Molecular Dynamics Study of Zn(Aβ) and Zn(Aβ)2

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Pan, Lurong ^a   Patterson, James C ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID BETA PROTEIN; ZINC;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; COVALENT BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; OLIGOMERIZATION; STRUCTURE ANALYSIS;

AMYLOID BETA-PEPTIDES; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; QUANTUM THEORY; ZINC;

EID: 84884687853     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070681     Document Type: Article

References (56)

1. Alzheimer's Association (2009) Alzheimer's Disease Facts and Figures Alzheimer's & Dementia 5: 3.
2. Masters CL, Simms G, Weinman NA, Multhaup G, McDonald BL, et al. (1985) Amyloid plaque core protein in Alzheimer disease and Down syndrome. Proc Natl Acad Sci U S A 82: 4245-4249.
3. Jarrett JT, Berger EP, Lansbury PT, (1993) The C-terminus of the beta protein is critical in amyloidogenesis. Ann N Y Acad Sci 695: 144-148.
4. Iwatsubo T, Odaka A, Suzuki N, Mizusawa H, Nukina N, et al. (1994) Visualization of A beta 42(43) and A beta 40 in senile plaques with end-specific A beta monoclonals: evidence that an initially deposited species is A beta 42(43). Neuron 13: 45-53.
5. Kim J, Onstead L, Randle S, Price R, Smithson L, et al. (2007) Abeta40 inhibits amyloid deposition in vivo. J Neurosci 27: 627-633.
6. Iijima K, Liu HP, Chiang AS, Hearn SA, Konsolaki M, et al. (2004) Dissecting the pathological effects of human Abeta40 and Abeta42 in Drosophila: a potential model for Alzheimer's disease. Proc Natl Acad Sci U S A 101: 6623-6628.
7. Hardy J, Selkoe DJ, (2002) The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science 297: 353-356.
8. Cleary JP, Walsh DM, Hofmeister JJ, Shankar GM, Kuskowski MA, et al. (2005) Natural oligomers of the amyloid-beta protein specifically disrupt cognitive function. Nat Neurosci 8: 79-84.
9. Becker JS, Zoriy MV, Pickhardt C, Palomero-Gallagher N, Zilles K, (2005) Imaging of copper, zinc, and other elements in thin section of human brain samples (hippocampus) by laser ablation inductively coupled plasma mass spectrometry. Anal Chem 77: 3208-3216.
10. Chen WT, Liao YH, Yu HM, Cheng IH, Chen YR, (2011) Distinct effects of Zn2+, Cu2+, Fe3+, and Al3+ on amyloid-beta stability, oligomerization, and aggregation: amyloid-beta destabilization promotes annular protofibril formation. J Biol Chem 286: 9646-9656.
11. Rajendran R, Minqin R, Ynsa MD, Casadesus G, Smith MA, et al. (2009) A novel approach to the identification and quantitative elemental analysis of amyloid deposits-insights into the pathology of Alzheimer's disease. Biochem Biophys Res Commun 382: 91-95.
12. Atwood CS, Moir RD, Huang X, Scarpa RC, Bacarra NM, et al. (1998) Dramatic aggregation of Alzheimer abeta by Cu(II) is induced by conditions representing physiological acidosis. J Biol Chem 273: 12817-12826.
13. Esler WP, Stimson ER, Jennings JM, Ghilardi JR, Mantyh PW, et al. (1996) Zinc-induced aggregation of human and rat beta-amyloid peptides in vitro. J Neurochem 66: 723-732.
14. Cherny RA, Atwood CS, Xilinas ME, Gray DN, Jones WD, et al. (2001) Treatment with a copper-zinc chelator markedly and rapidly inhibits beta-amyloid accumulation in Alzheimer's disease transgenic mice. Neuron 30: 665-676.
15. Cherny RA, Legg JT, McLean CA, Fairlie DP, Huang X, et al. (1999) Aqueous dissolution of Alzheimer's disease Abeta amyloid deposits by biometal depletion. J Biol Chem 274: 23223-23228.
16. Noy D, Solomonov I, Sinkevich O, Arad T, Kjaer K, et al. (2008) Zinc-amyloid beta interactions on a millisecond time-scale stabilize non-fibrillar Alzheimer-related species. J Am Chem Soc 130: 1376-1383.
17. Shin BK, Saxena S, (2008) Direct evidence that all three histidine residues coordinate to Cu(II) in amyloid-beta1-16. Biochemistry 47: 9117-9123.
18. Mekmouche Y, Coppel Y, Hochgräfe K, Guilloreau L, Talmard C, et al. (2005) Characterization of the ZnII binding to the peptide amyloid-beta1-16 linked to Alzheimer's disease. Chembiochem 6: 1663-1671.
19. Syme CD, Viles JH, (2006) Solution 1H NMR investigation of Zn2+ and Cd2+ binding to amyloid-beta peptide (Abeta) of Alzheimer's disease. Biochim Biophys Acta 1764: 246-256.
20. Zirah S, Kozin SA, Mazur AK, Blond A, Cheminant M, et al. (2006) Structural changes of region 1-16 of the Alzheimer disease amyloid beta-peptide upon zinc binding and in vitro aging. J Biol Chem 281: 2151-2161.
21. Danielsson J, Pierattelli R, Banci L, Gräslund A, (2007) High-resolution NMR studies of the zinc-binding site of the Alzheimer's amyloid beta-peptide. FEBS J 274: 46-59.
22. Liu ST, Howlett G, Barrow CJ, (1999) Histidine-13 is a crucial residue in the zinc ion-induced aggregation of the A beta peptide of Alzheimer's disease. Biochemistry 38: 9373-9378.
23. Miura T, Suzuki K, Kohata N, Takeuchi H, (2000) Metal binding modes of Alzheimer's amyloid beta-peptide in insoluble aggregates and soluble complexes. Biochemistry 39: 7024-7031.
24. Yang DS, McLaurin J, Qin K, Westaway D, Fraser PE, (2000) Examining the zinc binding site of the amyloid-beta peptide. Eur J Biochem 267: 6692-6698.
25. Kozin SA, Zirah S, Rebuffat S, Hoa GH, Debey P, (2001) Zinc binding to Alzheimer's Abeta(1-16) peptide results in stable soluble complex. Biochem Biophys Res Commun 285: 959-964.
26. Curtain CC, Ali F, Volitakis I, Cherny RA, Norton RS, et al. (2001) Alzheimer's disease amyloid-beta binds copper and zinc to generate an allosterically ordered membrane-penetrating structure containing superoxide dismutase-like subunits. J Biol Chem 276: 20466-20473.
27. Dong J, Shokes JE, Scott RA, Lynn DG, (2006) Modulating amyloid self-assembly and fibril morphology with Zn(II). J Am Chem Soc 128: 3540-3542.
28. Stellato F, Menestrina G, Serra MD, Potrich C, Tomazzolli R, et al. (2006) Metal binding in amyloid beta-peptides shows intra- and inter-peptide coordination modes. Eur Biophys J Biophy 35: 340-351.
29. Talmard C, Guilloreau L, Coppel Y, Mazarguil H, Faller P, (2007) Amyloid-beta peptide forms monomeric complexes with Cu-II and Zn-II prior to aggregation. Chembiochem 8: 163-165.
30. Gaggelli E, Janicka-Klos A, Jankowska E, Kozlowski H, Migliorini C, et al. (2008) NMR studies of the Zn2+ interactions with rat and human beta-amyloid (1-28) peptides in water-micelle environment. J Phys Chem B 112: 100-109.
31. Minicozzi V, Stellato F, Comai M, Dalla Serra M, Potrich C, et al. (2008) Identifying the minimal copper- and zinc-binding site sequence in amyloid-beta peptides. J Biol Chem 283: 10784-10792.
32. Faller P, Hureau C, (2009) Bioinorganic chemistry of copper and zinc ions coordinated to amyloid-beta peptide. Dalton T 2009: 1080-1094.
33. Talmard C, Leuma Yona R, Faller P, (2009) Mechanism of zinc(II)-promoted amyloid formation: Zinc(II) binding facilitates the transition from the partially alpha-helical conformer to aggregates of amyloid beta protein(1-28). J Biol Inorg Chem 14: 449-455.
34. Miller Y, Ma B, Nussinov R, (2010) Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A 107: 9490-9495.
35. Miller Y, Ma B, Nussinov R, (2010) Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in rugged energy landscape. Chem Rev 110: 4820-4838.
36. Shewmaker F, McGlinchey RP, Wickner RB, (2011) Structural insights into functional and pathological amyloid. J Biol Chem 286: 16533-16540.
37. Tomaselli S, Esposito V, Vangone P, van Nuland NA, Bonvin AM, et al. (2006) The alpha-to-beta conformational transition of Alzheimer's Abeta-(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of beta conformation seeding. ChemBioChem 7: 257-267.
38. Lührs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, et al. (2005) 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. PNAS 102: 17342-17347.
39. Lipscomb WN, Sträter N, (1996) Recent Advances in Zinc Enzymology. Chem Rev 96: 2375-2434.
40. Parkin G, (2004) Synthetic analogues relevant to the structure and function of zinc enzymes. Chem Rev 104: 699-767.
41. Sousa SF, Lopes AB, Fernandes PA, Ramos MJ, (2009) The Zinc proteome: a tale of stability and functionality. Dalton Trans 14: 7946-7956.
42. Parr RG, Gadre SR, Bartolotti LJ, (1979) Local density functional theory of atoms and molecules. Proc Natl Acad Sci U S A 76: 2522-2526.
43. Becke AD, Johnson ER, (2007) A unified density-functional treatment of dynamical, nondynamical, and dispersion correlations. J Chem Phys 127: 124108.
44. Stephens PJ, Devlin FJ, Chabalowski CF, Frisch MJ, (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J Phys Chem 98: 11623-11627.
45. Petersson GA, Bennett A, Tensfeldt TG, Al-Laham MA, Shirley WA, et al. (1988) A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row atoms. J Chem Phys 89: 2193-218.
46. Clark T, Chandrasekhar J, Spitznagel GW, Schleyer PR, (1983) Efficient diffuse function-augmented basis-sets for anion calculations. 3. The 3-21+G basis set for 1st-row elements, Li-F. J Comp Chem 4: 294-301.
47. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, et al. (2009) Gaussian 09, Revision A.02, Gaussian, Inc., Wallingford CT.
48. Becker OM, MacKerell AD Jr, Roux B, Watanabe M, Editors (2001) Computational Biochemistry and Biophysics. Marcel Dekker, Inc. New York. pp 7-38.
49. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (1996) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802.
50. Humphrey W, Dalke A, Schulten K, (1996) VMD- Visual Molecular Dynamics. J Molec Graphics 14: 33-38.
51. Lobanov MY, Bogatyreva NS, Galzitskaya OV, (2008) Radius of gyration as an indicator of protein structure compactness. Molecular Biology 42: 623-628.
52. Beauchemin D, Kisilevsky R, (1998) A method based on ICP-MS for the analysis of Alzheimer's amyloid plaques. Anal Chem 70: 1026-1029.
53. Deeth RJ, Randell K, (2008) Ligand field stabilization and activation energies revisited: molecular modeling of the thermodynamic and kinetic properties of divalent, first-row aqua complexes. Inorg Chem 47: 7377-7388.
54. Sciarretta KL, Gordon DJ, Petkova AT, Tycko R, Meredith SC, (2005) Abeta40-lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry 44: 6003-6014.
55. Petkova A, Yau WM, Tycko R, (2006) Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils. Biochemistry 45: 498-512.
56. Roychaudhuri R, Yang M, Deshpande A, Cole GM, Frautschy S, et al. (2013) C-terminal turn stability determines assembly differences between Aβ40 and Aβ42. J Mol Biol 2013 425: 292-308.