Structural determination of Aβ25-35 micelles by molecular dynamics simulations

Biophysical Journal

Volumn 99, Issue 2, 2010, Pages 666-674

  Yu, Xiang ^a   Wang, Qiuming ^a   Zheng, Jie ^a  

^a The University of Akron   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID BETA PROTEIN; LYSINE; PEPTIDE; WATER;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; HYDROGEN BOND; METABOLISM; MICELLE; MOLECULAR DYNAMICS; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; THERMODYNAMICS; TIME;

AMYLOID BETA-PROTEIN; COMPUTER SIMULATION; HUMANS; HYDROGEN BONDING; LYSINE; MICELLES; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS; TIME FACTORS; WATER;

EID: 77955187036     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.05.006     Document Type: Article

References (50)

1. Frozza, R. L., A. P. Horn,...., C. G. Salbego. 2009. A comparative study of β-amyloid peptides Aβ1-42 and Aβ25-35 toxicity in organotypic hippocampal slice cultures. Neurochem. Res. 34: 295-303.
2. Haass, C., and D. J. Selkoe. 2007. Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid β-peptide. Nat. Rev. Mol. Cell Biol. 8:101-112. (Pubitemid 46432529)
3. Kirkitadze, M. D., G. Bitan, and D. B. Teplow. 2002. Paradigm shifts in Alzheimer's disease and other neurodegenerative disorders: the emerging role of oligomeric assemblies. J. Neurosci. Res. 69:567-577.
4. Selkoe, D. J. 2008. Soluble oligomers of the amyloid β-protein impair synaptic plasticity and behavior. Behav. Brain Res. 192: 106-113.
5. Glabe, C. G. 2008. Structural classification of toxic amyloid oligomers. J. Biol. Chem. 283:29639-29643.
6. Paravastu, A. K., R. D. Leapman,..., R. Tycko. 2008. Molecular structural basis for polymorphism in Alzheimer's β-amyloid fibrils. Proc. Natl. Acad. Sci. USA. 105:18349-18354.
7. Kayed, R., A. Pensalfini, ..., C. Glabe. 2009. Annular protofibrils are a structurally and functionally distinct type of amyloid oligomer. J. Biol. Chem. 284:4230-4237.
8. Zheng, J., X. Yu,..., Q. Wang. 2010. Molecular modeling of two distinct triangular oligomers in amyloid β-protein. J. Phys. Chem. B. 114:463-470.
9. Takeda, T., and D. K. Klimov. 2009. Probing energetics of Aβ fibril elongation by molecular dynamics simulations. Biophys. J. 96: 4428-4437.
10. Reddy, G., J. E. Straub, and D. Thirumalai. 2009. Dynamics of locking of peptides onto growing amyloid fibrils. Proc. Natl. Acad. Sci. USA. 106:11948-11953.
11. Nguyen, H. D., and C. K. Hall. 2004. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. USA. 101:16180-16185. (Pubitemid 39552819)
12. Sawaya, M. R., S. Sambashivan,..., D. Eisenberg. 2007. Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature. 447:453-457.
13. Zheng, J., B. Ma,..., R. Nussinov. 2006. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys. J. 91:824-833.
14. Karsai, A., U. Murvai,..., M. S. Kellermayer. 2008. Oriented epitaxial growth of amyloid fibrils of the N27C mutant β 25-35 peptide. Eur. Biophys. J. 37: 1133-1137.
15. Chimon, S., M. A. Shaibat,..., Y. Ishii. 2007. Evidence of fibril-like [β]-sheet structures in a neurotoxic amyloid intermediate of Alzheimer's [β]-amyloid. Nat. Struct. Mol. Biol. 14:1157-1164. (Pubitemid 350223342)
16. Kayed, R., E. Head,..., C. G. Glabe. 2003. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science. 300:486-489. (Pubitemid 36444329)
17. Yong, W., A. Lomakin,..., G. B. Benedek. 2002. Structure determination of micelle-like intermediates in amyloid β-protein fibril assembly by using small angle neutron scattering. Proc. Natl. Acad. Sci. USA. 99:150-154. (Pubitemid 34060332)
18. Sabaté, R., and J. Estelrich, 2005. Evidence of the existence in the fibrillogenesis of β-amyloid peptide. J. Phys. Chem. B. 109:11027-11032. (Pubitemid 40844540)
19. Petkova, A. T., R. D. Leapman,..., R. Tycko. 2005. Self-propagating, molecular-level polymorphism in Alzheimer's β-amyloid fibrils. Science. 307: 262-265.
20. Yan, L., D. Philippe,..., W. Guanghong. 2009. Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent. Proteins. 75:954-963.
21. Dumoulin, M., and C. M. Dobson, 2004. Probing the origins, diagnosis and treatment of amyloid diseases using antibodies. Biochimie. 86:589-600. (Pubitemid 39535630)
22. Habicht, G., C. Haupt,..., M. Fändrich. 2007. Directed selection of a conformational antibody domain that prevents mature amyloid fibril formation by stabilizing Aβ protofibrils. Proc. Natl. Acad. Sci. USA. 104:19232-19237.
23. Valincius, G., F. Heinrich,..., M. Lösche. 2008. Soluble amyloid β-oligomers affect dielectric membrane properties by bilayer insertion and domain formation: implications for cell toxicity. Biophys. J. 95: 4845-4861.
24. Kayed, R., Y. Sokolov,..., C. G. Glabe. 2004. Permeabilization of lipid bilayers is a common conformation-dependent activity of soluble amyloid oligomers in protein misfolding diseases. J. Biol. Chem. 279:46363-46366. (Pubitemid 39518276)
25. Millucci, L., R. Raggiaschi,..., A. Santucci. 2009. Rapid aggregation and assembly in aqueous solution of A β (25-35) peptide. J. Biosci. 34:293-303.
26. Esposito, C., A. Tedeschi,..., A. M. D'ursi. 2006. Exploring interaction of β-amyloid segment (25-35) with membrane models through paramagnetic probes. J. Pept. Sci. 12: 766-774.
27. Suh, E. C., Y. J. Jung,..., K. E. Lee. 2008. A β 25-35 induces presynaptic changes in organotypic hippocampal slice cultures. Neurotoxicology. 29:691-699.
28. Wei, G., and J.-E. Shea. 2006. Effects of solvent on the structure of the Alzheimer amyloid-β (25-35) peptide. Biophys. J. 91:1638-1647. (Pubitemid 44352430)
29. Ma, B., and R. Nussinov. 2006. The stability of monomeric intermediates controls amyloid formation: Aβ25-35 and its N27Q mutant. Biophys. J. 90:3365-3374.
30. Kaminsky, Y. G., M. W. Marlatt,..., E. A. Kosenko. 2010. Subcellular and metabolic examination of amyloid-β peptides in Alzheimer disease pathogenesis: evidence for Aβ (25-35). Exp. Neurol. 221:26-37.
31. Im, W., M. S. Lee, and C. L. Brooks, 3rd. 2003. Generalized born model with a simple smoothing function. J. Comput. Chem. 24:1691-1702.
32. D'Ursi, A. M., M. R. Almenante,..., D. Picone. 2004. Solution structure of amyloid β-peptide (25-35) in different media. J. Med. Chem. 47:4231-4238.
33. Frishman, D., and P. Argos. 1995. Knowledge-based protein secondary structure assignment. Proteins. 23:566-579. (Pubitemid 26009520)
34. Cheon, M., I. Chang,..., G. Favrin. 2007. Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. PLOS Comput. Biol. 3:e173.
35. Auer, S., F. Meersman,..., M. Vendruscolo, 2008. A generic mechanism, of emergence of amyloid protofilaments from, disordered oligomeric aggregates. PLOS Comput. Biol. 4:e1000222.
36. Mukherjee, S., P. Chowdhury, and F. Gai. 2009. Effect of dehydration on the aggregation kinetics of two amyloid peptides. J. Phys. Chem. B. 113:531-535.
37. Krone, M. G., L. Hua, ..., J. E. Shea. 2008. Role of water in mediating the assembly of Alzheimer amyloid-β Aβ 16-22 protofilaments. J. Am. Chem. Soc. 130:11066-11072.
38. Karsai, A., A. Nagy,..., M. S. Kellermayer. 2005. Effect of lysine-28 side-chain acetylation on the nanomechanical behavior of Alzheimer amyloid β25-35 fibrils. J. Chem. Inf. Model. 45:1641-1646. (Pubitemid 41784734)
39. Houry, W. A., J. M. Sauder,..., H. A. Scheraga. 1998. Definition of amide protection factors for early kinetic intermediates in protein folding. Proc Natl. Acad. Sci. USA. 95:4299-4302.
40. Hensley, K., J. M. Carney,..., D. A. Butterfield. 1994. A model for β-amyloid aggregation and neurotoxicity based on free radical generation by the peptide: relevance to Alzheimer disease. Prot: Natl. Acad. Sci. USA. 91:3270-3274. (Pubitemid 24130218)
41. Karsai, Á., L. Grama,..., M. S. Z. Kellermayer. 2007. Potassium-dependent oriented growth of amyloid β25-35 fibrils on mica. Nanotechnology. 18:345102. (Pubitemid 47228434)
42. Liu, R., C. McAllister,..., M. R. Sierks. 2004. Residues 17-20 and 30-35 of β-amyloid play critical roles in aggregation, J. Neurosci. Res. 75:162-171. (Pubitemid 38049387)
43. Hughes, E., R. M. Burke, and A. J. Doig. 2000. Inhibition of toxicity in the β-amyloid peptide fragment β -(25-35) using N-methylated derivatives: a general strategy to prevent amyloid formation. J. Biol. Chem. 275:25109-25115.
44. Zheng, J., H. Jang,..., R. Nussinov. 2007. Modeling the Alzheimer Aβ17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys. J. 93:3046-3057. (Pubitemid 350103369)
45. Zheng, J., H. Jang, ..., R. Nussinov. 2008. Annular structures as intermediates in fibril formation of Alzheimer Aβ17-42. J. Phys. Chem. B. 112:6856-6865.
46. Buchete, N.-V., R. Tycko, and G. Hummer. 2005. Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments. J. Mol. Biol. 353:804-821. (Pubitemid 41460541)
47. Chebaro, Y., N. Mousseau, and P. Derreumaux. 2009. Structures and thermodynamics of Alzheimer's amyloid-β Aβ (16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Aβ fibrillation. J. Phys. Chem. B. 113:7668-7675.
48. Miles, L. A., K. S. Wun,..., M. W. Parker. 2008. Amyloid-β-anti- amyloid-β complex structure reveals an extended conformation in the immunodominant B-cell epitope. J. Mol. Biol. 377:181-192.
49. Schneidman-Duhovny, D., Y. Inbar,..., H. J. Wolfson. 2005. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33:W363-W367.
50. Mashiach, E., D. Schneidman-Duhovny,..., H. J. Wolfson. 2008. FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res. 36:W229-W232.