Energy landscapes of the monomer and dimer of the Alzheimer's peptide AΒ (1-28)

Journal of Chemical Physics

Volumn 128, Issue 12, 2008, Pages

  Dong, Xiao ^a,b   Chen, Wei ^a,b   Mousseau, Normand ^a   Derreumaux, Philippe ^b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b France   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AGGLOMERATION; AMINO ACIDS; DIMERS; DISEASES; PEPTIDES;

ALZHEIMER'S PEPTIDE; ENERGY LANDSCAPES;

MONOMERS;

AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN (1 28); AMYLOID BETA-PROTEIN (1-28); PEPTIDE FRAGMENT; SOLVENT; WATER;

ALZHEIMER DISEASE; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; COMPUTER SIMULATION; DIMERIZATION; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

ALZHEIMER DISEASE; AMYLOID BETA-PROTEIN; CIRCULAR DICHROISM; COMPUTER SIMULATION; DIMERIZATION; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SOLUTIONS; SOLVENTS; THERMODYNAMICS; WATER;

EID: 41549164349     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2890033     Document Type: Article

References (64)

1. H. A. Lashuel and P. T. J. Lansbury, Q. Rev. Biophys. 39, 167 (2006).
2. M. S. Goldberg and P. T. J. Lansbury, Nat. Cell Biol. 2, E115 (2000).
3. M. P. Lambert, A. K. Barlow, B. A. Chromy, C. Edwards, R. Freed, M. Liosatos, T. E. Morgan, I. Rozovsky, B. Trommer, K. L. Viola, P. Wals, C. Zhang, C. E. Finch, G. A. Krafft, and W. L. Klein, Proc. Natl. Acad. Sci. U.S.A. 95, 6448 (1998).
4. D. M. Walsh, I. Klyubin, J. V. Fadeeva, W. K. Cullen, R. Anwyl, M. S. Wolfe, M. J. Rowan, and D. J. Selkoe, Nature (London) 416, 535 (2002).
5. G. Bitan, M. D. Kirkitadze, A. Lomakin, S. S. Vollers, G. B. Benedek, and D. B. Teplow, Proc. Natl. Acad. Sci. U.S.A. 100, 330 (2003).
6. D. Flock, S. Colacino, G. Colombo, and A. Di Nola, Proteins 62, 183 (2006).
7. Y. Xu, J. Shen, X. Luo, W. Zhu, K. Chen, J. Ma, and H. Jiang, Proc. Natl. Acad. Sci. U.S.A. 102, 5403 (2005).
8. D. F. Raffa and A. Rauk, J. Phys. Chem. B 111, 3789 (2007).
9. A. Voegler Smith and C. K. Hall, Proteins 44, 344 (2001).
10. R. Malek and N. Mousseau, Phys. Rev. E 62, 7723 (2000).
11. S. Santini, N. Mousseau, and P. Derreumaux, J. Am. Chem. Soc. 126, 11509 (2004).
12. S. Santini, G. H. Wei, N. Mousseau, and P. Derreumaux, Structure (London) 12, 1245 (2004).
13. G. Favrin, A. Irback, and S. Mohanty, Biophys. J. 87, 3657 (2004).
14. S. A. Petty and S. M. Decatur, J. Am. Chem. Soc. 127, 13488 (2005).
15. N. D. Lazo, M. A. Grant, M. C. Condron, A. C. Rigby, and D. B. Teplow, Protein Sci. 14, 1581 (2005).
16. A. Baumketner, S. L. Bernstein, T. Wyttenbach, N. D. Lazo, D. B. Teplow, M. T. Bowers, and J. E. Shea, Protein Sci. 15, 1239 (2006).
17. W. Chen, N. Mousseau, and P. Derreumaux, J. Chem. Phys. 125, 084911 (2006).
18. A. Baumketner and J. E. Shea, J. Mol. Biol. 362, 567 (2006).
19. I. Daidone, F. Simona, D. Roccatano, R. A. Broglia, G. Tiana, G. Colombo, and A. Di Nola, Proteins 57, 198 (2004).
20. J. P. Lee, E. R. Stimson, J. R. Ghilardi, P. W. Mantyh, Y. A. Lu, A. M. Felix, W. Llanos, A. Behbin, M. Cummings, and M. Van Criekinge, Biochemistry 34, 5191 (1995).
21. W. Han and Y.-D. Wu, J. Am. Chem. Soc. 127, 15408 (2005).
22. B. Tarus, J. E. Straub, and D. Thirumalai, J. Mol. Biol. 345, 1141 (2005).
23. E. Mikros, D. Benaki, E. Humpfer, M. Spraul, S. Loukas, C. Stassinopoulou, and M. Pelecanou, Angew. Chem., Int. Ed. Engl. 40, 3603 (2001).
24. A. T. Petkova, Y. Ishii, J. J. Balbach, O. N. Antzutkin, R. D. Leapman, F. Delaglio, and R. Tycko, Proc. Natl. Acad. Sci. U.S.A. 99, 16742 (2002).
25. J. Talafous, K. J. Marcinowski, G. Klopman, and M. G. Zagorski, Biochemistry 33, 7788 (1994).
26. K. Ma, E. Clancy, Y. Zhang, D. Ray, K. Wollenberg, and M. Zagorski, J. Am. Chem. Soc. 121, 8698 (1999).
27. F. Eker, K. Griebenow, and R. Schweitzer-Stenner, Biochemistry 43, 6893 (2004).
28. C. L. Shen, G. L. Scott, F. Merchant, and R. M. Murphy, Biophys. J. 65, 2383 (1993).
29. A. Kapurniotu, A. Buck, M. Weber, A. Schmauder, T. Hirsch, J. Bernhagen, and M. Tatarek-Nossol, Chem. Biol. 10, 149 (2003).
30. B. Klajnert, M. Cortijo-Arellano, J. Cladera, and M. Bryszewska, Biochem. Biophys. Res. Commun. 345, 21 (2006).
31. B. Solomon, R. Koppel, D. Frankel, and E. Hanan-Aharon, Proc. Natl. Acad. Sci. U.S.A. 94, 4109 (1997).
32. C. D. Syme and J. H. Viles, Biochim. Biophys. Acta 1764, 246 (2006).
33. K. Kirshenbaum and V. Daggett, Biochemistry 34, 7629 (1995).
34. M. Valerio, A. Colosimo, F. Conti, A. Giuliani, A. Grottesi, C. Manetti, and J. P. Zbilut, Proteins 58, 110 (2005).
35. J. Kandoghin and C. L. Brooks, Proc. Natl. Acad. Sci. U.S.A. 104, 16880 (2007).
36. G. Barkema and N. Mousseau, Phys. Rev. Lett. 77, 4358 (1996).
37. G. Wei, N. Mousseau, and P. Derreumaux, J. Chem. Phys. 117, 11379 (2002).
38. J. Maupetit, P. Tuffery, and P. Derreumaux, Proteins 69, 394 (2007).
39. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953).
40. P. Derreumaux, J. Chem. Phys. 107, 1941 (1997).
41. P. Derreumaux, Phys. Rev. Lett. 85, 206 (2000).
42. N. Floquet, S. Pasco, L. Ramont, P. Derreumaux, J.-Y. Laronze, J.-M. Nuzillard, F. X. Maquart, A. J. P. Alix, and J.-C. Monboisse, J. Biol. Chem. 279, 2091 (2004).
43. G. Wei, N. Mousseau, and P. Derreumaux, Proteins 56, 464 (2004).
44. L. Holm and C. Sander, J. Mol. Biol. 233, 123 (1993).
45. L. Holm and C. Sander, Science 273, 595 (1996).
46. S. Wallin, J. Farwer, and U. Bastolla, Proteins 50, 144 (2003).
47. W. Kabsch and C. Sander, Biopolymers 22, 2577 (1983).
48. R. Srinivasan and G. D. Rose, Proc. Natl. Acad. Sci. U.S.A. 96, 14258 (1999).
49. P. Derreumaux and N. Mousseau, J. Chem. Phys. 126, 025101 (2007).
50. See EPAPS Document No. E-JCPSA6-007812 for supplementary Table: Secondary structure composition of the lowest-energy structure of the 10 dimer runs. For more information on EPAPS, see (http://www.aip.org/pubservs/epaps.html).
51. J. J. Balbach, Y. Ishii, O. N. Antzutkin, R. D. Leapman, N. W. Rizzo, F. Dyda, J. Reed, and R. Tycko, Biochemistry 39, 13748 (2000).
52. J. Danielsson, J. Jarvet, P. Damberg, and A. Graslund, FEBS J. 272, 3938 (2005).
53. J. Huang, Y. Yao, J. Lin, Y.-H. Ye, W.-Y. Sun, and W.-X. Tang, J. Biol. Inorg. Chem. 9, 627 (2004).
54. J. Danielsson, J. Jarvet, P. Damberg, and A. Graslund, Magn. Reson. Chem. 40, S89 (2002).
55. Y. Mu, D. Kosov, and G. Stock, J. Phys. Chem. B 107, 5064 (2003).
56. S. Gnanakaran and A. E. García, Proteins 59, 773 (2005).
57. F. Rao and A. Caflisch, J. Mol. Biol. 342, 299 (2004).
58. K. H. Lim, H. H. Collver, Y. T. H. Le, P. Nagchowdhuri, and J. M. Kenney, Biochem. Biophys. Res. Commun. 353, 443 (2007).
59. N. G. Sgourakis, Y. Yan, S. A. McCallum, C. Wang, and A. E. Garcia, J. Mol. Biol. 368, 1448 (2007).
60. B. Urbanc, L. Cruz, S. Yun, S. V. Buldyrev, G. Bitan, D. B. Teplow, and H. E. Stanley, Proc. Natl. Acad. Sci. U.S.A. 101, 17345 (2004).
61. B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan, Biophys. J. 87, 2310 (2004).
62. C. Liang, P. Derreumaux, and G. Wei, Biophys. J. 93, 3353 (2007).
63. T. Luhrs, C. Ritter, M. Adrian, D. Riek-Loher, B. Bohrmann, H. Dobeli, D. Schubert, and R. Riek, Proc. Natl. Acad. Sci. U.S.A. 102, 17342 (2005).
64. Y. Hori, T. Hashimoto, Y. Wakutani, K. Urakami, K. Nakashima, M. M. Condron, S. Tsubuki, T. C. Saido, D. B. Teplow, and T. Iwatsubo, J. Biol. Chem. 282, 4916 (2007).