Hydrophobic regions on protein surfaces

Perspectives in Drug Discovery and Design

Volumn 17, Issue , 1999, Pages 27-42

  Eisenhaber, Frank ^a,b  

^a RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Atomic solvation parameter; Docking; Hydration; Hydrophobic effect; Protein hydrophobic region

Indexed keywords

AQUEOUS SOLUTION; BINDING SITE; CONFORMATIONAL TRANSITION; HYDRATION; HYDROPHOBICITY; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; REVIEW; SOLVATION; SURFACE PROPERTY;

EID: 0033452432     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008766422140     Document Type: Review

References (105)

1. Eisenhaber, F., Persson, B. and Argos, P., Crit. Rev. Biochem. Mol. Biol., 30 (1995) 1.
2. Strynadka, N.C.J., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B.K., Kuntz, I.D., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., Zimmermann, F., Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M. and James, M.N.G., Nat. Struct. Biol., 3 (1996) 233.
3. Rupley, J.A. and Careri, G., Adv. Protein Chem., 41 (1991) 37.
4. Eisenhaber, F. and Argos, P., Protein Eng., 9 (1996) 1121.
5. Wüthrich, K., Otting, G. and Liepinsh, E., Faraday Discuss., 93 (1992) 35.
6. Levitt, M. and Park, B.H., Structure, 1 (1993) 223.
7. Steinhoff, H.-J., Kramm, B., Hess, G., Owerdieck, C. and Redhardt, A., Biophys. J., 65 (1993) 1486.
8. Phillips Jr., G.N. and Pettitt, B.M., Protein Sci., 4 (1995) 149.
9. Otting, G. and Liepinsh, E., Acc. Chem. Res., 28 (1995) 171.
10. Peemoeller, H., Yeomans, F.G., Kydon, D.W. and Sharp, A.R., Biophys. J., 49 (1986) 943.
11. Eisenmenger, F., Eisenhaber, F., Tumanyan, V.G. and Esipova, N.G., Studia Biophys., 98 (1984) 155.
12. Bryant, S.H., Proteins, 26 (1996) 172.
13. Herrmann, R.B., J. Phys. Chem., 76 (1972) 2754.
14. Reynolds, J.A., Gilbert, D.B. and Tanford, C., Proc. Natl. Acad. Sci. USA, 71 (1974) 2925.
15. Amidon, G.L., Yalkowsky, S.H., Anik, S.T. and Valvani, S.C., J. Phys. Chem., 79 (1975) 2239.
16. Valvani, S.C., Yalkowsky, S.H. and Amidon, G.L., J. Phys. Chem., 80 (1976) 829.
17. Herrmann, R.B., Proc. Natl. Acad. Sci. USA, 74 (1977) 4144.
18. Hopfinger, A.J., Macromolecules, 4 (1971) 731.
19. Hodes, Z.I., Nemethy, G. and Scheraga, H.A., Biopolymers. 18 (1979) 1565.
20. Hodes, Z.I., Nemethy, G. and Scheraga, H.A., Biopolymers, 18 (1979) 1611.
21. Kang, Y.K., Gibson, K.D., Nemethy, G. and Scheraga, H.A., J. Phys. Chem., 92 (1988) 4742.
22. Colonna-Cesari, F. and Sander, C., Biophys. J., 57 (1990) 1103.
23. Stouten, P.F.W., Frömmel, C., Nakamura, H. and Sander, C., Mol. Simul., 10 (1993) 97.
24. Luty, B.A., Wasserman, Z.R., Stouton, P.F.W., Hodge, C.N., Zacharias, M. and McCammon, J.A., J. Comput. Chem., 16 (1995) 454.
25. Augspurger, J.D. and Scheraga, H.A., J. Comput. Chem., 17 (1996) 1549.
26. Richards, P.M., Anna. Rev. Biophys. Bioeng., 6 (1995) 151.
27. Pauling, L., The Nature of the Chemical Bond, Cornell University, Ithaca, NY, 1960.
28. Bondi, A., Physical Properties of Molecular Crystals, Liquids and Glasses, Wiley, New York, NY, 1968.
29. Chothia, C., Nature, 254 (1975) 304.
30. Li, A. and Nussinov, R., Proteins, 18 (1998) 111.
31. Nyburg, S.C., Faerman, C.H. and Prasad, L., Acta Crystallogr., B43 (1987) 106.
32. Ikuta, S., Ishikawa, M., Katada, M. and Sano, H., Acta Crystallogr., B46 (1991) 23.
33. Steiner, T. and Saenger, W., Acta Crystallogr., B47 (1991) 1022.
34. Stone, A.J. and Tong, C.-S., J. Comput. Chem., 15 (1994) 1377.
35. Frömmel, C., J. Theor. Biol., 111 (1984) 247.
36. Eisenberg, D. and McLachlan, A.D., Nature, 319 (1986) 199.
37. Murphy, L.R., Matubayasi, N., Payne, V.A. and Levy, R.M., Folding Design, 3 (1998) 105.
38. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C. and Scharf, M., J. Comput. Chem., 16 (1995) 273.
39. Bliznyuk, A.A. and Gready, J.E., J. Comput. Chem., 17 (1996) 962.
40. Bliznyuk, A.A. and Gready, J.E., J. Comput. Chem., 17 (1996) 970.
41. Richmond, T.J., J. Mol. Biol., 178 (1984) 63.
42. Kundrot, C.E., Ponder, J.W. and Richards, F.M., J. Comput. Chem., 12 (1991) 402.
43. Perrot, G., Cheng, B., Gibson, K.D., Vila, J., Palmer, K.A., Nayeem, A., Maigret, B. and Scheraga, H.A., J. Comput. Chem., 13 (1992) 1.
44. Cossi, M., Mennucci, B. and Cammi, R., J. Comput. Chem., 17 (1996) 57.
45. Von Freyberg, B. and Braun, W., J. Comput. Chem., 14 (1993) 510.
46. Von Freyberg, B., Richmond, T.J. and Braun, W., J. Mol. Biol., 233 (1993) 275.
47. Mumenthaler, C. and Braun, W., J. Mol. Modelling, 1 (1995) 1.
48. Schiffer, C.A., Caldwell, J.W., Kollman, P.A. and Stroud, R.M., Mol. Simul., 10 (1993) 121.
49. Zhang, H., Wong, C.F., Thacher, T. and Rabitz, H., Proteins, 23 (1995) 218.
50. Juffer, A., Eisenhaber, F., Hubbard, S.J., Walther, D. and Argos, P., Protein Sci., 4 (1995) 2499.
51. Juffer, A.H., Eisenhaber, F., Hubbard, S.J., Walther, D. and Argos, P., Protein Sci., 5 (1996) 1748.
52. Cummings, M.D., Hart, T.N. and Read, R.J., Protein Sci., 4 (1995) 2087.
53. Karplus, P.A., Protein Sci., 6 (1997) 1307.
54. Vajda, S., Weng, Z. and DeLisi, C., Protein Eng., 8 (1995) 1081.
55. Audry, E., Dubost, J.P., Colleter, J.C. and Dallet, Ph., Eur. J. Med. Chem.-Chim. Ther., 21 (1986) 71.
56. Furet, P., Sele, A. and Cohen, N.C., J. Mol. Graph., 6 (1988) 182.
57. Fauchère, J.-L., Quarendon, P. and Kaetterer, L., J. Mol. Graph., 6 (1988) 203.
58. Croizet, F., Langlois, M.H., Dubost. J.P., Braquet, P., Audry, E., Dallet, Ph. and Colleter, J.C., J. Mol. Graph., 8 (1990) 153.
59. Brasseur, R., J. Biol. Chem., 266 (1991) 16120.
60. Heiden, W., Moeckel, G. and Brickmann, J., J. Comput.-Aided Mol. Design, 7 (1993) 503.
61. Young, L., Jernigan, R.L. and Covell, D.G., Protein Sci., 3 (1994) 717.
62. Du, Q. and Arteca, G.A., J. Comput.-Aided Mol. Design, 10 (1996) 133.
63. Du, Q., Arteca, G.A. and Mezey, P.G., J. Comput.-Aided Mol. Design, 11 (1997) 503.
64. Vedani, A. and Huhta, D., J. Am. Chem. Soc., 113 (1991) 5860.
65. Pitt, W.R., Murray-Rust, J. and Goodfellow, J.M., J. Comput. Chem., 14 (1993) 1007.
66. Zheng, Ch., Wong, Ch.F. and McCammon, J.A., Biopolymers, 29 (1990) 1877.
67. Eisenhaber, F., Mannik, J.H. and Tumanyan, V.G., Biopolymers, 29 (1990) 1453.
68. Eisenhaber, F., Tumanyan, V.G. and Abagyan, R.A., Biopolymers, 30 (1990) 563.
69. Eisenhaber, F. and Schulz, W., Biopolymers, 32 (1992) 1643.
70. Brunne, R.M., Liepinsh, E., Otting, G., Wüthrich. K. and van Gunsteren, W.F., J. Mol. Biol., 231 (1993) 1040.
71. Lounnas, V. and Pettitt, B.M., Proteins, 18 (1994) 133.
72. Lounnas, V. and Pettitt, B.M., Proteins, 18 (1994) 148.
73. Lounnas, V., Pettitt, B.M. and Phillips Jr., G.N., Biophys. J., 66 (1994) 601.
74. Rao, S.T., Wu, S., Satyshur, K.A., Ling, K.-Y., Kung, C. and Sundaralingam, M., Protein Sci., 2 (1993) 436.
75. Vogel, H.J., Biochem. Cell Biol., 72 (1994) 357.
76. Wintrode, P.L. and Privalov, P.L., J. Mol. Biol., 266 (1997) 1050.
77. Prange, T., Schiltz, M., Pernot, L., Colloc'h, N., Longhi, S., Bourguet, W. and Fourme, R., Proteins, 30 (1998) 61.
78. Rees, D C. and Wolfe, G.M., Protein Sci., 2 ( 1993) 1882.
79. Eisenhaber, F., Protein Sci., 5 (1996) 1676.
80. Ooi, T., Oobatake, M., Nemethy, G. and Scheraga, H.A., Proc. Natl. Acad. Sci. USA, 84 (1987) 3086.
81. Eisenberg, D., Wesson, M. and Yamashita, M., Chem. Scripta, 29A (1989) 217.
82. Wesson, L. and Eisenberg, D., Protein Sci., 1 (1992) 227.
83. Koehl, P. and Delarue, M., Proteins, 20 (1994) 264.
84. Eriksson, A.E., Baase, W.A., Zhang, X.-J., Heinz, D.W., Blaber, M., Baldwin, E.P. and Matthews, B.W., Science, 255 (1992) 178.
85. Eriksson, A.E., Baase, W.A. and Matthews, B.W., J. Mol. Biol., 229 (1993) 747.
86. Pinker, RJ., Rose, G.D. and Kallenbach, N.R., Protein Sci., 2 (1993) 1099.
87. Vallone, B., Miele, A.E., Vecchini, P., Chiancone, E. and Brunori, M., Proc. Natl. Acad. Sci. USA, 95 (1998) 6103.
88. Wang, Y., Zhang, H. and Scott, R.A., Protein Sci., 4 (1995) 1402.
89. Lemieux, R.U., Acc. Chem Res., 29 (1996) 373.
90. Argos, P., Protein Eng., 2 (1988) 101.
91. Janin, J., Miller, S. and Chothia, C., J. Mol. Biol., 204 (1988) 155.
92. Miller, S., Protein Eng., 3 (1989) 77.
93. Janin, J. and Chothia, C., J. Biol. Chem., 265 (1990) 1627.
94. Korn, A.P. and Burnett, R.M., Proteins, 9 (1991) 37.
95. Jones, S. and Thornton, J.M., Proc. Natl. Acad. Sci. USA, 93 (1996) 13.
96. Tsai, C.-J., Lin, S.L., Wolfson, H.J. and Nussinov, R., Crit. Rev. Biochem. Mol. Biol., 31 (1996) 127.
97. Jones, S. and Thornton, J.M., J. Mol. Biol., 272 (1997) 121.
98. Jones, S. and Thomton, J.M., J. Mol. Biol., 272 (1997) 133.
99. Tsai, C.-J., Lin, S L., Wolfson, H.J. and Nussinov, R., Protein Sci., 6 (1997) 53.
100. Conte, L.L., Chothia, C. and Janin, J., J. Mol. Biol., 285 (1999) 2177.
101. Lijnzaad, P. and Argos, P., Proteins, 28 (1997) 333.
102. Tisi, L.C. and Evans, P.A., J. Mol. Biol., 249 (1995) 251.
103. Uversky, V.N. and Ptitsyn, O.B., J. Mol. Biol., 255 (1996) 215.
104. Causette, M., Planche, H., Delepine, S., Monsan, P., Gaunand, A. and Lindet, B., Protein Eng., 10(1997) 1235.
105. Kuehner, D.E., Heyer, C., Rämsch, C., Fornefeld, U.M., Blanch, H.W. and Prausnitz, J M., Biophys J., 73 (1997) 3211.