Role of water in mediating the assembly of alzheimer amyloid-β Aβ16-22 protofilaments

Journal of the American Chemical Society

Volumn 130, Issue 33, 2008, Pages 11066-11072

  Krone, Mary Griffin ^a   Hua, Lan ^b   Soto, Patricia ^a   Zhou, Ruhong ^b,c   Berne, B J ^b,c   Shea, Joan Emma ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; GLYCOPROTEINS; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY;

ALZHEIMER AMYLOID; AMYLOID FIBRILS; BASIC BUILDING BLOCKS; MOLECULAR DYNAMICS SIMULATIONS; PROTOFILAMENT; PROTOFILAMENTS; ROLE OF WATER;

DYNAMICS;

AMYLOID; AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN[16-22]; PROTOFILAMENT; WATER;

ALZHEIMER DISEASE; ARTICLE; BETA SHEET; ENERGY TRANSFER; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR DYNAMICS; SIMULATION;

AMYLOID BETA-PROTEIN; COMPUTER SIMULATION; HYDROPHOBICITY; MODELS, CHEMICAL; MODELS, MOLECULAR; PHASE TRANSITION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; TEMPERATURE; WATER;

EID: 50249168222     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja8017303     Document Type: Article

References (57)

1. Teplow, D. B. Amyloid 1998, 5, 121-142.
2. Sunde, M.; Blake, C. Adv. Protein Chem. 1997, 50, 123-159.
3. Eanes, E. D.; Glenner, G. G. J. Histochem. Cytochem. 1968, 16, 673-677.
4. Dobson, C. M. Trends Biochem. Sci. 1999, 24, 329-332.
5. Caughey, B.; Lansbury, P. T. Annu. Rev. Neurosci. 2003, 26, 267-298.
6. Tseng, B. P.; Esler, W. P.; Clish, C. B.; Stimson, E. R.; Ghilardi, J. R.; Vinters, H. V.; Mantyh, P. W.; Lee, J. P.; Maggio, J. E. Biochemistry 1999, 38, 10424-10431.
7. Nichols, M. R.; Moss, M. A.; Reed, D. K.; Lin, W.-L.; Mukhopadhyay, R.; Hoh, J. H.; Rosenberry, T. L. Biochemistry 2002, 41, 6115-6127.
8. Berard, D. R.; Attard, P.; Patey, G. N. J. Chem. Phys. 1993, 98, 7236-7244.
9. Patey, G. N. Ber. Bunsen-Ges. Phys. Chem. 1996, 100, 885-888.
10. Wallqvist, A.; Berne, B. J. J. Phys. Chem. 1995, 99, 2893-2899.
11. Li, X.; Li, J.; Eleftheriou, M.; Zhou, R. J. Am. Chem. Soc. 2006, 128, 12439-47.
12. Zangi, R.; Hagen, M.; Berne, B. J. J. Am. Chem. Soc. 2007, 129, 4678-86.
13. Lum, K.; Luzar, A. Phys. Rev. E 1997, 56, R6283-R6286.
14. Hummer, G.; Garde, S. Phys. Rev. Lett. 1998, 80, 4193-4196.
15. Luzar, A.; Leung, K. J. Chem. Phys. 2000, 113, 5836-5844.
16. Ashbaugh, H. S.; Paulaitis, M. E. J. Am. Chem. Soc. 2001, 123, 10721-10728.
17. Bratko, D.; Curtis, R. A.; Blanch, H. W.; Prausnitz, J. M. J. Chem. Phys. 2001, 115, 3873-3877.
18. Huang, D. M.; Chandler, D. J. Phys. Chem. B 2002, 106, 2047-2053.
19. Lum, K.; Chandler, D.; Weeks, J. D. J. Phys. Chem. B 1999, 103, 4570-4577.
20. Wallqvist, A.; Gallicchio, E.; Levy, R. M. J. Phys. Chem. B 2001, 105, 6745-6753.
21. Huang, X.; Margulis, C. J.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 11953-11958.
22. Hua, L.; Huang, X.; Liu, P.; Zhou, R.; Berne, B. J. J. Phys. Chem. B 2007, 111, 9069-9077.
23. Liu, P.; Huang, X. H.; Zhou, R. H.; Berne, B. J. Nature 2005, 437, 159-162.
24. Cheung, M. S.; Garcia, A. E.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 685-690.
25. Guo, W.; Lampoudi, S.; Shea, J.-E. Biophys. J. 2003, 85, 61-69.
26. Shea, J.-E., III Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16064-16068.
27. Cummings, J. L. N. Engl. J. Med. 2004, 351, 56-67.
28. Hardy, J.; Selkoe, D. J. Science 2002, 297, 353-356.
29. Balbach, J. J.; Ishii, Y.; Antzutkin, O. N.; Leapman, R. D.; Rizzo, N. W.; Dyda, F.; Reed, J.; Tycko, R. Biochemistry 2000, 39, 13748-13759.
30. Soto, P.; Griffin, M. A.; Shea, J.-E. Biophys. J. 2007, 93, 3015-3025.
31. Choudhury, N.; Pettit, B. M. J. Am. Chem. Soc. 2005, 127, 3556-3567.
32. Zhou, R. H.; Huang, X. H.; Margulis, C. J.; Berne, B. J. Science 2004, 305, 1605-1609.
33. Wolde, P. R. t.; Chandler, D. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6539-6543.
34. Huang, D. M.; Chandler, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8324-8327.
35. Finkelstein, E. V.; Shaknovich, E. I. Biopolymers 1989, 28, 1681-1694.
36. Azriel, R.; Gazit, E. J. Biol. Chem. 2001, 276, 34156-34161.
37. Cheng, Y. K.; Rossky, P. J. Nature 1998, 392, 696-699.
38. Lee, C. Y.; McCammon, J. A.; Rossky, P. J. J. Chem. Phys. 1984, 80, 4448-4454.
39. Southall, N. T.; Dill, K. A. J. Phys. Chem. B 2000, 104, 1326-1331.
40. Choudhury, N.; Pettit, B. M. J. Am. Chem. Soc. 2007, 129, 4847-4852.
41. MacCallum, J. L.; Moghaddam, M. S.; Chan, H. S.; Tieleman, D. P. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 6206-6219.
42. Ma, B.; Nussinov, R. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 14126-31.
43. Buchete, N. V.; Tycko, R.; Hummer, G. J. Mol. Biol. 2005, 353, 804-21.
44. Zheng, J.; Jang, H.; Ma, B.; Tsai, C. J.; Nussinov, R. Biophys. J. 2007, 93, 3046-57.
45. Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Madsen, A. O.; Riekel, C.; Grothe, R.; Eisenberg, D. Nature 2005, 435, 773-8.
46. Favrin, G.; Irback, A.; Mohanty, S. Biophys. J. 2004, 87, 3657-3664.
47. Gnanakaran, S.; Nussinov, R.; Garcia, A. E. J. Am. Chem. Soc. 2006, 128, 2158-2159.
48. Klimov, D. K.; Thirumalai, D. Structure 2003, 11, 295-307.
49. Santini, S.; Wei, G. H.; Mousseau, N.; Derreumaux, P. Structure 2004, 12, 1245-1255.
50. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Intermolecular Forces; Reidel: Dordrech, 1981.
51. Scott, W. R. P.; Hunenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, T.; Kruger, P.; van Gunsteren, W. F. J. Phys. Chem. A 1999, 103, 3596-3607.
52. Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
53. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472.
54. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962.
55. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
56. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56.
57. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.