Probing the initial stage of aggregation of the Aβ10-35- protein: Assessing the propensity for peptide dimerization

Journal of Molecular Biology

Volumn 345, Issue 5, 2005, Pages 1141-1156

  Tarus, Bogdan ^a   Straub, John E ^a   Thirumalai, D ^b  

^a USA ^*  (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

Alzheimer's disease; amyloid protein; dimer; molecular dynamics simulation; potential of mean force

Indexed keywords

AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN[10-35]; UNCLASSIFIED DRUG;

ALZHEIMER DISEASE; AMINO ACID SEQUENCE; AQUEOUS SOLUTION; ARTICLE; DIMERIZATION; ELECTRICITY; ENERGY; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR PROBE; NUCLEAR MAGNETIC RESONANCE; OLIGOMERIZATION; PRESSURE; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; TEMPERATURE DEPENDENCE;

EID: 11844255790     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.11.022     Document Type: Article

References (50)

1. G.G. Glenner, and C.W. Wong Alzheimer's disease: initial report of the purification and characterization of a novel cerebrovascular amyloid protein Biochem. Biophys. Res. Commun. 120 1984 885 890
2. C.L. Masters, G. Simms, N.A. Weinman, G. Multhaup, B.L. McDonald, and K. Beyreuther Amyloid plaque core protein in Alzheimer disease and Down syndrome Proc. Natl Acad. Sci. USA 82 1985 4245 4249
3. D.J. Selkoe Alzheimer's disease: a central role for amyloid J. Neuropath. 53 1991 438 447
4. A.E. Roher, M.J. Ball, S.V. Bhave, and A.R. Wakade β-Amyloid from Alzheimer disease brains inhibits sprouting and survival of sympathetic neurons Biochem. Biophys. Res. Commun. 174 1991 572 579
5. D. Games, D. Adams, R. Alessrini, R. Barbour, P. Bathelette, and C. Blackwell Alzheimer-type neuropathology in transgenic mice overexpressing V717F β-amyloid precursor protein Nature 373 1995 523 527
6. F.M. LaFerla, B.T. Tinkle, C.J. Bieberich, C.C. Hudenschild, and G. Jay The Alzheimer Aβ peptide induces neurodegeneration and apoptotic cell death in transgenic mice Nature Genet. 9 1995 21 29
7. 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
8. 1-42 are potent central nervous system neurotoxins Proc. Natl Acad. Sci. USA 95 1998 6448 6453
9. D.M. Walsh, D.M. Hartley, Y. Kusumoto, Y. Fezoui, M.M. Condron, and A. Lomakin Amyloid β-protein fibrillogenesis. Structure and biological activity of protofibrillar intermediates J. Biol. Chem. 274 1999 25945 25952
10. J.D. Harper, and P.T. Lansbury Models of amyloid seeding in Alzheimer's disease and scrapie: mechanistic truths and physiological consequences of the time-dependent solubility of amyloid proteins Annu. Rev. Biochem. 66 1997 385 407
11. G. Bitan, M.D. Kirkitadze, A. Lomakin, S.S. Vollers, G.B. Benedek, and D.B. Teplow Amyloid β-protein (Aβ) assembly: Aβ40 and Aβ42 oligomerize through distinct pathways Proc. Natl Acad. Sci. USA 100 2003 330 335
12. F. Massi, D. Klimov, D. Thirumalai, and J.E. Straub Charge states rather than propensity for β-structure determine enhanced fibrillogenesis in wild-type Alzheimer's β-amyloid peptide compared to E22Q Dutch mutant Protein Sci. 11 2002 1639 1647
13. G. Bitan, B. Tarus, S.S. Vollers, H.A. Lashuel, M.M. Condron, J.E. Straub, and D.B. Teplow A molecular switch in amyloid assembly: Met35 and amyloid β-protein oligomerization J. Am. Chem. Soc. 125 2003 15359 15365
14. J.T. Jarrett, E.P. Berger, and P.T. Lansbury Jr The carboxy terminus of the β amyloid protein is critical for the seeding of amyloid formation: Implications for the pathogenesis of Alzheimer's disease Biochemistry 32 1993 4693 4697
15. J.T. Jarrett, E.P. Berger, and P.T. Lansbury Jr The C-terminus of the beta protein is critical in amyloidogenesis Ann. N.Y. Acad. Sci. 695 1993 144 148
16. D. Thirumalai, D.K. Klimov, and R.I. Dima Emerging ideas on the molecular basis of protein and peptide aggregation Curr. Opin. Struct. Biol. 13 2003 146 159
17. T.S. Burkoth, T. Benzinger, V. Urban, D.M. Morgan, D.M. Gregory, and P. Thiyagarajan Structure of the β-amyloid(10-35) fibril J. Am. Chem. Soc. 122 2000 7883 7889
18. O.N. Antzutkin, J.J. Balbach, R.D. Leapman, N.W. Rizzo, J. Reed, and R. Tycko Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of β-sheets in Alzheimer's β-amyloid fibrils Proc. Natl Acad. Sci. USA 97 2000 13045 13050
19. A.T. Petkova, Y. Ishii, J.J. Balbach, O.N. Antzutkin, R.D. Leapman, F. Delaglio, and R. Tycko A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR Proc. Natl Acad. Sci. USA 99 2002 16742 16747
20. M.D. Kirkitadze, M.M. Condron, and D.B. Teplow Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis J. Mol. Biol. 312 2001 1103 1119
21. D.K. Klimov, and D. Thirumalai Dissecting the assembly of Aβ 16-22 amyloid peptides into antiparallel β-sheets Structure 11 2003 295 307
22. S. Zhang, K. Iwata, M.J. Lachenmann, J.W. Peng, S. Li, and E.R. Stimson The Alzheimer's peptide A (adopts a collapsed coil structure in water J. Struct. Biol. 130 2000 130 141
23. W.P. Esler, A.M. Felix, E.R. Stimson, M.J. Lachenmann, J.R. Ghilardi, and Y.A. Lu Activation barriers to structural transition determine deposition rates of Alzheimer's disease Aβ amyloid J. Struct. Biol. 130 2000 174 183
24. E. Katchalski-Katzir, I. Shariv, M. Eisenstein, A.A. Friesem, C. Aflalo, and I.A. Vakser Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques Proc. Natl Acad. Sci. USA 89 1992 2195 2199
25. J.G. Kirkwood Statistical mechanics of fluid mixtures J. Chem. Phys. 3 1935 300 313
26. G.M. Torrie, and J.P. Valleau Nonphysical sampling distribution in Monte Carlo free-energy estimation: umbrella sampling J. Comp. Phys. 23 1977 187 199
27. C. Zhang, G. Vasmatzis, J.L. Cornette, and C. DeLisi Determination of atomic desolvation energies from the structures of crystallized proteins J. Mol. Biol. 267 1997 707 726
28. F. Massi, J.W. Peng, J.P. Lee, and J.E. Straub Simulation study of the structure and dynamics of the Alzheimer's amyloid peptide congener in solution Biophys. J. 80 2001 31 44
29. F. Massi, and J.E. Straub Energy landscape theory for Alzheimer's amyloid β-peptide fibril elongation Proteins: Struct. Funct. Genet. 42 2001 217 229
30. F. Chiti, M. Stefani, N. Taddei, G. Ramponi, and C.M. Dobson Rationalization of the effects of mutations on peptide and protein aggregation rates Nature 424 2003 805 808
31. R. Chen, L. Li, and Z. Weng ZDOCK: an initial-stage protein-docking algorithm Proteins: Struct. Funct. Genet. 52 2003 80 87
32. R. Chen, and Z. Weng Docking unbound proteins using shape complementarity, desolvation, and electrostatics Proteins: Struct. Funct. Genet. 47 2002 281 294
33. L. Miravalle, T. Tokuda, R. Chiarle, G. Giaccone, O. Bugiani, and F. Tagliavini Substitutions at codon 22 of Alzheimer's Aβ peptide induce diverse conformational changes and apoptotic effects in human cerebral endothelial cells J. Biol. Chem. 275 2000 27110 27116
34. F. Massi, and J.E. Straub Probing the origins of incresed activity of the E22Q "Dutch" mutant Alzheimer's β-amyloid peptide Biophys. J. 81 2001 697 709
35. B. Lee, and F.M. Richards Interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
36. W. Im, D. Beglov, and B. Roux Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Comput. Phys. Commun. 111 1998 59 75
37. S. Zhang, N. Casey, and J.P. Lee Residual structure in the Alzheimer's disease peptide: probing the origin of a central hydrophobic cluster Fold. Des. 3 1998 414 422
38. B. Widom, P. Bhimalapuram, and K. Koga The hydrophobic effect Phys. Chem. Chem. Phys. 5 2003 3085 3093
39. B.R. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaninathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization and dynamics calculations J. Comp. Phys. 4 1983 187 217
40. A.D. MacKerell Jr, D. Bashford, M. Bellott, R.L. Dunbrack Jr, J.D. Evanseck, and M.J. Field All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
41. S. Miyazawa, and R.L. Jernigan Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation Macromolecules 18 1985 534 552
42. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
43. S.E. Feller, Y. Zhang, R.W. Pastor, and B.R. Brooks Constant pressure molecular dynamics simulation: the Langevin piston method J. Chem. Phys. 103 1995 4613 4621
44. W.G. Hoover Cannonical dynamics: equilibrium phase-space distributions Phys. Rev. A 31 1985 1695 1697
45. T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an N log (N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
46. J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical-integration of Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comp. Phys. 23 1977 327 341
47. J. Kottalam, and D.A. Case Dynamics of ligand escape from the heme pocket of myoglobin J. Am. Chem. Soc. 110 1988 7690 7697
48. S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comp. Chem. 13 1992 1011 1021
49. B. Roux The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 91 1995 275 282
50. V. Munoz, and L. Serrano Intrinsic secondary structure propensities of the amino acids, using statistical φ-ψ matrices: comparison with experimental scales Proteins: Struct. Funct. Genet. 20 1994 301 311