Combinatorial approaches to probe the sequence determinants of protein aggregation and amyloidogenicity

Protein and Peptide Letters

Volumn 13, Issue 3, 2006, Pages 279-286

  Wurth, Christine ^a,b   Kim, Woojin ^a   Hecht, Michael H ^a  

^a PRINCETON UNIVERSITY   (United States)

^b F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

Amyloid; Combinatorial libraries; Protein aggregation; Protein design

Indexed keywords

AMYLOID; PEPTIDE LIBRARY;

AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; REVIEW; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; AMYLOID; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 33645513791     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986606775338506     Document Type: Review

References (72)

1. Kelly, J. (1996) Curr. Opin. Struct. Biol., 6, 11-17.
2. Prusiner, S.B. (1997) Science, 278, 245-251.
3. Selkoe, D. (2001) Physiol. Rev., 81, 741-766.
4. Dobson, C.M. (1999) Trends Biochem. Sci., 24, 329-332.
5. Dobson, C.M. (2003) Nature, 426, 884-890.
6. Serpell, L.C. (2000) Biochim. Biophys. Acta, 1502, 16-30.
7. Lynn, D. and Meredith, S. (2000) J. Struct. Biol., 130, 153-173.
8. Hammarström, P., Jiang, X., Hurshman, A., Powers, E. and Kelly, J. (2002) Proc. Natl. Acad. Sci. USA, 99, 16427-16432.
9. Villegas, V., Zurdo, J., Filimonov, V.V., Aviles, F.X., Dobson, C.M. and Serrano, L. (2000) Protein Sci., 9, 1700-1708.
10. Esler, W., Stimson, E., Ghilardi, J., Lu, Y., Felix, A., Vinters, H., Mantyh, P., Lee, J. and Maggio, J. (1996) Biochemistry, 35, 13914-13921.
11. Fay, D., Fluet, A., Johnson, C. and Link, C. (1998) J. Neurochem., 71, 1616-1625.
12. Fraser, P., McLachlan, D., Surewicz, W., Mizzen, C., Snow, A., Nguyen, J. and Kirschner, D. (1994) J. Mol. Biol., 244, 64-73.
13. Päiviö, A., Nordling, E., Kallberg, Y., Thyberg, J. and Johansson, J. (2004) Protein Sci., 13, 1251-1259.
14. Lim, W. and Sauer, R. (1989) Nature 339, 31-36.
15. Lim, W. and Sauer, R. (1991) J. Mol. Biol., 219, 359-376.
16. Axe, D., Foster, N. and Fersht, A. (1996) Proc. Natl. Acad. Sci. USA, 93, 5590-5594.
17. Gu, H., Yi, Q., Bray, S., Riddle, D., Shiau, A. and Baker, D. (1995) Protein Sci., 4, 1108-1117.
18. Munson, M., O'Brien, R., Sturtevant, J. and Regan, L. (1994) Protein Sci., 3, 2015-2022.
19. Palzkill, T. and Botstein, D. (1992) Proteins, 14, 29-44.
20. Mandecki, W. (1990) Protein Eng., 3, 221-226.
21. Davidson, A. and Sauer, R. (1994) Proc. Natl. Acad. Sci. USA, 91, 2146-2150.
22. Kamtekar, S., Schiffer, J., Xiong, H., Babik, J. and Hecht, M. (1993) Science, 262, 1680-1685.
23. Wei, Y., Liu, T., Sazinsky, S., Moffet, D., Pelczer, I. and Hecht, M. (2003a) Protein Sci., 12, 92-102.
24. Wei, Y., Kim, S., Fela, D., Baum, J. and Hecht, M. (2003b) Proc. Natl. Acad. Sci. USA, 100, 13270-13273.
25. Ventura, S. and Serrano, L. (2004) Proteins, 56, 1-10.
26. Hecht, M., Das, A., Go, A., Bradley, L. and Wei, Y. (2004) Protein Sci., 13, 1711-1723.
27. Lahr, S., Broadwater, A., Carter, C., Collier, M., Hensley, L., Waldner, J., Pielak, G. and Edgel, M. (1999) Proc. Natl. Acad. Sci. USA, 96, 14860-14865.
28. Creighton, T. (1992) in Proteins 2nd Ed. pp.171-199. W.H. Freeman and Company, New York.
29. Schulman, B. and Kim, P. (1996) Nat. Struct. Biol., 3, 682-687.
30. Morimoto, A., Irie, K., Murakami, K., Ohigashi, H., Shindo, M., Nagao, M., Shimizu, T. and Shirasawa, T. (2002) Biochem. Biophys. Res. Com., 295, 306-311.
31. Murakami, K., Irie, K., Morimoto, A., Ohigashi, H., Shindo, M., Nagao, M., Shimizu, T. and Shirasawa, T. (2002) Biochem. Biophys. Res. Com., 294, 5-10.
32. Wood, S.J., Wetzel, R., Martin, J.D. and Hurle, M.R. (1995) Biochemistry, 34, 724-730.
33. Williams, A.D., Portelius, E., Kheterpal, I., Guo, J., Cook, K.D., Xu, Y. and Wetzel, R. (2004) J. Mol. Biol., 335, 833-842.
34. Petkova, A., Ishii, Y., Balbach, J., Antzutkin, O., Leapman, R., Delaglio, F. and Tycko, R. (2002) Proc. Natl. Acad. Sci. USA, 99, 16742-16747.
35. von Bergen, M., Friedhoff, P., Biernat, J., Heberle, J., Mandelkow, E.M. and Mandelkow, E. (2000) Proc. Natl. Acad. Sci. USA, 97, 5129-5134.
36. Westermark, P., Wernstedt, C., Wilander, E., Hayden, D., O'Brien, T. and Johnson, K. (1987) Proc. Natl. Acad. Sci. USA, 84, 3881-3885.
37. Cooper, G., Willis, A., Clark, A., Turner, R., Sim, R. and Reid, K. (1987) Proc. Natl. Acad. Sci. USA, 84, 8628-8632.
38. Moriarty, D. and Raleigh, D. (1999) Biochemistry, 38, 1811-1818.
39. Azriel, R. and Gazit, E. (2001) J. Biol. Chem., 276, 34156-34161.
40. Cunningham, B. and Wells, J. (1989) Science, 244, 1081-1085.
41. Hilbich, C., Kisters-Woike, B., Reed, J., Masters, C. and Beyreuther, K. (1992) J. Mol. Biol., 228, 460-473.
42. Tjernberg, L.O., Näslund, J., Lindqvist, F., Johansson, J., Karlström, A., Thyberg, J., Terenius, L. and Nordstedt, C. (1996) J. Biol. Chem., 271, 8545-8548.
43. Wurth, C., Guimard, N.K. and Hecht, M.H. (2002) J. Mol. Biol., 319, 1279-1290.
44. Salmona, M., Morbin, M., Massignan, T., Colombo, L., Mazzoleni, G., Capobianco, R., Diomede, L., Thaler, F., Mollica, L., Musco, G., Kourie, J.J., Bugiani, O., Sharma, D., Inouye, H., Kirschner, D.A., Forloni, G. and Tagliavini, F. (2003) J. Biol. Chem., 278, 48146-48153.
45. Roy, S., Helmer, K.J. and Hecht, M.H. (1997) Fold Des., 2, 89-92.
46. Rosenbaum, D.M., Roy, S. and Hecht, M.H. (1999) J. Am. Chem. Soc., 121, 9509-9513.
47. Keefe, A. and Szostak, J. (2001) Nature, 410, 715-718.
48. Matsuura, T., Ernst, A. and Plückthun, A. (2002) Protein Sci., 11, 2631-2643.
49. Matsuura, T., Ernst, A., Zechel, D. and Plückthun, A. (2004) Chem. Biochem. 5, 177-182.
50. Lin, H. and Cornish, V. (2002) Angew. Chemie Int. Ed., 41, 4402-4425.
51. Zaccolo, M., Williams, D., Brown, D. and Gherardi, E. (1996) J. Mol. Biol., 255, 589-603.
52. Kunichika, K., Hashimoto, Y. and Imoto, T. (2002) Protein Eng., 15, 805-809.
53. Waldo, G.S. (2003) Curr. Opin. Chem. Biol., 7, 33-38.
54. Wigley, W.C., Stidham, R.D., Smith, N.M., Hunt, J.F. and Thomas, P.J. (2001) Nat. Biotech., 19, 131-136.
55. Waldo, G.S., Standish, B.M., Berendzen, J. and Terwilliger, T.C. (1999) Nat. Biotech., 17, 691-695.
56. Koscielska-Kasprzak, K. and Otlewski, J. (2003) Protein Sci., 12, 1675-1685.
57. Chiti, F., Stefani, M., Taddei, N., Ramponi, G. and Dobson, C.M. (2003) Nature, 424, 805-808.
58. West, M.W., Wang, W., Patterson, J., Mancias, J.D., Beasley, J.R. and Hecht, M.H. (1999) Proc. Natl. Acad. Sci. USA, 96, 11211-11216.
59. Xiong, H., Buckwalter, B., Shieh, H. and Hecht, M. (1995) Proc. Natl. Acad. Sci. USA, 92, 6349-6353.
60. Brack, A. and Spach, G. (1981) J. Am. Chem. Soc., 103, 6319-6323.
61. Zhang, S., Holmes, T., Lockshin, C. and Rich, A. (1993) Proc. Natl. Acad. Sci., USA 90, 3334-3338.
62. Wang, W. and Hecht, M.H. (2002) Proc. Natl. Acad. Sci. USA, 99, 2760-2765.
63. DuBay, K.F., Pawar, A.P., Chiti, F., Zurdo, J., Dobson, C.M. and Vendruscolo, M. (2004) J. Mol. Biol., 341, 1317-1326.
64. Broome, B. and Hecht, M. (2000) J. Mol. Biol., 296, 961-968.
65. Kammerer, R., Kostrewa, D., Zurdo, J., Detken, A., Garcia-Echeverria, C., Green, J.D., Müller, S.A., Meier, B.H., Dobson, C.M. and Steinmetz, M. (2003) Proc. Natl. Acad. Sci. USA, 101, 4435-4440.
66. Lopez de la Paz, M., Goldie, K., Zurdo, J., Lacroix, E., Dobson, C.M., Hoenger, A. and Serrano, L. (2002) Proc. Natl. Acad. Sci. USA, 99, 16052-16057.
67. Lopez de la Paz, M. and Serrano, L. (2004) Proc. Natl. Acad. Sci. USA, 101, 87-92.
68. Fändrich, M., Fletcher, M. and Dobson, C.M. (2001) Nature, 410, 165-166.
69. Tjernberg, L., Hosia, W., Bark, N., Thyberg, J. and Johansson, J. (2002) J. Biol. Chem., 277, 43243-43246.
70. Richardson, J.S. and Richardson, D.C. (2002) Proc. Natl. Acad. Sci. USA, 99, 2754-2759.
71. Fernandez-Escamilla, A., Rousseau, F., Schymkowitz, J. and Serrano, L. (2004) Nat. Biotech., 22, 1302-1306.
72. Kim, W. and Hecht, M.H. (2005) J. Biol. Chem., 280, 35069-35076.