Engineering Novel Bioactive Mini-Proteins from Small Size Natural and de Novo Designed Scaffolds

Current Protein and Peptide Science

Volumn 1, Issue 4, 2000, Pages 403-430

  Martin, Loïc ^a   Vita, Claudio ^a  

^a CEA SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA;

ENZYME INHIBITOR; EPIDERMAL GROWTH FACTOR; IMMUNOGLOBULIN; PEPTIDE;

AMINO ACID SEQUENCE; ANIMAL; BINDING SITE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN ENGINEERING; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; REVIEW; SYNTHESIS;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; ENZYME INHIBITORS; EPIDERMAL GROWTH FACTOR; HUMANS; IMMUNOGLOBULINS; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN ENGINEERING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 0034584872     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389203003381306     Document Type: Article

References (144)

1. Gallop, M.A., Barrett, R.W., Dowex, W.J., Fodor, S.P.A. and Gordon, E.M. (1994) J. Med. Chem. 37, 1233-1251.
2. Wentworth Jr, P. and Janda, K.D. (1998) Curr. Opin. Biotechnol. 9, 109-115.
3. Smith, G.P. (1991) Curr. Opin. Biotechnol. 2, 688-673.
4. Zwick, M.B., Shen, J. and Scott, J.K. (1998) Curr. Opin. Biotechnol. 9, 427-436.
5. Marshall, G.R. (1992) Curr. Opin. Struct. Biol. 2, 904-919.
6. Hruby, V.J., Al-Obeidi, F., Kazmierski, W. (1990) Biochem. J. 268, 249-262.
7. Rizo, J. and Gierasch, L.M. (1992) Annu. Rev. Biochem. 61, 387-418.
8. Olsen, G.L., Bolin, D.R., Bonner, M.P., Bös, M., Cook, C.M., Fry, D.C., Graves, B.J., Hatada, M., Hill, D.E., Kahn, M., Madison, V.S., Rusiecki, V.K., Sarabu, R., Sepinwall, J., Vincent, G.P. and Voss, M.E. (1993) J. Med. Chem. 36, 3039-3049.
9. Hruby, V.J., Li, G., Haskell-Luevano, C. and Shenderovich, M. (1997) Biopolymers (Peptide Science) 43, 219-266.
10. Ménez, A., Bontems, F., Roumestand, C., Gilquin, B. and Toma, F. (1992) Proc. R. Soc. Edinburgh 99B, 83-103.
11. Laskowski, M. and Kato, I. (1980) Annu. Rev. Biochem. 49, 593-626.
12. Le Nguyen, D., Heitz, A., Chiche, L., Castro, B., Boigegrain, R.A., Favel, A. and Coletti-Previero, M.A. (1990) Biochimie 72, 431-435.
13. Klug, A. and Schwabe, J.W. (1995) FASEB J. 9, 597-604.
14. Schwabe, J.W. and Klug, A. (1994) Nature Struct. Biol. 1, 345-349
15. Landschultz, W.H., Johnson, P.F. and McKnight, S.L. (1988) Science 240, 1759-1764.
16. Campbell, I.D. and Bork, P. (1993) Curr. Opin. Struct. Biol. 3, 385-392.
17. Nygren, P.A. and Uhlén, M. (1997) Curr. Opin. Struct. Biol. 7, 463-469.
18. Vita, C., Vizzavona, J., Drakopoulou, E., Zinn-Justin, S., Gilquin, B. and Ménez, A. (1998) Biopolymers (Peptide Science) 47, 93-100.
19. Vita, C. (1997) Curr. Opin. Biotechnol. 8, 429-434.
20. Solazzo, M., Bianchi, E., Felici, F., Cortese, R. and Pessi, A. (1996) in Combinatorial libraries. Synthesis, screening and application potential (Cortese, R. Ed.), pp127-143, Walter de Gruyter, New York
21. Cunningham, B.C. and Wells, J.A. (1997) Curr. Opin. Struct. Biol. 7, 457-462.
22. Mutter, M. (1988) Trends Biochem. Sci. 13, 261-265.
23. Mutter, M. and Vuilleumier, S. (1989) Angew. Chem. Int. Ed. Engl. 28, 535-554.
24. Tuchscherer, G., Scheibler, L., Dumy, P. and Mutter, M. (1998) Biopolymers (Peptide Science) 47, 63-73.
25. Bork, P., Holm, L. and Sander, C. (1994) J. Mol. Biol. 242, 309-320..
26. Gerstein, M. and Levitt, M. (1997) Proc. Natl. Acad. Sci. USA 94, 11911-11916.
27. Huston, J.S., Levinson, D., Meredith, M., Tai, M.S., Novotny, J., Margolies, M.N., Ridge, R.J., Bruccoleri, R.E., Haber, E., Crea, R. and Oppermann, F. (1988) Proc. Natl. Acad. Sci. USA 85, 5879-5883.
28. Davies, J. and Riechmann, L. (1995) Biotechnol. 13, 475-478.
29. Ward, S.E., Gussow, D., Griffiths, A.D., Jones, P.T. and Winter, G. (1989) Nature 341, 544-546.
30. Hammers-Casterman, C., Atahouch, T., Muyldermans, S., Robinson, G., Hamers, C., Bayama Songa, E., Bendahman, N. and Hamers, R. (1993) Nature 363, 446-448.
31. Desmyter, A., Transue, T.R., Ghahroudi, M.A., Thi, M.H.D., Poortmans, F., Hamers, R., Muyldermans, S. and Wyns, L. (1996) Nature Struct. Biol. 3, 803-811.
32. Pessi, A., Bianchi, E., Crameri, A., Venturini, S., Tramontano, A. and Solazzo, M. (1993) Nature 362, 367-369.
33. Bianchi, E., Venturini, S., Pessi, A., Tramontano, A. and Solazzo, M. (1994) J. Mol. Biol. 236, 649-659.
34. Martin, F., Toniatti, C., Salvati, A.L., Venturini, S., Ciliberto, G., Cortese, R. and Solazzo, M. (1994) EMBO J. 13, 5303-5309.
35. Martin, F., Toniatti, C., Salvati, A.L., Ciliberto, G., Cortese, R. and Solazzo, M. (1996) J. Mol. Biol. 255, 86-97.
36. Dimasi, N., Martin, F., Volpari, C., Brunetti, M., Biasol, G., Altamura, S., Cortese, R., De Francesco, R., Steinkühler, C. and Solazzo, M. (1997) J. Virol. 71, 7461-7469.
37. Martin, F., Steinkühler, C., Brunetti, M., Pessi, A., Cortese, R., De Francesco, R. and Solazzo, M. (1999) Protein Eng. 12, 1005-1011.
38. Gentz, R., Rauscher III, F.J., Abate, C. and Curran, T. (1989) Science 243: 1695-1699.
39. Cohen, C. and Parry, D.A.D. (1990) Proteins Struct. Funct. Genet. 7, 1-15.
40. Jones, N. (1990) Cell 61, 9-11.
41. Adamson, J.G., Zhou, N.E. and Hodges, R.S. (1993) Curr. Opin. Biotechnol. 4, 428-437.
42. DeGrado, W.F., Wasserman, Z.R. and Lear, J.D. (1989) Science 243, 622-628.
43. Hecht, M.H., Richardson, J.S., Richardson, D.C. and Ogden, R.C. (1990) Science 249, 884-891.
44. Zhou, N.E., Kay, C.M. and Hodges, R.S. (1992) J. Biol. Chem. 267, 2664-2670.
45. Zhou, N.E., Kay, C.M. and Hodges, R.S. (1992) Biochemistry 31, 5739-5746.
46. Myszka, D.F. and Chaiken, I.M. (1994) Biochemistry 33, 2363-2372.
47. Fezoui, Y., Weaver, D.L. and Osterhout, J.J. (1994) Proc. Natl. Acad. Sci. USA 91, 3675-3679.
48. Walsh, S.T.R., Cheng, H., Bryson, J.W., Roder, H. and DeGrado, W.F. (1999) Proc. Natl. Acad. Sci. USA 96, 5486-5491.
49. Schafmeister, C.E., LaPorte, S.L., Miercke, J.W. and Stroud, R.M. (1997) Nature Struct. Biol. 4, 1039-1046.
50. Su, J.Y., Hodges, R.S. and Kay, C.M. (1994) Biochemistry 33, 15501-15510.
51. Houston, M.E. Jr., Wallace, A., Bianchi, E., Pessi, A. and Hodges, R.S. (1996) J. Mol. Biol. 262, 270-282.
52. Bianchi, E., Fogolari, A., Wallace, A., Nicotra, M., Acali, S., Phalipon, A., Barbato, G., Bazzo, R., Cortese, R., Felici, F. and Pessi, A.(1994) J. Mol. Biol. 236, 649-659.
53. Miceli, R., Myszka, D., Mao, J., Sathe, G. and Chaiken, I.M. (1996) Drug Design Discovery 13, 95-105.
54. Mutter, M. and Tuchscherer, G. (1997) Cell. Mol. Life Sci. 53, 851-863.
55. Tuchscherer, G., Grell, D., Mathieu, M. and Mutter, M. (1998) J. Peptide Res. 54, 185-194.
56. Mutter, M., Dumy, P., Garouste, P., Lehmann, C., Mathieu, M., Peggion, C., Peluso, S., Razaname, A. and Tuchscherer, G. (1996) Angew. Chem. Int. Ed. Engl. 35, 1482-1485.
57. Grouzmann, E., Buclin, T., Martire, M., Cannizzaro, C., Dörner, B., Razaname, A. and Mutter, M. (1997) J. Biol. Chem. 272, 7699-7706.
58. Keller, T.A., Duscl, C., Kröner, D., Sévin, A.F., Vogel, H., Cervigni, S.E. and Dumy, P. (1995) Supramol. Sci. 2, 166-170.
59. Tuchscherer, G., Lehmann, C. and Mathieu, M. (1998) Angew. Chem. Int. Ed. Engl. 37, 2990-2993.
60. Scheibler, L. Dumy, P., Stamou, D., Duscl, C., Vogel, H. and Mutter, M. (1998) Tetrahedron Lett. 54, 3725-3734.
61. Duschl, C., Sévin-Landais, A.F. and Vogel, H. (1996) Biophys. J. 70, 1985-1995.
62. Malis, D.D., Grouzmann, E., Morel, D.R., Mutter, M. and Lacroix J.S. (1999) Br. J. Pharmacol. 126, 989-996.
63. Bontems, F., Roumestand, C., Gilquin, B., Ménez, A. and Toma, F. (1991) Science 254, 1521-1523.
64. Bonmatin, J.M., Bonnat, J.L., Gallet, X., Vovelle, F., Ptak, M., Reichhart, J.M., Hoffmann, J.A., Keppi, E., Legrain, M. and Achstetter, T. (1992) J. Biol. NMR 2, 235-256.
65. Bruix, M., Jiménez, M. A., Santoro, J., Gonzàlez, C., Collila, F. J., Méndez, E. and Rico, M. (1993) Biochemistry 32, 715-724.
66. Caldwell, J.E., Abildgaad, F., Dzakula, Z., Ming, D., Hellekant, G. and Markley, J.L. (1998) Nature Struct. Biol. 5, 427-431.
67. Vita, C., Roumestand, C., Toma, F. and Ménez, A. (1995) Proc. Natl. Acad. Sci. USA 92, 6404-6408.
68. Vita, C., Bontems, F., Bouet, F., Tauc, M., Poujeol, P., Vatanpour, H., Harvey, A.L., Ménez, A. and Toma, F. (1993) Eur. J. Biochem. 217, 157-169.
69. Pierret, B., Virelizier, H. and Vita, C. (1995) Int. J. Peptide Protein Res. 46, 471-479.
70. Drakopoulou, E., Zinn-Justin, S., Guenneugues, M., Gilquin, B., Ménez, A. and Vita, C. (1996) J. Biol. Chem. 271, 11979-11987.
71. Zinn-Justin, S., Roumestand, C., Gilquin, B., Bontems, F., Ménez, A. and Toma, F. (1995) Biochemistry 31, 11335-11347.
72. Trémeau, O., Lemaire, C., Drevet, P., Pinkasfeld, P., Ducancel, F., Boulain, J. C. and Ménez, A. (1995) J. Biol. Chem. 270, 9362-9369.
73. Zinn-Justin, S. Guenneugues, M., Drakopoulou, E., Gilquin, B., Vita, C. and Ménez, A. (1996) Biochemistry 35, 8535-8543.
74. Drakopoulou, E., Vizzavona, J. and Vita, C. (1998) Lett. Peptide Sci. 5, 241-245.
75. Vita, C., Drakopoulou, E., Vizzavona, J., Rochette, S., Martin, L., Ménez, A., Roumestand, C., Yang, Y.S., Ylistagui, L., Benjouad, A. and Gluckman , J.C. (1999) Proc. Natl. Acad. Sci. USA, 96, 13091-13096.
76. Dalgleish, A.G., Beverley, A.C., Clapham, P.R., Crawford, D.H., Greaves, M.F., and Weiss, R.A. (1984) Nature 312, 763-767.
77. Klatzmann, D., Champagne, E., Chamaret, S., Gruest, J., Guetard, D., Hercend, T. , Gluckman, J.C. and Montagnier, L. (1984) Nature 312, 767-768.
78. Berger, E.A. (1997) AIDS 11, S3-S16.
79. Littman, D.R. (1998) Cell 93, 677-680.
80. Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J. and Hendrickson, W.A. (1998) Nature 393, 648-659.
81. Sweet, R.W., Truneh, A. and Hendrickson, W.A. (1991) Curr. Opin. Biotechnol. 2, 622-633.
82. Ryu, S.E., Truneh, A., Sweet, R.W. and Hendrickson, W.A. (1994) Structure 2, 59-74.
83. Kellenberger, E., Mer, G., Kellenberger, C., Marguerie, G. and Lefèvre, J.F. (1999) Eur. J. Biochem. 260, 810-817.
84. Mer, G., Kellenberger, C. and Lefèvre, J.F. (1998) J. Mol. Biol. 281, 235-240.
85. O'Shea, E.K, Klemm, J.D., Kim, P.S., Alber, T. (1991) Science 254, 539-544.
86. Saudek, V., Pastore, A., Morelli, M.A., Frank, R., Gausepohl, H. and Gibson, T. (1991) Protein Eng. 4, 519-529.
87. Butcher, D.J., Kowalska, M.A., Li, S., Luo, Z., Shan, S., Lu, Z., Niewarowski, S. and Huang, Z. (1997) FEBS Lett. 409, 183-187.
88. Domingues, H., Gregut, D., Sebald, W., Oschkinat, H. and Serrano, L. (1999) Nature Struct. Biol. 6, 652-656.
89. Smith, J.W., Tachias, K. and Madison, E.L. (1995) J. Biol. Chem. 270, 39486-30490.
90. Vella, F., Hernandez, J.F., Molla, A., Block, M.R. and Arlaud, G.J. (1999) J. Peptide Res. 54, 415-426.
91. Pellegrino, G.R. and Berg, J.M. (1991) Proc. Natl. Acad. Sci. USA 88, 671-675.
92. Pavletich, N.P. and Pabo, C.O. (1991) Science 252, 809-817.
93. Choo, Y. and Klug, A. (1995) Curr. Opin. Biotechnol. 6, 431-436.
94. Bianchi, E., Fogolari, A., Wallace, A., Nicotra, M., Acali, S., Phalipon, A., Barbato, G., Bazzo, R., Cortese, R., Felici, F. and Pessi, A. (1995) J. Mol. Biol. 247, 154-160.
95. Barbato, G., Cicero, D.O., Bianchi, E., Pessi, A. and Bazzo, R. (1996) J. Biomol. NMR 8, 36-48.
96. Nilsson, B., Moks, T., Jansson, B., Abrahmsén, L., Elmblad, A., Holmgren, E., Henrichsson, C., Jones, T.A. and Uhlén, M. (1987) Protein Eng. 1, 107-113.
97. Deisenhofer, J. (1981) Biochemistry 20, 2361-2370.
98. Gouda, H., Torigoe, H., Saito, A., Sato, M., Arata, Y., Shimada, I. (1992) Biochemistry 31, 9665-9672.
99. Lyons, B.A., Tashino, M., Cedergren, L., Nilsson, B., and Montelione, G. (1993) Biochemistry 32, 7839-7845.
100. Nord, K., Nilsson, J., Nilsson, B., Uhlén, M. and Nygren, P.A. (1995) Protein Eng. 8, 601-608.
101. Nord, K, Gunneriusson, E., Ringdahl, J., Stahl, S., Uhlén, M. and Nygren, P.A (1997) Nature Biotechnol. 15, 772-777.
102. Vertesy, L., Oeding, V., Bender, R., Zepf, K. and Nesermann, G. (1984) Eur. J. Biochem. 141, 505-512.
103. Kline, A.D., Braun, W. and Wutrich, K. (1986) J. Mol. Biol. 189, 377-382.
104. Pfugrath, J.W., Wiegand, G., Huber, R. and Vertesy, L. (1986) J. Mol. Biol. 189, 383-386.
105. McConnell, S.J. and Hoess, R.H. (1995) J. Mol. Biol. 250, 460-470.
106. Smith, G.P., Patel, S.U., Windass, J.D., Thornton, J.M., Winter, G. and Griffiths, A.D. (1998) J. Mol. Biol. 277, 317-332.
107. Roberts, B.L., Markland, W., Ley, C.L., Kent, R.B., White, D.W., Guterman, S.K., and Ladner, R.C. (1992) Proc. Natl. Acad. Sci. USA 89, 2429-2433.
108. Markland, W., Ley, A.C. and Ladner, R.C. (1996) Biochemistry 35, 8045-8057.
109. Markland, W., Ley, A.C. and Ladner, R.C. (1996) Biochemistry 35, 8058-8067.
110. Dennis, M.S., Herzka, A. and Lazarus, R.A. (1995) J. Biol. Chem. 270, 25411-25417.
111. Dennis, M.S. and Lazarus, R.A. (1994) J. Biol. Chem. 269, 22129-22136.
112. Dennis, M.S. and Lazarus, R.A. (1994) J. Biol. Chem. 269, 22137-22144.
113. Szadenings, M., Vasel, B., Hecht, H. and Schomburg, D. (1995) Protein Eng. 8, 45-52.
114. Martin, F., Dimasi, N., Volpari, C., Perreraz, C., Di Marco, S., Brunetti, M., Steinkühler, C., De Francesco, R. and Solazzo, M. Biochemistry 37, 11459-11468.
115. Li, B., Tom, J.Y.K., Oare, D., Yen, R., Fairbrother, W.J., Wells, J.A. and Cunningham, B.C. (1995) Science 270, 1657-1660.
116. Braisted, A., and Wells, J.A. (1996) Proc. Natl. Acad. Sci. USA 93, 5688-5692.
117. Starovasnik, M.A., Braisted, A., and Wells, J.A. (1997) Proc. Natl. Acad. Sci. USA 94, 10080-10085.
118. Reinecke, U., Sabat, R., Misselwitz, R., Welfle, H., Volk, H.D. and Schneider-Mergener, J. (1999) Nature Biotechnol. 17, 271-275.
119. Friedler, A., Zakai, N., Karni, O., Broder, Y.C., Baraz, L., Kotler, M., Loyter, A. and Gilon, C. (1998) Biochemistry, 37, 5616-5622.
120. Kasher, R., Oren, D.A., Barda, Y. and Gilon, C. (1999) J. Mol. Biol. 292, 421-429.
121. Jones, P.T., Dear, P.H., Foote, J., Neuberg, M.S. and Winter, G. (1986) Nature 321, 522-525.
122. Nixon, A.E., Ostermeier, M. and Benkovic, S.J. (1998) Trends Biotechnol. 16, 258-264.
123. Dumy, P., Eggleston, I.M., Esposito, G., Nicola, S. and Mutter, M. (1996) Biopolymers 39, 297-308.
124. LeSauter, L., Wei, L., Gibbs, B.F. and Saragovi, H.U. (1995) J. Biol. Chem. 270, 6564-6569.
125. Monfardini, C., Kieber-Emmons, T., Voet, D., Godillot, A.P., Weiner, D.B. and Williams, W.V. (1996) J. Biol. Chem. 271, 2966-2971.
126. Zhang, X., Piatier-Tonneau, D., Auffray, C., Muraly, R., Mahapatra, A., Zhang, F.Q., Maier, C.C., Saragovi, U. and Greene, M. (1996) Nature Biotechnol. 14, 472-475.
127. Zhang, X., Gaubin, M., Briant, L., Srikantan, V., Murali, R., Saragovi, U., Weiner, D., Devaux, C., Auterio, M., Piatier-Tonneau, D. and Greene, M. (1996) Nature Biotechnol. 15, 150-154.
128. O'Neil, K.T., Hoess, R.H., Jackson, S.A., Ramachandran, N.S., Mousa, S.A. and DeGrado, W. (1992) Proteins Struct. Funct. Genet. 14, 509-515.
129. Wrighton, N.C., Farrell, F.X., Chang, R., Kashyap, A.K., Barbone, F.P., Mulcahy, L.S., Johnson, D.L., Barret, R.W., Jolliffe, L.K. and Dower, W.J. (1996) Science 273, 458-464.
130. Livnah, O., Stura, E.A., Johnson, D.L., Middleton, S.A., Mulcahy, L.S., Wrighton, N.C., Dower, W.J., Jolliffe, L.K. and Wilson, I.A. (1996) Science 273, 464-471.
131. Hirschmann, R., Yao, W., Cascieri, M.A., Strader, C.D., Maeschler, L., Cichy-Knight, M.A., Hynes, J. Jr, van Rijn, R.D., Sprengler, P.A. and Smith, A.B. III (1996) J. Med. Chem. 39, 2441-2448.
132. McBride, J.D., Freeman, N., Domingo, G.J. and Leatherbarrow, R.J. (1996) J. Mol. Biol. 259, 819-827.
133. Clackson, T. and Wells, J.A. (1995) Science 267, 383-386.
134. MacLennan, J. (1995) Nature Biotechnol 13, 1180-1182
135. Lister-James, J., Moyer, B. Jr and Dean R.T. (1997) Q. .J. Nucl. Med. 41, 111-118.
136. Ladner, R.C. (1999) Q. J. Nucl. Med. 43, 119-124.
137. Longo, F.L. and Mobley, W.C. (1996) Nature Biotechnol. 14, 1092.
138. LeSauteur, L., Cheubg, N.K.V., Lisbona, R. and Saragovi, H.U. (1996) Nature Biotechnol. 14, 1120-1122.
139. Chen, S., Chrusciel, R.A., Nakanishi, H., Raktabutr, A., Johnson, M.E., Sato, A., Weiner, D., Hoxie, J., Saragovi, H.U., Greene, M.I. and Khan, M. (1992) Proc. Natl. Acad. Sci. USA 89, 5872-5876.
140. Moore, J.P. and Sweet, R.W. (1993) Perspectives Drug Discovery Design 1, 235-250.
141. McDovvell, R.S., Blackburn, B.K., Gadek, T.R., McGee, L.R., Rawson, T., Reynolds, M.E., Robarge, K.D., Somers, T.C., Thorsen, E.D., Tischler, M., Tom, J.Y.R., Webb, T.R. and Burnier, J.P. (1994) J. Am. Chem. Soc. 116, 5069-5076.
142. Chu-Biao, X., Roderick, J., Eyermann, C.G., Mousa, S., Olson, R.E. and DeGrado, W.F. (1994) Bioorg. Med. Chem. 2, 897-908.
143. Zhao, B., Helms, L.R., DesJarlais, R.L., Abdel-Meguid, S.S. and Wetzel, R. (1995) Nature Struct. Biol. 2, 1131-1137.
144. Koradi, R., Billeter, M. and Wütrich, K. (1996) J. Mol. Graphics 14, 51-55.