Citation: ZHOU Xiao-Ying, XI Wen-Hui, WEI Guang-Hong. Molecular Dynamics Simulations on the Binding of Fullerene to Amyloid-β Oli mers[J]. Acta Physico-Chimica Sinica, ;2014, 30(8): 1587-1596. doi: 10.3866/PKU.WHXB201405291 shu

Molecular Dynamics Simulations on the Binding of Fullerene to Amyloid-β Oli mers

1.
Department of Physics, Fudan University, Key Laboratory for Computational Physical Sciences Ministry of Education, State Key Laboratory of Surface Physics, Shanghai 200433, P. R. China

Received Date: 11 April 2014
Available Online: 29 May 2014
Fund Project:

We investigated the binding process of fullerene to fibril-like Aβ42 oli mers by performing multiple molecular dynamics simulations. It was observed that the C₆₀ molecule searched a series of positions on the surfaces of the Aβ42 oli mers before finding a stable binding state. Multi-binding sites have been identified and these can be classified into six types according to the type of residue in contact with the fullerene. The sites near the central hydrophobic core (CHC) (¹⁷LVFFA²¹) and the turn region (²⁷NKGAI³¹) were identified as the most suitable sites with the lowest associated binding energies. These bound states were primarily stabilized by van der Waals interactions, while the solvation effect acted as a destabilizing factor.
- Multi-site binding,
- Binding energy,
- Secondary structure disruption,
- Hydrophobic cave,
- Groove-rolling mechanism
1. [1]
  
  (1) Chiti, F.; Dobson, C. M. Annu. Rev. Biochem. 2006, 75, 333. doi: 10.1146/annurev.biochem.75.101304.123901
2. [2]
  (2) Selkoe, D. J. Nature 2003, 426, 900. doi: 10.1038/nature02264
3. [3]
  (3) Selkoe, D. J. Physiol. Rev. 2001, 81, 741.
4. [4]
  (4) Selkoe, D. J. Jama-J. Am. Med. Assoc. 2000, 283, 1615. doi: 10.1001/jama.283.12.1615
5. [5]
  (5) Blennow, K.; de Leon, M. J.; Zetterberg, H. Lancet 2006, 368, 387. doi: 10.1016/S0140-6736(06)69113-7
6. [6]
  (6) Selkoe, D. J. Nature 1999, 399, A23.
7. [7]
  (7) Hardy, J.; Selkoe, D. J. Science 2002, 297, 353. doi: 10.1126/science.1072994
8. [8]
  (8) LaFerla, F. M.; Green, K. N.; Oddo, S. Nat. Rev. Neurosci. 2007, 8, 499. doi: 10.1038/nrn2168
9. [9]
  (9) Reinhard, C.; Hebert, S. S.; De Strooper, B. Embo. J. 2005, 24, 3996. doi: 10.1038/sj.emboj.7600860
10. [10]
  (10) Finder, V. H.; Glockshuber, R. Neurodegener. Dis. 2007, 4, 13. doi: 10.1159/000100355
11. [11]
  (11) Rauk, A. Chem. Soc. Rev. 2009, 38, 2698. doi: 10.1039/b807980n
12. [12]
  (12) Luhrs, T.; Ritter, C.; Adrian, M.; Riek-Loher, D.; Bohrmann, B.; Doeli, H.; Schubert, D.; Riek, R. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 17342. doi: 10.1073/pnas.0506723102
13. [13]
  (13) Tycko, R. Annu. Rev. Phys. Chem. 2011, 62, 279. doi: 10.1146/annurev-physchem-032210-103539
14. [14]
  (14) Straub, J. E.; Thirumalai, D. Annu. Rev. Phys. Chem. 2011, 62, 437. doi: 10.1146/annurev-physchem-032210-103526
15. [15]
  (15) Walsh, D. M.; Selkoe, D. J. J. Neurochem. 2007, 101, 1172. doi: 10.1111/j.1471-4159.2006.04426.x
16. [16]
  (16) Ma, K.; Clancy, E. L.; Zhang, Y. B.; Ray, D. G.;Wollenberg, K.; Za rski, M. G. J. Am. Chem. Soc. 1999, 121, 8698. doi: 10.1021/ja990864o
17. [17]
  (17) Peralvarez-Marin, A.; Barth, A.; Graslund, A. J. Mol. Biol. 2008, 379, 589. doi: 10.1016/j.jmb.2008.04.014
18. [18]
  (18) Liu, F. F.; Dong, X. Y.; Sun, Y. Acta. Phys. -Chim. Sin. 2010, 26, 1643. [刘夫锋, 董晓燕, 孙彦. 物理化学学报, 2010, 26, 1643.] doi: 10.3866/PKU.WHXB20100613
19. [19]
  (19) Saraiva, A. M.; Cardoso, I.; Pereira, M. C.; Coelho, M. A.; Saraiva, M. J.; Mohwald, H.; Brezesinski, G. ChemBioChem 2010, 11, 1905. doi: 10.1002/cbic.201000237
20. [20]
  (20) Bitan, G.; Kirkitadze, M. D.; Lomakin, A.; Vollers, S. S.; Benedek, G. B.; Teplow, D. B. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 330. doi: 10.1073/pnas.222681699
21. [21]
  (21) Cabaleiro-La , C.; Quinlan-Pluck, F.; Lynch, I.; Dawson, K. A.; Linse, S. ACS Chem. Neurosci. 2010, 1, 279. doi: 10.1021/cn900027u
22. [22]
  (22) Cummings, J. L. New Engl. J. Med. 2004, 351, 56. doi: 10.1056/NEJMra040223
23. [23]
  (23) Kolosnjaj, J.; Szwarc, H.; Moussa, F. Toxicity Studies of Fullerenes and Derivatives. In Bio-Applications of Nanoparticles; Springer: New York, 2007; p 168.
24. [24]
  (24) Geckeler, K. E.; Samal, S. Polym. Int. 1999, 48, 743. doi: 10.1002/(SICI)1097-0126(199909)48:9<743::AID-PI246>3.0.CO;2-4
25. [25]
  (25) Jensen, A.W.;Wilson, S. R.; Schuster, D. I. Bioorgan. Med. Chem. 1996, 4, 767. doi: 10.1016/0968-0896(96)00081-8
26. [26]
  (26) Li, C. X.; Mezzenga, R. Nanoscale 2013, 5, 6207. doi: 10.1039/c3nr01644g
27. [27]
  (27) Todorova, N.; Makarucha, A. J.; Hine, N. D. M.; Mostofi, A. A.; Yarovsky, I. PLoS Comput. Biol. 2013, 9 (12), e1003360.
28. [28]
  (28) Podolski, I. Y.; Podlubnaya, Z. A.; Kosenko, E. A.; Mugantseva, E. A.; Makarova, E. G.; Marsagishvili, L. G.; Shpagina, M. D.; Kaminsky, Y. G.;Andrievsky, G. V.; Klochkov, V. K. J. Nanosci. Nanotechnol. 2007, 7, 1479. doi: 10.1166/jnn.2007.330
29. [29]
  (29) Huang, H. M.; Ou, H. C.; Hsieh, S. J.; Chiang, L. Y. Life Sciences 2000, 66, 1525. doi: 10.1016/S0024-3205(00)00470-7
30. [30]
  (30) Guo, J.; Li, J.; Zhang, Y.; Jin, X.; Liu, H.; Yao, X. Plos One 2013, 8, e65579.
31. [31]
  (31) Zuo, G.; Zhou, X.; Huang, Q.; Fang, H.; Zhou, R. J. Phys. Chem. C 2011, 115, 23323-23328. doi: 10.1021/jp208967t
32. [32]
  (32) Kim, J. E.; Lee, M. Biochem. Biophys. Res. Commun. 2003, 303, 576. doi: 10.1016/S0006-291X(03)00393-0
33. [33]
  (33) Andujar, S. A.; Lugli, F.; Hofinger, S.; Enriz, R. D.; Zerbetto, F. Phys. Chem. Chem. Phys. 2012, 14, 8599. doi: 10.1039/c2cp40680b
34. [34]
  (34) Petkova, A. T.; Yau,W. M.; Tycko, R. Biochemistry 2006, 45, 498. doi: 10.1021/bi051952q
35. [35]
  (35) Lu, J. X.; Qiang,W.; Yau,W. M.; Schwieters, C. D.; Meredith, S. C.; Tycko, R. Cell 2013, 154, 1257. doi: 10.1016/j.cell.2013.08.035
36. [36]
  (36) Ma, B. Y.; Nussinov, R. Curr. Opin. Chem. Biol. 2006, 10, 445. doi: 10.1016/j.cbpa.2006.08.018
37. [37]
  (37) Hezaveh, S.; Samanta, S.; Milano, G.; Roccatano, D. J. Chem. Phys. 2011, 135 (16), 164501. doi: 10.1063/1.3643417
38. [38]
  (38) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435.
39. [39]
  (39) van Gunsteren,W. F.; Billeter, S.; Eising, A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott,W.; Tironi, I. G. Biomolecular Simulation: the GROMOS96 Manual and User Guide; Vdf Hochschulverlag AG an der ETH Zürich: Zürich, 1996.
40. [40]
  (40) Berendsen, H.; Postma, J.; Van Gunsteren,W.; Hermans, J. Intermolecular Forces 1981, 11, 331.
41. [41]
  (41) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089. doi: 10.1063/1.464397
42. [42]
  (42) Hess, B.; Bekker, H.; Berendsen, H. J.; Fraaije, J. G. J. Comput. Chem. 1997, 18, 1463. doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
43. [43]
  (43) Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952. doi: 10.1002/jcc.540130805
44. [44]
  (44) Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.;Wang, J.; Duke, R. E.; Luo, R.;Walker, R. C.; Zhang,W.; Merz, K. M.; Roberts, B. P.;Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvai, I.;Wong, K. F.; Paesani, F.; Vanicek, J.; Liu, J.;Wu, X.; Brozell, S. R.; Steinbrecher, T.; hlke, H.; Cai, Q.; Ye, X.;Wang, J.; Hsieh, M. J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 11; University of California: San Francisco, 2010.
45. [45]
  (45) Kabsch,W.; Sander, C. Biopolymers 1983, 22, 2577. doi: 10.1002/bip.360221211
46. [46]
  (46) Connolly, M. L. J. Appl. Crystallorg. 1983, 16, 548. doi: 10.1107/S0021889883010985
47. [47]
  (47) Shao, J. Y.; Tanner, S.W.; Thompson, N.; Cheatham, T. E. J. Chem. Theory Comput. 2007, 3, 2312.
48. [48]
  (48) Onufriev, A.; Bashford, D.; Case, D. A. J. Phys. Chem. B 2000, 104, 3712.
49. [49]
  (49) Kopitz, H.; Zivkovic, A.; Engels, J.W.; hlke, H. ChemBioChem 2008, 9, 2619. doi: 10.1002/cbic.200800461
50. [50]
  (50) Tjernberg, L. O.; Näslund, J.; Lindqvist, F.; Johansson, J.; Karlström, A. R.; Thyberg, J.; Terenius, L.; Nordstedt, C. J. Biol. Chem. 1996, 271, 8545. doi: 10.1074/jbc.271.15.8545
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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

Molecular Dynamics Simulations on the Binding of Fullerene to Amyloid-β Oli mers

南开大学师唯/华北电力大学（保定）刘景维：二维配位聚合物中有序的亲锂冠醚位点用于无枝晶锂沉积

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通讯作者: 陈斌, bchen63@163.com