Binding of congo red to amyloid protofibrils of the alzheimer Aβ9-40 peptide probed by molecular dynamics simulations

Biophysical Journal

Volumn 103, Issue 3, 2012, Pages 550-557

  Wu, Chun ^a   Scott, Justin ^a   Shea, Joan Emma ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID BETA PROTEIN; CONGO RED;

ARTICLE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE; ROTATION; STATIC ELECTRICITY;

AMYLOID BETA-PEPTIDES; CONGO RED; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; ROTATION; STATIC ELECTRICITY;

EID: 84864695671     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.07.008     Document Type: Article

References (52)

1. M. Goedert, and M.G. Spillantini A century of Alzheimer's disease Science 314 2006 777 781 (Pubitemid 44706636)
2. A. Drzezga Amyloid-plaque imaging in early and differential diagnosis of dementia Ann. Nucl. Med. 24 2010 55 66
3. J. Hardy, and D.J. Selkoe The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics Science 297 2002 353 356 (Pubitemid 34790756)
4. M. Hashimoto, and E. Rockenstein E. Masliah Role of protein aggregation in mitochondrial dysfunction and neurodegeneration in Alzheimer's and Parkinson's diseases Neuromolecular Med. 4 2003 21 36
5. A. Lorenzo, and B. Razzaboni B.A. Yankner Pancreatic islet cell toxicity of amylin associated with type-2 diabetes mellitus Nature 368 1994 756 760 (Pubitemid 24153418)
6. M. Bucciantini, and E. Giannoni M. Stefani Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases Nature 416 2002 507 511 (Pubitemid 34288846)
7. M. Bucciantini, and G. Calloni M. Stefani Prefibrillar amyloid protein aggregates share common features of cytotoxicity J. Biol. Chem. 279 2004 31374 31382 (Pubitemid 39037804)
8. H. Benhold Specific staining of amyloid by Congo red Muenchen. Med. Wochenschr. 1922 1537 1538
9. P. Divry Histochemical study of senile plaques J. Neurol. Psychiatry 27 1927 643 657
10. W.E. Klunk, R.F. Jacob, and R.P. Mason Quantifying amyloid β-peptide (Abeta) aggregation using the Congo red-Abeta (CR-abeta) spectrophotometric assay Anal. Biochem. 266 1999 66 76 (Pubitemid 29024609)
11. W.E. Klunk, J.W. Pettegrew, and D.J. Abraham Quantitative evaluation of Congo red binding to amyloid-like proteins with a β-pleated sheet conformation J. Histochem. Cytochem. 37 1989 1273 1281 (Pubitemid 19186029)
12. A. Lorenzo, and B.A. Yankner Beta-amyloid neurotoxicity requires fibril formation and is inhibited by Congo red Proc. Natl. Acad. Sci. USA 91 1994 12243 12247 (Pubitemid 24368641)
13. A.J. Howie, and D.B. Brewer Optical properties of amyloid stained by Congo red: history and mechanisms Micron 40 2009 285 301
14. L.W. Jin, and K.A. Claborn B. Kahr Imaging linear birefringence and dichroism in cerebral amyloid pathologies Proc. Natl. Acad. Sci. USA 100 2003 15294 15298 (Pubitemid 38020982)
15. R.P. Linke Highly sensitive diagnosis of amyloid and various amyloid syndromes using Congo red fluorescence Virchows Arch. 436 2000 439 448 (Pubitemid 30312159)
16. S. Sen, and G. Başdemir Diagnosis of renal amyloidosis using Congo red fluorescence Pathol. Int. 53 2003 534 538 (Pubitemid 37076294)
17. A.J. Howie, and D.B. Brewer A.P. Jones Physical basis of colors seen in Congo red-stained amyloid in polarized light Lab. Invest. 88 2008 232 242 (Pubitemid 351311279)
18. M.O. Pedersen, and K. Mikkelsen N.C. Nielsen NMR reveals two-step association of Congo red to amyloid β in low-molecular-weight aggregates J. Phys. Chem. B 114 2010 16003 16010
19. C. Lendel, and B. Bolognesi A. Gräslund Detergent-like interaction of Congo red with the amyloid β peptide Biochemistry 49 2010 1358 1360
20. P.P. Bose, and U. Chatterjee P.I. Arvidsson Effects of Congo red on Aβ(1-40) fibril formation process and morphology ACS Chem. Neuros. 1 2010 315 324
21. A.T. Petkova, W.M. Yau, and R. Tycko Experimental constraints on quaternary structure in Alzheimer's β-amyloid fibrils Biochemistry 45 2006 498 512 (Pubitemid 43100415)
22. C. Wu, M.T. Bowers, and J.E. Shea On the origin of the stronger binding of PIB over thioflavin T to protofibrils of the Alzheimer amyloid-β peptide: a molecular dynamics study Biophys. J. 100 2011 1316 1324
23. N.V. Buchete, and G. Hummer Structure and dynamics of parallel β-sheets, hydrophobic core, and loops in Alzheimer's Aβ fibrils Biophys. J. 92 2007 3032 3039 (Pubitemid 46684564)
24. J. Zheng, and B.Y. Ma R. Nussinov Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association Front. Biosci. 13 2008 3919 3930 (Pubitemid 351594670)
25. Y. Duan, and C. Wu P. Kollman A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24 2003 1999 2012
26. V. Hornak, and R. Abel C. Simmerling Comparison of multiple amber force fields and development of improved protein backbone parameters Proteins 65 2006 712 725 (Pubitemid 44583220)
27. W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparisons of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
28. C. Wu, and Z.X. Wang Y. Duan Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations J. Am. Chem. Soc. 129 2007 1225 1232 (Pubitemid 46208593)
29. J.M. Wang, and R.M. Wolf D.A. Case Development and testing of a general amber force field J. Comput. Chem. 25 2004 1157 1174
30. U. Essmann, and L. Perera L.G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 1995 8577 8593
31. J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
32. P. Procacci, and B.J. Berne Multiple time-scale methods for constant-pressure molecular-dynamics simulations of molecular-systems Mol. Phys. 83 1994 255 272
33. H.J.C. Berendsen, and J.P.M. Postma J.R. Haak Molecular dynamics with coupling to an external bath J. Comput. Phys. 81 1984 3684 3690
34. S.W. Chiu, and M. Clark E. Jakobsson Collective motion artifacts arising in long-duration molecular dynamics simulations J. Comput. Chem. 21 2000 121 131
35. S.C. Harvey, R.K.Z. Tan, and T.E. Cheatham The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition J. Comput. Chem. 19 1998 726 740
36. X. Daura, and K. Gademann A.E. Mark Peptide folding: when simulation meets experiment Angew. Chem. Int. Ed. 38 1999 236 240 (Pubitemid 29051239)
37. B. Stopa, and B. Piekarska M. Król The structure and protein binding of amyloid-specific dye reagents Acta Biochim. Pol. 50 2003 1213 1227 (Pubitemid 38608849)
38. M. Sunde, and L.C. Serpell C.C. Blake Common core structure of amyloid fibrils by synchrotron x-ray diffraction J. Mol. Biol. 273 1997 729 739 (Pubitemid 27488813)
39. R. Tycko Molecular structure of amyloid fibrils: insights from solid-state NMR Q. Rev. Biophys. 39 2006 1 55 (Pubitemid 44566373)
40. B.Y. Ma, and R. Nussinov Stabilities and conformations of Alzheimer's β -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): sequence effects Proc. Natl. Acad. Sci. USA 99 2002 14126 14131 (Pubitemid 35257636)
41. N.V. Buchete, R. Tycko, and G. Hummer Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments J. Mol. Biol. 353 2005 804 821 (Pubitemid 41460541)
42. J. Zheng, and H. Jang R. Nussinov Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities Biophys. J. 93 2007 3046 3057 (Pubitemid 350103369)
43. M.R.H. Krebs, E.H.C. Bromley, and A.M. Donald The binding of thioflavin-T to amyloid fibrils: localization and implications J. Struct. Biol. 149 2005 30 37 (Pubitemid 40051399)
44. A.R. Katritzky, S. Sild, and M. Karelson Correlation and prediction of the refractive indices of polymers by QSPR J. Chem. Inf. Comput. Sci. 38 1998 1171 1176 (Pubitemid 128591283)
45. A.V. Kajava, U. Baxa, and A.C. Steven β arcades: recurring motifs in naturally occurring and disease-related amyloid fibrils FASEB J. 24 2010 1311 1319
46. L.S. Wolfe, and M.F. Calabrese Y. Xiong Protein-induced photophysical changes to the amyloid indicator dye thioflavin T Proc. Natl. Acad. Sci. USA 107 2010 16863 16868
47. V.I. Stsiapura, and A.A. Maskevich O.V. Buganov Charge transfer process determines ultrafast excited state deactivation of thioflavin T in low-viscosity solvents J. Phys. Chem. A 114 2010 8345 8350
48. V.I. Stsiapura, and A.A. Maskevich I.M. Kuznetsova Computational study of thioflavin T torsional relaxation in the excited state J. Phys. Chem. A 111 2007 4829 4835 (Pubitemid 46960782)
49. C. Wu, and Z.X. Wang J.E. Shea The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations J. Mol. Biol. 384 2008 718 729
50. C. Wu, and M. Biancalana J.E. Shea Binding modes of thioflavin-T to the single-layer β-sheet of the peptide self-assembly mimics J. Mol. Biol. 394 2009 627 633
51. E.P. Raman, T. Takeda, and D.K. Klimov Molecular dynamics simulations of Ibuprofen binding to Abeta peptides Biophys. J. 97 2009 2070 2079
52. T. Takeda, and W.L.E. Chang D.K. Klimov Binding of nonsteroidal anti-inflammatory drugs to Aβ fibril Proteins 78 2010 2849 2860