Common attributes of native-state structures of proteins, disordered proteins, and amyloid

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 18, 2006, Pages 6883-6888

  Hoang, Trinh X ^a   Marsella, Luca ^b,c   Trovato, Antonio ^c   Seno, Flavio ^c   Banavar, Jayanth R ^d   Maritan, Amos ^c  

^a INSTITUTE OF PHYSICS   (Viet Nam)

^b SISSA   (Italy)

^c UNIVERSITY OF PADOVA   (Italy)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Amyloid formation; Presculpted free energy landscape; Protein design; Protein folding

Indexed keywords

AMYLOID; GLOBULAR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; GEOMETRY; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

AMYLOID; HUMANS; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; TEMPERATURE;

EID: 33646466620     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0601824103     Document Type: Article

References (45)

1. Hoang, T. X., Trovato, A., Seno, F., Jayanth, J. R. & Maritan, A. (2004) Proc. Natl. Acad. Sci. USA 101, 7960-7964.
2. Banavar, J. R., Hoang, T. X., Maritan, A., Seno, F. & Trovato, A. (2004) Phys. Rev. E 70, 041905
3. Chothia, C. (1992) Nature 357, 543-544.
4. DeGrado, W. F., Wasserman, Z. R. & Lear, J. D. (1989) Science 243, 622-628.
5. Kamtekar, S., Schiffer, J. M., Xiong, H. J., Babik, J. M. & Hecht, M. H. (1993) Science 262, 1680-1685.
6. Bryson, J. W., Betz, S. F., Lu, H. S., Suich, D. J., Zhou, H. X., O'Neil, K. T. & DeGrado, W. F. (1995) Science 270, 935-941.
7. Dahiyat, B. I. & Mayo, S. L. (1997) Science 278, 82-87.
8. Koehl, P. & Levitt, M. (1999) J. Mol. Biol. 293, 1161-1181.
9. Koehl, P. & Levitt, M. (1999) J. Mol. Biol. 293, 1183-1193.
10. Wang, W. X. & Hecht, M. H. (2002) Proc. Natl. Acad. Sci. USA 99, 2760-2765.
11. Wei, Y., Kim, S., Fela, D., Baum, J. & Hecht, M. H. (2003) Proc. Natl. Acad. Sci. USA 100, 13270-13273.
12. Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L. & Baker, D. (2003) Science 302, 1364-1368.
13. Wright, P. E. & Dyson, H. J. (1999) J. Mol. Biol. 293, 7960-7964.
14. Dunker, A. K., Lawson, J. D., Brown, C. J., Williams, R. M., Romero, P., Oh, J. S., Oldfield, C. J., Campen, A. M., Ratcliff, C. M., Hipps, K. W., et al. (2001) J. Mol. Graphics Model. 19, 26-59.
15. Dunker, A. K. & Obradovic, Z. (2001) Nat. Biotechnol. 19, 805-806.
16. Dyson, H. J. & Wright, P. E. (2002) Curr. Opin. Struct. Biol. 12, 54-60.
17. Tompa, P. (2002) Trends Biochem. Sci. 27, 527-533.
18. Uversky, V. N. (2002) Eur. J. Biochem. 269, 2-12.
19. Fuxreiter, M., Simon, I., Friedrich, P. & Tompa, P. (2004) J. Mol. Biol. 338, 1015-1026.
20. Kelly, J. W. (1998) Curr. Opin. Struct. Biol. 8, 101-106.
21. Prusiner, S. B. (1998) Proc. Natl. Acad. Sci. USA 95, 13363-13383.
22. Petkova, A. T., Ishii, Y., Balbach, J. J., Antzutkin, O. N., Leapman, R. D., Delaglio, F. & Tycko, R. (2002) Proc. Natl. Acad. Sci. USA 99, 16742-16747.
23. Bucciantini, M., Giannoni, E., Chiti, F., Baroni, F., Formigli, L., Zurdo, J. S., Taddei, N., Ramponi, G., Dobson, C. M. & Stefani, M. (2002) Nature 416, 507-511.
24. Dobson, C. M. (2003) Nat. Rev. Drug Discov. 2, 154-160.
25. Chiti, F., Stefani, M., Taddei, N., Ramponi, G. & Dobson, C. M. (2003) Nature 424, 805-808.
26. Govaerts, C., Wille, H., Prusiner, S. B. & Cohen, F. E. (2004) Proc. Natl. Acad. Sci. USA 101, 8342-8347.
27. Dubay, K. F., Pawar, A. P., Chiti, F., Zurdo, J., Dobson, C. M. & Vendruscolo, M. (2004) J. Mol. Biol. 341, 1317-1326.
28. Dobson, C. M. (2004) Science 304, 1259-1262.
29. Petkova, A. T., Leapman, R. D., Guo, Z., Yau, W. M., Mattson, M. P. & Tycko, R. (2005) Science 307, 262-265.
30. Nelson, R., Sawaya, M. R., Balbirnie, M.. Madsen, A. O., Riekel, C., Grothe, R. & Eisenberg, D. (2005) Nature 435, 773-778.
31. Bernal, J. D. (1939) Nature 143, 663-667.
32. Wolynes, P. G., Onuchic, J. N. & Thirumalai, D. (1995) Science 267, 1619-1620.
33. Dill, K. A. & Chan, H. S. (1997) Nat. Struct. Biol. 4, 10-19.
34. Lau, K. F. & Dill, K. A. (1989) Macromolecules 22, 3986-3997.
35. West, M. W., Wang, W., Patterson, J., Manda, J. D., Beasley, J. R. & Hecht, M. H. (1999) Proc. Natl Acad. Sci. USA 96, 11211-11216.
36. West, M. W. & Hecht, M. H. (1995) Protein Sci. 4, 2032-2039.
37. Shi, Z., Olson, C. A., Rose, G. D., Baldwin, R. L. & Kallenbach, N. R. (2002) Proc. Natl. Acad. Sci. USA 99, 9190-9195.
38. Yue, K. & Dill, K. A. (1995) Proc. Natl. Acad. Sci. USA 92, 146-150.
39. Chan, H. S. & Dill, K. A. (1990) Proc. Natl. Acad. Sci. USA 87, 6388-6392.
40. Tsai, C. J., Ma, B., Sham, Y. Y., Kumar, S. & Nussinov, R. (2001) Proteins 44, 418-427.
41. Broome, B. M. & Hecht, M. H. (2000) J. Mol. Biol. 296, 961-968.
42. Fitzkee, N. C., Fleming, P. J., Gong, H., Panasick, N., Street, T. O. & Rose, G. D. (2005) Trends Biochem. Sci. 30, 73-80.
43. Kazmierkiewicz, R., Liwo, A. & Scheraga, H. A. (2002) J. Comput. Chem. 23, 715-723.
44. Liwo, A., Kazmierkiewicz, R., Czaplewski, C., Groth, M., Oldziej, S., Rackovski, R. J., Pincus, M. R. & Scheraga, H. A. (1998) J. Comput. Chem. 19, 259-276.
45. Sokal, A. D. (1996) Nucl. Phys. B 47, Suppl., 172-179.