Model amyloid peptide B18 monomer and dimer studied by replica exchange molecular dynamics simulations

Journal of Physical Chemistry B

Volumn 114, Issue 39, 2010, Pages 12701-12707

  Knecht, Volker ^a  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DICHROISM; GLYCOPROTEINS; MOLECULAR DYNAMICS; MONOMERS; OLIGOMERS; PEPTIDES; SOLUTIONS;

AMYLOID DISEASE; AMYLOID FIBRIL; AMYLOID PEPTIDES; AQUEOUS SOLUTIONS; CIRCULAR DICHROISM SPECTRA; FIBRIL FORMATION; FIBRILLIZATION; LAG PHASE; MISFOLDING; REPLICA EXCHANGE MOLECULAR DYNAMICS; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; STATISTICAL WEIGHT; THERAPEUTIC STRATEGY; U-SHAPED; U-SHAPED CONFORMATIONS;

CONFORMATIONS;

EID: 77957292370     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp1048698     Document Type: Article

References (51)

1. Westermark, P. FEBS J. 2005, 272, 5942-5949
2. Chiti, F.; Dobson, C. M. Annu. Rev. Biochem. 2006, 75, 333-366
3. Ulrich, A. S.; Otter, M.; Glabe, C. G.; Hoekstra, D. J. Biol. Chem. 1998, 273, 16748-16755
4. Maltseva, E. Model membrane interactions with ions and peptides at the air/water interface. Ph.D. thesis, Universität Potsdam, 2005.
5. Knecht, V.; Möhwald, H.; Lipowsky, R. J. Phys. Chem. B 2007, 111, 4161-4170
6. van Gunsteren, W. F. Angew. Chem., Int. Ed. 2006, 45, 4064-4092
7. Urbanc, B.; Cruz, L.; Yun, S.; Buldyrev, S. V.; Bitan, G.; Teplow, D. B.; Stanley, H. E. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17345-17350
8. Simona, F.; Tiana, G.; Broglia, R. A.; Colombo, G. J. Mol. Graph. 2004, 23, 263-273
9. Daidone, I.; Simona, F.; Roccatano, D.; Broglia, R.; Tiana, G.; Colombo, G.; Di Nola, A. Proteins 2004, 57, 198-204
10. Han, W.; Wu, Y. D. J. Am. Chem. Soc. 2005, 127, 15408-15416
11. Xu, Y. C.; Shen, J. J.; Luo, X. M.; Zhu, W. L.; Chen, K. X.; Ma, J. P.; Jiang, H. L. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 5403-5407
12. Daidone, I.; Amadei, A.; Di Nola, A. Proteins 2005, 59, 510-518
13. Villa, A.; Mark, A. E.; Saracino, G. A. A.; Cosentino, U.; Pitea, D.; Moro, G.; Salmona, M. J. Phys. Chem. B 2006, 110, 1423-1428
14. Wei, G. H.; Shea, J. E. Biophys. J. 2006, 91, 1638-1647
15. Tomaselli, S.; Esposito, V.; Vangone, P.; van Nuland, N. A. J.; Bonvin, A. M. J. J.; Guerrini, R.; Tancredi, T.; Temussi, P. A.; Picone, D. ChemBioChem 2006, 7, 257-267
16. Khandogin, J.; Brooks, C. L. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 16880-16885
17. Raffa, D. F.; Rauk, A. J. Phys. Chem. B 2007, 111, 3789-3799
18. Sgourakis, N. G.; Yan, Y.; McCallum, S. A.; Wang, C.; Garcia, A. E. J. Mol. Biol. 2007, 368, 1448-1457
19. Knecht, V. J. Phys. Chem. B 2008, 112, 9476-9483
20. Liang, C.; Derreumaux, P.; Mousseau, N.; Wei, G. Biophys. J. 2008, 95, 510-517
21. Chebaro, Y.; Mousseau, N.; Derreumaux, P. J. Phys. Chem. B 2009, 113, 7668-7675
22. Jang, S.; Shin, S. J. Phys. Chem. B 2006, 110, 1955-1958
23. Harrison, P.; Chan, H.; Prusiner, S.; Cohen, F. Protein Sci. 2001, 10, 819-835
24. Dong, X.; Chen, W.; Mousseau, N.; Derreumaux, P. J. Chem. Phys. 2008, 128, 125108-1
25. Wei, G.; Jewett, A. I.; Shea, J.-E. Phys. Chem. Chem. Phys. 2010, 12, 3622-3629
26. Papanikolopoulou, K.; Schoehn, G.; Forge, V.; Forsyth, V. T.; Riekel, C.; Hernandez, J. F.; Ruigrok, R. W. H.; Mitraki, A. J. Biol. Chem. 2005, 280, 2481-2490
27. Liang, C.; Derreumaux, P.; Wei, G. Biophys. J. 2007, 93, 3353-3362
28. Ulrich, A. S.; Tichelaar, W.; Forster, G.; Zschornig, O.; Weinkauf, S.; Meyer, H. W. Biophys. J. 1999, 77, 829-841
29. Lepere, M.; Muenter, A. H.; Chevallard, C.; Guenoun, P.; Brezesinski, G. Colloid Surf., A 2007, 303, 73-78
30. Wu, C.; Lei, H.; Duan, Y. Biophys. J. 2004, 87, 3000-3009
31. Boucher, G.; Mousseau, N.; Derreumaux, P. Proteins 2006, 65, 877-888
32. Reich, L. Folding dynamics and stability of proteins. Ph.D. thesis, Universität Potsdam, 2009.
33. Petty, S.; Decatur, S. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 14272-14277
34. Yan, Y.; Wang, C. J. Mol. Biol. 2006, 364, 853-862
35. Eisenberg, D.; McLachlan, A. D. Nature 1986, 319, 199-203
36. Glaser, R. W.; Grune, M.; Wandelt, C.; Ulrich, A. S. Biochemistry 1999, 38, 2560-2569
37. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott,W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v.: Zürich, Groningen, 1996.
38. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction Models for Water in Relation to Protein Hydration. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Company: Dordrecht, 1981; pp 331 - 342.
39. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Impey, R.; Klein, M. J. Chem. Phys. 1983, 79, 926-935
40. Hermans, J.; Berendsen, H. J. C.; van Gunsteren, W. F.; Postma, J. P. M. Biopolymers 1984, 23, 1513-1518
41. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718
42. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472
43. Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. J. Comput. Chem. 1999, 20, 786-798
44. Feenstra, K. A.; Peter, C.; Scheek, R. M.; van Gunsteren, W. F.; Mark, A. E. J. Biomol. NMR 2002, 23, 181-194
45. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
46. Hünenberger, P. Lattice-sum methods for computing electrostatic interactions in molecular simulations. In Simulation and theory of electrostatic interactions in solution: Computational chemistry, biophysics, and aqueous solutions; Pratt, L.; Hummer, G., Eds.; American Institute of Physics: Melville, NY, 1999; pp 17 - 83.
47. Berendsen, H.; Postma, J.; van Gunsteren, W.; Di Nola, A.; Haak, J. J. Chem. Phys. 1984, 81, 3684-3690
48. Frishman, D.; Argos, P. Proteins 1995, 23, 566-579
49. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Angew. Chem., Int. Ed. 1999, 38, 236-240
50. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14, 33-38
51. Connolly, M. L. Science 1983, 221, 709-713