The importance of steric zipper on the aggregation of the mvggvv peptide derived from the amyloid β peptide

Journal of Biomolecular Structure and Dynamics

Volumn 28, Issue 1, 2010, Pages 39-50

  Chang, Liang Kai ^a   Zhao, Jian Hua ^a   Liu, Hsuan Liang ^a   Wu, Josephine W ^a   Chuang, Chih Kuang ^a,b,c   Liu, Kung Tien ^d   Chen, Jenn Tzong ^d   Tsai, Wei Bor ^e   Ho, Yih ^f  

^a NATIONAL TAIPEI UNIVERSITY OF TECHNOLOGY   (Taiwan)

^b MACKAY MEMORIAL HOSPITAL   (Taiwan)

^c FU JEN CATHOLIC UNIVERSITY   (Taiwan)

^d INSTITUTE OF NUCLEAR ENERGY RESEARCH   (Taiwan)

^e NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^f TAIPEI MEDICAL UNIVERSITY   (Taiwan)

Author keywords

Alzheimer's disease; Amyloid fibril; Amyloid peptide; Molecular dynamics (MD) simulation; Parkinson's disease; Steric zipper

Indexed keywords

AMYLOID BETA PROTEIN; METHIONYLVALYLGLYCYLGLYCYLVALYLVALINE; PEPTIDE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; HYDROPHOBICITY; INTROSPECTION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN STABILITY; PROTEIN STRUCTURE; STEREOCHEMISTRY;

AMINO ACID SEQUENCE; AMYLOID BETA-PEPTIDES; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MUTATION; NEURODEGENERATIVE DISEASES; PEPTIDES; PROTEIN CONFORMATION;

EID: 77956544501     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2010.10507342     Document Type: Article

References (51)

1. Westermark, P., 2005. FEBS J, 272:5942–5949.
2. Dobson, C. M., 2005. Nature, 435:747–749.
3. Groenning, M., Norrman, M., Flink, J. M., van de Weert, M., Bukrinsky, J. T., Schluckebier, G., and Frokjaer, S., 2007. J Struct Biol, 159:483–497.
4. Makin, O. S., and Serpell, L. C., 2005. Methods Mol Biol, 299:67–80.
5. Nilsson, M. R., 2004. Methods, 34:151–160.
6. Rochet, J. C., and Lansbury, P. T., Jr. 2000. Curr Opin Struct Biol, 10:60–68.
7. Sipe, J. D., and Cohen, A. S., 2000. J Struct Biol, 130:88–98.
8. Bucciantini, M., Giannoni, E., Chiti, F., Baroni, F., Formigli, L., Zurdo, J., Taddei, N., Ramponi, G., Dobson, C. M., and Stefani, M., 2002. Nature, 416:507–511.
9. Bucciantini, M., Calloni, G., Chiti, F., Formigli, L., Nosi, D., Dobson, C. M., and Stefani, M., 2004. J Biol Chem, 279:31374–31382.
10. Hardy, J., and Selkoe, D. J., 2002. Science, 97:353–356.
11. Klein, W. L., 2002. Neurochem int, 41:345–352.
12. Hepler, R. W., Grimm, K. M., Nahas, D. D., Breese, R., Dodson, E. C., Acton, P., Keller, P. M., Yeager, M., Wang, H., Shughrue, P., Kinney, G., and Joyce, J. G., 2006. Biochemistry, 45:15157–15167.
13. Lesne, S., Koh, M. T., Kotilinek, L., Kayed, R., Glabe, C. G., Yang, A., Gallagher, M., and Ashe, K. H., 2006. Nature, 440:352–357.
14. Cohen, F. E., and Kelly, J. W., 2003. Nature, 426:905–909.
15. Wang, S. S.-S., and Good, T. A., 2005. J Chin Inst Chem Engrs, 35:533–559.
16. Kim, W., and Hecht, M. H., 2006. Proc Nat l Acad Sci USA, 103:15824–15829.
17. Kheterpal, I., Williams, A., Murphy, C., Bledsoe, B., and Wetzel, R., 2001. Biochemistry, 40:11757–11767.
18. Williams, A. D., Portelius, E., Kheterpal, I., Guo, J. T., Cook, K. D., Xu, Y., and Wetzel, R., 2004. J Mol Biol, 335:833–842.
19. Wurth, C., Guimard, N. K., and Hecht, M. H., 2002. J Mol Biol, 319:1279–1290.
20. Buchete, N. V., Tycko, R., and Hummer, G., 2005. J Mol Biol, 353:804–821.
21. Zheng, J., Jang, H., Ma, B., Tsai, C. J., and Nussinov, R., 2007. Biophys J, 93:3046–3057.
22. Sawaya, M. R., Sambashivan, S., Nelson, R., Ivanova, M. I., Sievers, S. A., Apostol, M. I., Thompson, M. J., Balbirnie, M., Wiltzius, J. J., McFarlane, H. T., Madsen, A. Ø., Riekel, C., and Eisenberg, D., 2007. Nature, 447:453–457.
23. Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. O., Riekel, C., Grothe, R., and Eisenberg, D., 2005. Nature, 435:773–778.
24. Chang, L.-K., Zhao, J.-H., Liu, H.-L., Liu, K.-T., Chen, J.-T., Tsai, W.-B., and Ho, Y., 2009. J Biomol Struct Dyn, 26:731–740.
25. Zhao, J.-H., Liu, H.-L., Liu, Y.-F., Lin, H.-Y., Fang, H.-W., Ho, Y., and Tsai, W.-B. 2009. J Biomol Struct Dyn, 26:481–490.
26. Fang, P.-S., Zhao, J.-H., Liu, H.-L., Liu, K.-T., Chen, J.-T., Lin, H.-Y., Huang, C.-H., and Fang, H.-W., 2009. J Biomol Struct Dyn, 26:549–559.
27. Mehrnejad, F., and Chaparzadeh, N., 2008. J Biomol Struct Dyn, 26:255–262.
28. Yoon, J., Park, J., Jang, S., Lee, K., and Shin, S., 2008. J Biomol Struct Dyn, 25:505–515.
29. Hwang, M. J., Ni, X., Waldman, M., Ewig, C. S., and Hagler, A. T., 1998. Biopolymers, 45:435–468.
30. Allen, M. P., and Tildesley, D. J., 1987. Computer simulation of liquids. Oxford:Clarendon Press.
31. Andersen, H. C., 1983. J Comput Phys, 52:24–34.
32. Tsai, H. H., Zanuy, D., Haspel, N., Gunasekaran, K., Ma, B., Tsai, C. J., and Nussinov, R., 2004. Biophys J, 87:146–158.
33. Cavalli, A., Ferrara, P., and Caflisch, A., 2002. Proteins, 47:305–314.
34. Rao, F., and Caflisch, A., 2003. J Comput Phys, 119:4035–4042.
35. Zheng, J., Zanuy, D., Haspel, N., Tsai, C. J., Aleman, C., and Nussinov, R., 2007. Biochemistry, 46:1205–1218.
36. Rohrig, U. F., Laio, A., Tantalo, N., Parrinello, M., and Petronzio, R., 2006. Biophys J, 91:3217–3229.
37. Zheng, J., Ma, B., Tsai, C. J., and Nussinov, R., 2006. Biophys J, 91:824–833.
38. Wu, C., Lei, H., and Duan, Y., 2005. Biophys J, 88:2897–2906.
39. Li, D. W., Mohanty, S., Irback, A., and Huo, S., 2008. PLoS Comput Biol, 4:e1000238
40. Bouchard, M., Zurdo, J., Nettleton, E. J., Dobson, C. M., and Robinson, C. V., 2000. Protein Sci, 9:1960–1967.
41. Chothia, C., 1973. J Mol Biol, 75:295–302.
42. Jimenez, J. L., Nettleton, E. J., Bouchard, M., Robinson, C. V., Dobson, C. M., and Saibil, H. R., 2002. Proc Natl Acad Sci USA, 99:9196–9201.
43. Haspel, N., Zanuy, D., Ma, B., Wolfson, H., Nussinov, R., and Mol, J., 2005. Biol, 345:1213–1227.
44. Wang, J., Gulich, S., Bradford, C., Ramirez-Alvarado, M., and Regan, L., 2005. Structure, 13:1279–1288.
45. De Simone, A., Pedone, C., and Vitagliano, L., 2008. Biochem Biophys Res Commun, 366:800–806.
46. Esposito, L., Pedone, C., and Vitagliano, L., 2006. Proc Natl Acad Sci USA, 103:11533–11538.
47. Periole, X., Rampioni, A., Vendruscolo, M., and Mark, A. E., 2009. J Phys Chem B, 113:1728–1737.
48. Cohen, A. S., Shirahama, T., and Skinner, M., 1982. Electron microscopy of proteins, 3:165–205.
49. Serpell, L. C., Sunde, M., Benson, M. D., Tennent, G. A., Pepys, M. B., and Fraser, P. E., 2000. J Mol Biol, 300:1033–1039.
50. Sato, T., Kienlen-Campard, P., Ahmed, M., Liu, W., Li, H., Elliott, J. I., Aimoto, S., Constantinescu, S. N., Octave, J. N., and Smith, S. O., 2006. Biochemistry, 45:5503–5516.
51. Fradinger, E. A., Monien, B. H., Urbanc, B., Lomakin, A., Tan, M., Li, H., Spring, S. M., Condron, M. M., Cruz, L., Xie, C. W., Benedek, G. B., and Bitan, G., 2008. Proc Natl Acad Sci USA, 105:14175–14180.