Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation

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

Volumn 103, Issue 31, 2006, Pages 11533-11538

  Esposito, Luciana ^a,b   Pedone, Carlo ^a,b   Vitagliano, Luigi ^a,b  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b Centro Interuniversitario di Ricerca Sui Peptidi Bioattivi (CIRPEB)   (Italy)

Author keywords

Amyloid fiber; Neurodegenerative diseases; Prion

Indexed keywords

AMYLOID; GLYCYLASPARAGINYLASPARAGINYLGLUTAMINYLGLUTAMINYLASPARAGINYLTYROSINE; PEPTIDE; PRION PROTEIN; UNCLASSIFIED DRUG;

ALZHEIMER DISEASE; ARTICLE; BETA SHEET; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DEGENERATIVE DISEASE; ELECTRON MICROSCOPY; HYDRATION; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR SIZE; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN STRUCTURE; STEREOCHEMISTRY;

AMINO ACID SEQUENCE; AMYLOID; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 33746800825     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0602345103     Document Type: Article

References (37)

1. Ross, C. A. & Poirier, M. A. (2004) Nat. Med. 10, S10-S17.
2. Miranker, A. D. (2004) Proc. Natl. Acad. Sci. USA 101, 4335-4336.
3. Zerovnik, E. (2002) Eur. J. Biochem. 269, 3362-3371.
4. Dobson, C. M. (1999) Trends Biochem. Sci. 24, 329-332.
5. Wuthrich, K. & Riek, R. (2001) Adv. Protein Chem. 57, 55-82.
6. DeMarco, M. L. & Daggett, V. (2005) C. R. Biol. 328, 847-862.
7. Rousseau, F., Schymkowitz, J. & Serrano, L. (2006) Curr. Opin. Struct. Biol. 16, 118-126.
8. Temussi, P. A., Masino, L. & Pastore, A. (2003) EMBO J. 22, 355-361.
9. Wetzel, R. (2002) Structure (London) 10, 1031-1036.
10. Dobson, C. M. (2005) Nature 435, 747-749.
11. Makin, O. S. & Serpell, L. C. (2005) Methods Mol. Biol. 299, 67-80.
12. Makin, O. S. & Serpell, L. C. (2005) FEBS. J. 272, 5950-5961.
13. Zanuy, D., Ma, B. & Nussinov, R. (2003) Biophys. J. 84,1884-1894.
14. Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. O., Riekel, C., Grothe, R. & Eisenberg, D. (2005) Nature 435, 773-778.
15. Balbirnie, M., Grothe, R. & Eisenberg, D. S. (2001) Proc. Natl. Acad. Sci. USA 98, 2375-2380.
16. Diaz-Avalos, R., Long, C., Fontano, E., Balbirnie, M., Grothe, R., Eisenberg, D. & Caspar, D. L. (2003) J. Mol. Biol. 330, 1165-1175.
17. Perutz, M. F., Johnson, T., Suzuki, M. & Finch, J. T. (1994) Proc. Natl. Acad. Sci. USA 91, 5355-5358.
18. Perutz, M. F., Finch, J. T., Berriman, J. & Lesk, A. (2002) Proc. Natl. Acad. Sci. USA 99, 5591-5595.
19. Berman, H. M., Bhat, T. N., Bourne, P. E., Feng, Z., Gilliland, G., Weissig, H. & Westbrook, J. (2000) Nat. Struct. Biol. 7, 957-959.
20. Fernandez, A. (2005) FEBS Lett. 579, 6635-6640.
21. Chothia, C. (1973) J. Mol. Biol. 75, 295-302.
22. Wang, J., Gulich, S., Bradford, C., Ramirez-Alvarado, M. & Regan, L. (2005) Structure (London) 13, 1279-1288.
23. Soto, P., Cladera, J., Mark, A. E. & Daura, X. (2005) Angew. Chem. 117, 1089-1091.
24. Merlino, A., Esposito, L. & Vitagliano, L. (2006) Proteins 63, 918-927.
25. Merlino, A., Ceruso, M. A., Vitagliano, L. & Mazzarella, L. (2005) Biophys. J. 88, 2003-2012.
26. 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.
27. Klimov, D. K. & Thirumalai, D. (2003) Structure (London) 11, 295-307.
28. Zanuy, D., Haspel, N., Tsai, H. H., Ma, B., Gunasekaran, K., Wolfson, H. J. & Nussinov, R. (2004) Phys. Biol. 1, 89-99.
29. Gsponer, J., Haberthur, U. & Caflisch, A. (2003) Proc. Natl. Acad. Sci. USA 100, 5154-5159.
30. Sunde, M., Serpell, L. C., Bartlam, M., Fraser, P. E., Pepys, M. B. & Blake, C. C. (1997) J. Mol. Biol. 273, 729-739.
31. Sambashivan, S., Liu, Y., Sawaya, M. R., Gingery, M. & Eisenberg, D. (2005) Nature 437, 266-269.
32. Thompson, M. J., Sievers, S. A., Karanicolas, J., Ivanova, M. I., Baker, D. & Eisenberg, D. (2006) Proc. Natl Acad. Sci. USA 103, 4074-4078.
33. van der Spoel, D., Lindhal, E., Berk, H., Groenhof, G., Mark, A. E. & Berendsen, H. J. C. (2005) J. Comput. Chem. 26, 1701-1718.
34. Berendsen, H. J. C., van der Spoel, D. & van der Drunen, R. (1995) Comp. Phys. Comm. 91, 45-56.
35. Hess, B., Bekker, H., Berendsen, H. J. C. & Freaje, J. G. E. M. (1997) J. Comput. Chem. 18, 1463-1472.
36. Humphrey, W., Dalke, A. & Schulten, K. (1996) J. Mol. Graphics. 14, 33-38.
37. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.