Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water

Journal of Computational Chemistry

Volumn 32, Issue 2, 2011, Pages 349-355

  Lee, Chewook ^a   Ham, Sihyun ^a  

^a Sookmyung Women's University   (South Korea)

Author keywords

aggregation prone structure; Alzheimer's disease; amyloid beta protein; protein aggregation; protein misfolding

Indexed keywords

AGGREGATION-PRONE STRUCTURE; ALZHEIMER'S DISEASE; AMYLOID BETAS; PROTEIN AGGREGATION; PROTEIN MISFOLDING;

AGGLOMERATION; CONFORMATIONS; DISEASES; GLYCOPROTEINS; MOLECULAR DYNAMICS; MONOMERS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHASE SHIFTERS;

PROTEINS;

AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN (1 42); AMYLOID BETA PROTEIN[1-40]; AMYLOID BETA-PROTEIN (1-42); PEPTIDE FRAGMENT; WATER;

ALZHEIMER DISEASE; ARTICLE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN FOLDING;

ALZHEIMER DISEASE; AMYLOID BETA-PEPTIDES; HUMANS; MOLECULAR DYNAMICS SIMULATION; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; PROTEIN FOLDING; WATER;

EID: 78650086243     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21628     Document Type: Article

References (82)

1. Hartmann, T., Bieger, S. C., Brühl, B., Tienari, P. J., Ida, N., Allsop, D., Roberts, G. W., Masters, C. L., Dotti, C. G., Unsicker, K., Beyreuther, K., Nature Med 1997, 3, 1016.
2. Kayed, R., Head, E., Thompson, J. L., McIntire, T. M., Milton, S. C., Cotman, C. W., Glabe, C. G., Science 2003, 300, 486.
3. Tiraboschi, P., Hansen, L. A., Thal, L. J., Corey-Bloom, J., Neurology 2004, 62, 1984.
4. Bonelli, R. M., Wenning, G. K., Curr Pharm Des 2006, 12, 2701.
5. Gusella, J. F., Wexler, N. S., Conneally, P. M., Naylor, S. L., Anderson, M. A., Tanzi, R. E., Watkins, P. C., Ottina, K., Wallace, M. R., Sakaguchi, A. Y., Young, A. B., Shoulson, I., Bonilla, E., Marti, J. B., Nature 1983, 306, 234.
6. Imarisio, S., Carmichael, J., Korolchuk, V., Chen, C.-W., Saiki, S., Rose, C., Krishna, G., Davies, J. E., Ttofi, E., Underwood, B. R., Rubinsztein, D. C., Biochem J 2008, 412, 191.
7. Betarbet, R., Sherer, T. B., MacKenzie, G., Garcia-Osuna, M., Panov, A. V., Greenamyre, J. T., Nat Neurosci 2000, 3, 1301.
8. Hardy, J. A., Higgins, G. A., Science 1992, 256, 184.
9. Harper, J. D., Peter, T. L. J., Annu Rev Biochem 1997, 66, 385.
10. Rochet, J.-C., Peter, T. L. J., Curr Opin Struct Biol 2000, 10, 60.
11. Jarrett, J. T., Lansbury. P. T. J., Cell 1993, 73, 1055.
12. Mucke, L., Masliah, E., Yu, G. Q., Mallory, M., Rockenstein, E. M., Tatsuno, G., Hu, K., Kholodenko, D., Johnson-Wood, K., McConlogue, L., J Neurosci 2000, 20, 4050.
13. Schmechel, A., Zentgraf, H., Scheuermann, S., Fritz, G., Pipkorn, R. D., Reed, J., Beyreuther, K., Bayer, T. A., Multhaup, G., J Biol Chem 2003, 278, 35317.
14. Zhang, Y., McLaughlin, R., Goodyer, C., LeBlanc, A., J Cell Biol 2002, 156, 519.
15. Walsh, D. M., Selkoe, D. J., J Neurochem 2007, 101, 1172.
16. Barrow, C. J., Yasuda, A., Kenny, P. T., Zagorski, M. G., J Mol Biol 1992, 225, 1075.
17. Bitan, G., Kirkitadze, M. D., Lomakin, A., Vollers, S. S., Benedek, G. B., Teplow, D. B., Proc Natl Acad Sci USA 2003, 100, 330.
18. Jarrett, J. T., Berger, E. P., Peter, T. L. J., Biochemistry 1993, 32, 4693.
19. Riek, R., Guntert, P., Dobeli, H., Wipf, B., Wuthrich, K., Eur J Biochem 2001, 268, 5930.
20. Baumketner, A., Krone, M. G., Shea, J.-E., Proc Natl Acad Sci USA 2008, 105, 6027.
21. Cruz, L., Urbanc, B., Borreguero, J. M., Lazo, N. D., Teplow, D. B., Stanley, H. E., Proc Natl Acad Sci USA 2006, 12, 118263.
22. Fawzi, N. L., Phillips, A. H., Ruscio, J. Z., Doucleff, M., Wemmer, D. E., Head-Gordon, T., J Am Chem Soc 2008, 130, 6145.
23. Gnanakaran, S., Nussinov, R., García, A. E., J Am Chem Soc 2006, 128, 2158.
24. Han, W., Wu, Y. D., J Am Chem Soc 2005, 127, 15408.
25. Hwang, W., Zhang, S., Kamm, R. D., Karplus, M., Proc Natl Acad Sci USA 2002, 101, 12916.
26. Khandogin, J., Brooks, C. L., Proc Natl Acad Sci USA 2007, 104, 16880.
27. Klimov, D. K., Straub, J. E., Thirumalai, D., Proc Natl Acad Sci USA 2004, 101, 14760.
28. Krone, M. G., Hua, L., Soto, P., Zhou, R., Berne, B. J., Shea, J.-E., J Am Chem Soc 2008, 130, 11066.
29. Lakdawala, A. S., Morgan, D. M., Liotta, D. C., Lynn, D. G., Snyder, J. P., J Am Chem Soc 2002, 124, 15150.
30. Ma, B. Y., Nussinov, R., Proc Natl Acad Sci USA 2002, 99, 14126.
31. Nguyen, P. H., Li, M. S., Stock, G., Straub, J. E., Thirumalai, D., Proc Natl Acad Sci USA 2007, 104, 111.
32. Santini, S., Mousseau, N., Derreumaux, P., J Am Chem Soc 2004, 126, 11509.
33. Tarus, B., Straub, J. E., Thirumalai, D., J Am Chem Soc 2006, 125, 16159.
34. Wu, C., Wang, Z., Lei, H., Zhang, W., Duan, Y., J Am Chem Soc 2007, 129, 1225.
35. Bernstein, S. L., Wyttenbach, T., Baumketner, A., Shea, J.-E., Bitan, G., Teplow, D. B., Bowers, M. T., J Am Chem Soc 2005, 127, 2075.
36. Dong, X., Chen, W., Mousseau, N., Derreumaux, P., J Chem Phys 2008, 128, 125108.
37. Itoh, S. G., Okamoto, Y., J Phys Chem B 2008, 112, 2767.
38. Jang, S., Shin, S., J Phys Chem B 2006, 110, 1955.
39. Lam, A. R., Teplow, D. B., Stanley, H. E., Urbanc, B., J Am Chem Soc 2008, 130, 17413.
40. Urbanc, B., Cruz, L., Yun, S., Buldyrev, S. V., Bitan, G., Teplow, D. B., Stanley, H. E., Proc Natl Acad Sci USA 2004, 101, 17345.
41. Borreguero, J. M., Urbanc, B., Lazo, N. D., Buldyrev, S. V., Teplow, D. B., Stanley, H. E., Proc Natl Acad Sci USA 2005, 102, 6015.
42. Jang, H. B., Hall, C. K., Zhou, Y. Q., Biophys J 2004, 86, 31.
43. Peng, S., Ding, F., Urbanc, B., Buldyrev, S. V., Cruz, L., Stanley, H. E., Dokholyan, N. V., Phys Rev E 2004, 69, 041908.
44. Urbanc, B., Cruz, L., Ding, F., Sammond, D., Khare, S., Buldyrev, S. V., Stanley, H. E., Dokholyan, N. V., Biophys J 2004, 87, 2310.
45. Yun, S., Urbanc, B., Cruz, L., Bitan, G., Teplow, D. B., Stanley, H. E., Biophys J 2007, 92, 4064.
46. Crescenzi, O., Tomaselli, S., Guerrini, R., Salvadori, S., D'Ursi, A. M., Temussi, P. A., Picone, D., Eur J Biochem 2002, 269, 5642.
47. Case, D. A., Darden, T. A., Cheatam, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, K. M., Pearlman, D. A., Crowley, M., Walker, R. C., Zhang, W., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Wong, K. F., Paesani, F., Wu, X., Brozell, S., Tsui, V., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Beroza, P., Mathews, D. H., Schafmeister, C., Ross, W. S., Kollman, P. A., AMBER 9. University of California: San Francisco, 2006.
48. Wang, J., Cieplak, P., Kollman, P. A., J Comput Chem 2000, 21, 1049.
49. Berendsen, H. J. C., Postma, J. P. M., Vangunsteren, W. F., Dinola, A., Haak, J. R., J Chem Phys 1984, 81, 3684.
50. Best, R. B., Buchete, N.-V., Hummer, G., Biophys J 2008, 95, L07.
51. Sgourakis, N. G., Yan, Y. L., McCallum, S. A., Wang, C Y., Garcia, A. E., J Mol Biol 2007, 368, 1448.
52. Lim, K. H., Collver, H. H., Le, Y. T. H., Nagchowdhuri, P., Kenney, J. M., Biochem Biophys Res Commun 2007, 353, 443.
53. Lührs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Doeli, H., Schubert, D., Riek, R., Proc Natl Acad Sci USA 2005, 102, 17342.
54. Luttmann, E., Fels, G., Chem Phys 2006, 323, 138.
55. Triguero, L., Singh, R., Prabhakar, R., J Phys Chem B 2008, 112, 2159.
56. Triguero, L., Singh, R., Prabhakar, R., J Phys Chem B 2008, 112, 7123.
57. Wood, S. J., Maleeff, B., Hart, T., Wetzel, R., J Mol Biol 1996, 256, 870.
58. Yan, Y., Wang, C. Y., J Mol Biol 2006, 364, 853.
59. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., Klein, M. L., J Chem Phys 1983, 79, 926.
60. Darden, T., York, D., Pedersen, L., J Chem Phys 1993, 98, 10089.
61. Ryckaert, J. P., Ciccotti, G., Berendsen, H. J. C., J Comput Phys 1977, 23, 327.
62. Karplus, M., J Chem Phys 1959, 30, 11.
63. Hu, J.-S., Bax, A., J Am Chem Soc 1997, 119, 6360.
64. Kabsch, W., Sander, C., Biopolymers 1983, 22, 2577.
65. Lee, B., Richards, FM., J Biol Chem 1971, 55, 379.
66. Kyte, J., Doolittle, R. F., J Mol Biol 1982, 157, 105.
67. Feig, M., Karanicolas, J., Brooks, C. L., J Mol Graph Model 2004, 22, 377.
68. D'Ursi, A. M., Armenante, M. R., Guerrini, R., Salvadori, S., Sorrentino, G., Picone, D., J Med Chem 2004, 47, 4231.
69. Fraser, P. E., Nguyen, J. T., Surewicz, W. K., Kirschner, D. A., Biophys J 1991, 60, 1190.
70. Massi, F., Straub, J. E., J Comput Chem 2003, 24, 143.
71. Picotti, P., de Franceschi, G., Frare, E., Spolaore, B., Zambonin, M., Chiti, F., de Laureto, P. P., Fontana, A., J Mol Biol 2007, 367, 1237.
72. Shen, C. L., Murphy, R. M., Biophys J 1995, 69, 640.
73. Zhang, S., Iwata, K., Lachenmann, M. J., Peng, J. W., Li, S., Stimson, E. R., Lu, Y.-A., Felix, A. M., Maggio, J. E., Lee, J. P., J Struct Biol 2000, 130, 130.
74. Lim, K. H., Henderson, G. L., Jha, A., Louhivuori, M., ChemBioChem 2007, 8, 1251.
75. Morimoto, A., Irie, K., Murakami, K., Masuda, Y., Ohigashi, H., Nagao, M., Fukuda, H., Shimizu, T., Shirasawa, T., J Biol Chem 2004, 279, 52781.
76. Cheon, M., Chang, I., Mohanty, S., Luheshi, L. M., Dobson, C. M., Vendruscolo, M., Favrin, G., Plos Comput Biol 2007, 3, 1727.
77. Chimon, S., Ishii, Y., J Am Chem Soc 2005, 127, 13472.
78. Shen, L., Ji, H.-F., Zhang, H.-Y., J Phys Chem B 2008, 112, 3164.
79. Chiti, F., Dobson, C. M., Annu Rev Biochem 2006, 75, 333.
80. Dobson, C. M., Trends Biochem Sci 1999, 24, 329.
81. Dobson, C. M., Nature 2003, 426, 884.
82. Hoyer, W., Gronwall, C., Jonsson, A., Stahl, S., Hard, T., Proc Natl Acad Sci USA 2008, 105, 5099.