Stability of Iowa mutant and wild type Aβ-peptide aggregates

Journal of Chemical Physics

Volumn 141, Issue 17, 2014, Pages

  Alred, Erik J ^a   Scheele, Emily G ^a   Berhanu, Workalemahu M ^a   Hansmann, Ulrich H E ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGGREGATES; DISEASE CONTROL; GLYCOPROTEINS; HYDROPHOBICITY; MOLECULAR DYNAMICS; OLIGOMERS; PEPTIDES; STABILITY; THERMODYNAMIC STABILITY;

AMYLOID-BETA PEPTIDES; ANTIPARALLEL CONFORMATIONS; HYDROPHOBIC INTERACTIONS; MOLECULAR DYNAMICS SIMULATIONS; PATHOLOGICAL EFFECTS; RELATIVE STABILITIES; STRUCTURAL DIFFERENCES; STRUCTURAL VARIATIONS;

NEURODEGENERATIVE DISEASES;

AMYLOID BETA PROTEIN; PROTEIN AGGREGATE;

CHEMISTRY; GENETICS; MOLECULAR DYNAMICS; MUTATION; PROTEIN STABILITY;

AMYLOID BETA-PEPTIDES; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN AGGREGATES; PROTEIN STABILITY;

EID: 84908689237     PISSN: 00219606     EISSN: 10897690     Source Type: Journal    
DOI: 10.1063/1.4900892     Document Type: Article

References (60)

1. D. Eisenberg and M. Jucker, Cell 148 (6), 1188-1203 (2012). 10.1016/j.cell.2012.02.022
2. M. Ahmed, J. Davis, D. Aucoin, T. Sato, S. Ahuja, S. Aimoto, J. I. Elliott, W. E. Van Nostrand, and S. O. Smith, Nat. Struct. Mol. Biol. 17 (5), 561-556 (2010). 10.1038/nsmb.1799
3. M. R. Sawaya, S. Sambashivan, R. Nelson, M. I. Ivanova, S. A. Sievers, M. I. Apostol, M. J. Thompson, M. Balbirnie, J. J. W. Wiltzius, H. T. McFarlane, A. O. Madsen, C. Riekel, and D. Eisenberg, Nature (London) 447 (7143), 453-457 (2007). 10.1038/nature05695
4. O. N. Antzutkin, J. J. Balbach, R. D. Leapman, N. W. Rizzo, J. Reed, and R. Tycko, Proc. Natl. Acad. Sci. U.S.A. 97 (24), 13045-13050 (2000). 10.1073/pnas.230315097
5. A. T. Petkova, R. D. Leapman, Z. H. Guo, W. M. Yau, M. P. Mattson, and R. Tycko, Science 307 (5707), 262-265 (2005). 10.1126/science.1105850
6. A. W. P. Fitzpatrick, G. T. Debelouchina, M. J. Bayro, D. K. Clare, M. A. Caporini, V. S. Bajaj, C. P. Jaroniec, L. C. Wang, V. Ladizhansky, S. A. Muller, C. E. MacPhee, C. A. Waudby, H. R. Mott, A. De Simone, T. P. J. Knowles, H. R. Saibil, M. Vendruscolo, E. V. Orlova, R. G. Griffin, and C. M. Dobson, Proc. Natl. Acad. Sci. U.S.A. 110 (14), 5468-5473 (2013). 10.1073/pnas.1219476110
7. M. R. Smaoui, F. Poitevin, M. Delarue, P. Koehl, H. Orland, and J. Waldispuhl, Biophys. J. 104 (3), 683-693 (2013). 10.1016/j.bpj.2012.12.037
8. Y. Miller, B. Y. Ma, and R. Nussinov, Biophys. J. 97 (4), 1168-1177 (2009). 10.1016/j.bpj.2009.05.042
9. W. M. Berhanu and U. H. E. Hansmann, PLoS One 7 (7), e0041479 (2012). 10.1371/journal.pone.0041479
10. C. Nilsberth, A. Westlind-Danielsson, C. B. Eckman, M. M. Condron, K. Axelman, C. Forsell, C. Stenh, J. Luthman, D. B. Teplow, S. G. Younkin, J. Naslund, and L. Lannfelt, Nat. Neurosci. 4 (9), 887-893 (2001). 10.1038/nn0901-887
11. K. Murakami, K. Irie, A. Morimoto, H. Ohigashi, M. Shindo, M. Nagao, T. Shimizu, and T. Shirasawa, J. Biol. Chem. 278 (46), 46179-46187 (2003). 10.1074/jbc.M301874200
12. A. T. Petkova, W. M. Yau, and R. Tycko, Biochemistry 45 (2), 498-512 (2006). 10.1021/bi051952q
13. R. Tycko, K. L. Sciarretta, J. Orgel, and S. C. Meredith, Biochemistry 48 (26), 6072-6084 (2009). 10.1021/bi9002666
14. W. Qiang, W. M. Yau, Y. Q. Luo, M. P. Mattson, and R. Tycko, Proc. Natl. Acad. Sci. U.S.A. 109 (12), 4443-4448 (2012). 10.1073/pnas.1111305109
15. L. E. Buchanan, J. K. Carr, A. M. Fluitt, A. J. Hoganson, S. D. Moran, J. J. Pablo, J. L. Skinner, and M. T. Zanni, Proc. Natl. Acad. Sci. U.S.A. 111 (16), 5796-5801 (2014). 10.1073/pnas.1401587111
16. R. Tycko, Annu. Rev. Phys. Chem. 62, 279-299 (2011). 10.1146/annurev-physchem-032210-103539
17. A. Schmechel, H. Zentgraf, S. Scheuermann, G. Fritz, R. D. Pipkorn, J. Reed, K. Beyreuther, T. A. Bayer, and G. Multhaup, J. Biol. Chem. 278 (37), 35317-35324 (2003). 10.1074/jbc.M303547200
18. S. Piana, K. Lindorff-Larsen, and D. E. Shaw, Proc. Natl. Acad. Sci. U.S.A. 109 (44), 17845-17850 (2012). 10.1073/pnas.1201811109
19. U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 14, 1333-1338 (1993). 10.1002/jcc.540141110
20. U. H. E. Hansmann, Chem. Phys. Lett. 281, 140-150 (1997). 10.1016/S0009-2614(97)01198-6
21. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314 (1-2), 141-151 (1999). 10.1016/S0009-2614(99)01123-9
22. J. C. F. Schulz, L. Schmidt, R. B. Best, J. Dzubiella, and R. R. Netz, J. Am. Chem. Soc. 134 (14), 6273-6279 (2012). 10.1021/ja211494h
23. I. C. Lin and M. E. Tuckerman, J. Phys. Chem. B 114 (48), 15935-15940 (2010). 10.1021/jp109865y
24. L. B. Wright and T. R. Walsh, Phys. Chem. Chem. Phys. 15 (13), 4715-4726 (2013). 10.1039/c3cp42921k
25. D. M. Huang and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 97 (15), 8324-8327 (2000). 10.1073/pnas.120176397
26. J. Zhao, X. Yu, G. Liang, and J. Zheng, Biomacromolecules 12 (1), 210-220 (2011). 10.1021/bm101159p
27. N. Foloppe and A. D. MacKerell, J. Comput. Chem. 21 (2), 86-104 (2000). 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G
28. A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 102 (18), 3586-3616 (1998). 10.1021/jp973084f
29. A. D. MacKerell, M. Feig, and C. L. Brooks III, J. Comput. Chem. 25 (11), 1400-1415 (2004). 10.1002/jcc.20065
30. U. Zachariae, R. Schneider, R. Briones, Z. Gattin, J. P. Demers, K. Giller, E. Maier, M. Zweckstetter, C. Griesinger, S. Becker, R. Benz, B. L. de Groot, and A. Lange, Structure 20 (9), 1540-1549 (2012). 10.1016/j.str.2012.06.015
31. C. Kutzner, H. Grubmuller, B. L. de Groot, and U. Zachariae, Biophys. J. 101 (4), 809-817 (2011). 10.1016/j.bpj.2011.06.010
32. H. Jang, L. Connelly, F. T. Arce, S. Ramachandran, B. L. Kagan, R. Lal, and R. Nussinov, J. Chem. Theory Comput. 9 (1), 822-833 (2013). 10.1021/ct300916f
33. Y. Miller, B. Y. Ma, and R. Nussinov, J. Am. Chem. Soc. 133 (8), 2742-2748 (2011). 10.1021/ja1100273
34. S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl, Struct. Bioinf. 29 (7), 845-854 (2013). 10.1093/bioinformatics/btt055
35. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98 (12), 10089-10092 (1993). 10.1063/1.464397
36. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103 (19), 8577-8593 (1995). 10.1063/1.470117
37. B. Hess, J. Chem. Theory Comput. 4 (1), 116-122 (2008). 10.1021/ct700200b
38. S. Miyamoto and P. A. Kollman, J. Comput. Chem. 13 (8), 952-962 (1992). 10.1002/jcc.540130805
39. G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. 126 (1), 014101 (2007). 10.1063/1.2408420
40. G. Bussi, T. Zykova-Timan, and M. Parrinello, J. Chem. Phys. 130 (7), 074101 (2009). 10.1063/1.3073889
41. M. Parrinello and A. Rahman, J. Appl. Phys. 52 (12), 7182-7190 (1981). 10.1063/1.328693
42. W. L. DeLano, " PyMOL molecular graphics system," Version 1.3.0.4 Schrödinger, LLC, 2002.
43. N. A. Bernhardt, W. M. Berhanu, and U. H. E. Hansmann, J. Phys. Chem. B 117 (50), 16076-16085 (2013). 10.1021/jp409777p
44. O. N. Antzutkin, D. Iuga, A. V. Filippov, R. T. Kelly, J. Becker-Baldus, S. P. Brown, and R. Dupree, Angew. Chem.-Int. Ed. 51 (41), 10289-10292 (2012). 10.1002/anie.201203595
45. W. M. Berhanu and A. E. Masunov, J. Mol. Model. 18 (3), 1129-1142 (2012). 10.1007/s00894-011-1123-3
46. J. L. Guo and V. M. Y. Lee, Nat. Med. 20 (2), 130-138 (2014). 10.1038/nm.3457
47. Y. Miller, B. Y. Ma, and R. Nussinov, Chem. Rev. 110 (8), 4820-4838 (2010). 10.1021/cr900377t
48. A. Kahler, H. Sticht, and A. H. C. Horn, PLoS One 8 (7), e70521 (2013). 10.1371/journal.pone.0070521
49. D. W. Wright, B. A. Hall, O. A. Kenway, S. Jha, and P. V. Coveney, J. Chem. Theory Comput. 10 (3), 1228-1241 (2014). 10.1021/ct4007037
50. W. M. Berhanu, F. Yasar, and U. H. E. Hansmann, ACS Chem. Neurosci. 4 (11), 1488-1500 (2013). 10.1021/cn400141x
51. W. M. Berhanu and U. H. E. Hansmann, Prot.: Struct., Funct., Bioinf. 81 (9), 1542-1555 (2013). 10.1002/prot.24302
52. D. Spiliotopoulos, A. Spitaleri, and G. Musco, PLoS One 7 (10), e46902 (2012). 10.1371/journal.pone.0046902
53. B. R. Miller, T. D. McGee, J. M. Swails, N. Homeyer, H. Gohlke, and A. E. Roitberg, J. Chem. Theory Comput. 8 (9), 3314-3321 (2012). 10.1021/ct300418h
54. N. Homeyer and H. Gohlke, Mol. Inf. 31 (2), 114-122 (2012). 10.1002/minf.201100135
55. J. Park, B. Kahng, and W. Hwang, PLoS Comput. Biol. 5 (9), e1000492 (2009). 10.1371/journal.pcbi.1000492
56. A. Laganowsky, C. Liu, M. R. Sawaya, J. P. Whitelegge, J. Park, M. L. Zhao, A. Pensalfini, A. B. Soriaga, M. Landau, P. K. Teng, D. Cascio, C. Glabe, and D. Eisenberg, Science 335 (6073), 1228-1231 (2012). 10.1126/science.1213151
57. J. Wereszczynski and J. A. McCammon, Q. Rev. Biophys. 45, 1-25 (2012). 10.1017/S0033583511000096
58. R. Tycko, Prot. Sci. 23, 1528-1539 (2014). 10.1002/pro.2544
59. A. Okamoto, A. Yano, K. Nomura, S. Higai, and N. Kurita, J. Mol. Graph. Model. 50, 113-124 (2014). 10.1016/j.jmgm.2014.03.004
60. L. Jiang, C. Liu, D. Leibly, M. Landau, M. L. Zhao, M. P. Hughes, and D. S. Eisenberg, eLife 2, e00857 (2013). 10.7554/eLife.00857