The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

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

Volumn 100, Issue 9, 2003, Pages 5154-5159

  Gsponer, Jörg ^a   Haberthür, Urs ^a   Caflisch, Amedeo ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Energy landscape; Misfolding; Protein aggregation

Indexed keywords

AMIDE; AMYLOID; HEPTAPEPTIDE; PEPTIDE; PROTEIN; PROTEIN SUP35; TYROSINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; ENERGY TRANSFER; ENTHALPY; HYDROGEN BOND; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; PRION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN STRUCTURE; SIMULATION; X RAY DIFFRACTION; YEAST;

ALANINE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMYLOID; FUNGAL PROTEINS; PRIONS; PROTEIN CONFORMATION; SACCHAROMYCES CEREVISIAE PROTEINS; TYROSINE;

MUS;

EID: 0037627715     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0835307100     Document Type: Article

References (35)

1. Dobson, C. M. (1999) Trends Biochem. Sci. 24, 329-332.
2. Perutz, M. F. (1999) Trends Biochem. Sci. 24, 58-63.
3. Blake, C. & Serpell, L. (1996) Structure (London) 4, 989-998.
4. Malinchik, S. B., Inouye, H., Szumowski, K. E. & Kirschner, D. A. (1998) Biophys. J. 74, 537-545.
5. Broglia, R. A., Tiana, G., Pasquali, S., Roman, H. E. & Vigezzi, E. (1998) Proc. Natl. Acad. Sci. USA 95, 12930-12933.
6. Giugliarelli, G., Micheletti, C., Banavar, J. R. & Maritan, A. (2000) J. Chem. Phys. 113, 5072-5077.
7. Harrison, P. M., Chan, H. S., Prusiner, S. B. & Cohen, F. E. (1999) J. Mol. Biol. 286, 593-606.
8. Smith, A. V. & Hall, C. K. (2001) J. Mol. Biol. 312, 187-202.
9. Fernandez, A. & Boland, M. (2002) FEBS Lett. 529, 298-302.
10. Ma, B. & Nussinov, R. (2002) Protein Sci. 11, 2335-2350.
11. Ma, B. & Nussinov, R. (2002) Proc. Natl. Acad. Sci. USA 99, 14126-14131.
12. Balbirnie, M., Grothe, R. & Eisenberg, D. (2001) Proc. Natl. Acad. Sci. USA 98, 2375-2380.
13. Bucciantini, M., Giannoni, E., Chiti, F., Baroni, F., Formigli, L., Zurdo, J., Taddei, N., Ramponi, G., Dobson, C. M. & Stefani, M. (2002) Nature 416, 507-511.
14. Ferrara, P., Apostolakis, J. & Caflisch, A. (2002) Proteins Struct. Funct. Genet. 46, 24-33.
15. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comput. Chem. 4, 187-217.
16. Ferrara, P. & Caflisch, A. (2000) Proc. Natl. Acad. Sci. USA 97, 10780-10785.
17. Ferrara, P. & Caflisch, A. (2001) J. Mol. Biol. 306, 837-850.
18. Hiltpold, A., Ferrara, P., Gsponer, J. & Caflisch, A. (2000) J. Phys. Chem. B 104, 10080-10086.
19. Gsponer, J. & Caflisch, A. (2001) J. Mol. Biol. 309, 285-298.
20. Gsponer, J. & Caflisch, A. (2002) Proc. Natl. Acad. Sci. USA 99, 6719-6724.
21. Ferrara, P., Apostolakis, J. & Caflisch, A. (2000) J. Phys. Chem. B 104, 5000-5010.
22. Eaton, W. A., Munoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., Henry, E. R. & Hofrichter, J. (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 327-359.
23. Cavalli, A., Ferrara, P. & Caflisch, A. (2002) Proteins Struct. Funct. Genet. 47, 305-314.
24. De Alba, E., Santoro, J., Rico, M. & Jiménez, M. A. (1999) Protein Sci. 8, 854-865.
25. Beglov, D. & Roux, B. (1994) J. Chem. Phys. 100, 9050-9063.
26. Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. (1977) J. Comp. Phys. 23, 327-341.
27. Yang, A. S. & Honig, B. (1995) J. Mol. Biol. 252, 366-376.
28. Tjernberg, L. O., Naslund, J., Lindqvist, F., Johansson, J., Karlstrom, A. R., Thyberg, J., Terenius, L. & Nordstedt, C. (1996) J. Biol. Chem. 271, 8545-8548.
29. Lazaridis, T. & Karplus, M. (1999) Proteins Struct. Funct. Genet. 35, 133-152.
30. Vasquez, M., Nemethy, G. & Scheraga, H. (1994) Chem. Rev. 94, 2183-2239.
31. Gazit, E. (2002) FASEB J. 16, 77-83.
32. Chelli, R., Gervasio, F. L., Procacci, P. & Schettino, V. (2002) J. Am. Chem Soc. 124, 6133-6143.
33. Azriel, R. & Gazit, E. (2001) J. Biol. Chem. 276, 34156-34161.
34. Ferrone, F. (1999) Methods Enzymol. 309, 256-274.
35. Lopez de la Paz, M., Goldie, K., Zurdo, J., Lacroix, E., Dobson, C. M., Hoenger, A. & Serrano, L. (2002) Proc. Natl. Acad. Sci. USA 99, 16052-16057.