USA. 83:1986;8069.
82. Palliser C.C., Parry D.A.D. Proteins Struct. Funct. Genet. 42:2001;243.
83. Trinquier G., Sanejouand Y.-H. Protein Eng. 11:1998;153.
84. Cooper A. Curr. Opin. Chem. Biol. 3:1999;557.
85. Dill K.A. J Biol. Chem. 272:1997;701.
86. Tanaka S., Scheraga H.A. Macromolecules. 9:1976;945.
87. Pochapsky T.C., Pereira de Araujo A.F., Joughin B. Biophys. J. 76:1999;2319.
88. Ben-Naim A. J. Chem. Phys. 107:1997;3698.
89. Thomas P.D., Dill K.A. J. Mol. Biol. 257:1996;457.
90. Palecz B. J. Am. Chem. Soc. 124:2002;6003.
91. Ringo M.C., Evans C.E. Anal. Chem. 70:1998;315A.
92. Lin F.-Y., Chen W.-Y., Hearn M.T.W. J. Mol Recogn. 15:2002;55.
93. Cserhati T., Szogyi M. J. Chromatogr. 355:1986;211.
94. Cserhati T., Szogyi M. J. Chromatogr. 434:1988;455.
95. Vailaya A., Horvath Cs. Ind. Eng. Chem. Res. 35:1996;2964.
96. Peyrin E., Guillaume Y.C., Guinchard C. Anal. Chem. 69:1997;4979.
97. Basiuk V.A., Gromovoy T.Y. Coll. Surf. A. 118:1996;127.
98. Pochapsky T.C., Gopen Q. Protein Sci. 1:1992;786.
99. Wimley W.C., White S.H. Biochemistry. 39:2000;4432.
100. Wimley W.C. Protein Sci. 11:2002;301.