Hydrophobic Cooperativity as a Mechanism for Amyloid Nucleation

Journal of Molecular Biology

Volumn 368, Issue 3, 2007, Pages 894-901

  Hills Jr , Ronald D ^a   Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

amyloid fibril; cooperativity; critical nucleus; fibril formation kinetics; replica exchange molecular dynamics

Indexed keywords

AMYLOID; HEXAPEPTIDE; PEPTIDE;

ARTICLE; BETA SHEET; CELL NUCLEUS; ELECTRICITY; ENERGY TRANSFER; FIBER; HYDROPHOBICITY; MATHEMATICAL PARAMETERS; MOLECULAR DYNAMICS; MOLECULAR MODEL; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN AGGREGATION; SIMULATION; SOLVATION;

EID: 34047157022     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.02.043     Document Type: Article

References (37)

1. Sunde M., Serpell L.C., Bartlam M., Fraser P.E., Pepys M.B., and Blake C.C.F. Common core structure of amyloid fibrils by synchrotron X-ray diffraction. J. Mol. Biol. 273 (1997) 729-739
2. Hurshman A.R., White J.T., Powers E.T., and Kelly J.W. Transthyretin aggregation under partially denaturing conditions is a downhill polymerization. Biochemistry 43 (2004) 7365-7381
3. Massi F., and Straub J.E. Energy landscape theory for Alzheimer's amyloid beta-peptide fibril elongation. Proteins: Struct. Funct. Genet. 42 (2001) 217-229
4. Thirumalai D., Klimov D.K., and Dima R.I. Emerging ideas on the molecular basis of protein and peptide aggregation. Curr. Opin. Struct. Biol. 13 (2003) 146-159
5. Tiana G., Simona F., Brogliaa R.A., and Colombo G. Thermodynamics of beta-amyloid fibril formation. J. Chem. Phys. 120 (2004) 8307-8317
6. Powers E.T., and Powers D.L. The kinetics of nucleated polymerizations at high concentrations: amyloid fibril formation near and above the "supercritical concentration". Biophys. J. 91 (2006) 122-132
7. Kagan B.L., Azimov R., and Azimova R. Amyloid peptide channels. J. Membr. Biol. 202 (2004) 1-10
8. Kawahara M., Kuroda Y., Arispe N., and Rojas E. Alzheimer's beta-amyloid, human islet amylin, and prion protein fragment evoke intracellular free calcium elevations by a common mechanism in a hypothalamic GnRH neuronal cell line. J. Biol. Chem. 275 (2000) 14077-14083
9. Kayed R., Sokolov Y., Edmonds B., McIntire T.M., Milton S.C., Hall J.E., and Glabe C.G. Permeabilization of lipid bilayers is a common conformation-dependent activity of soluble amyloid oligomers in protein misfolding diseases. J. Biol. Chem. 279 (2004) 46363-46366
10. Quist A., Doudevski L., Lin H., Azimova R., Ng D., Frangione B., et al. Amyloid ion channels: a common structural link for protein-misfolding disease. Proc. Natl Acad. Sci. USA 102 (2005) 10427-10432
11. Cecchini M., Rao F., Seeber M., and Caflisch A. Replica exchange molecular dynamics simulations of amyloid peptide aggregation. J. Chem. Phys. 121 (2004) 10748-10756
12. Klimov D.K., and Thirumalai D. Dissecting the assembly of A beta(16-22) amyloid peptides into antiparallel beta sheets. Structure 11 (2003) 295-307
13. Wu C., Lei H.X., and Duan Y. Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations. Biophys. J. 87 (2004) 3000-3009
14. Nguyen H.D., and Hall C.K. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl Acad. Sci. USA 101 (2004) 16180-16185
15. Pellarin R., and Caflisch A. Interpreting the aggregation kinetics of amyloid peptides. J. Mol. Biol. 360 (2006) 882-892
16. Fay N., Inoue Y.J., Bousset L., Taguchi H., and Melki R. Assembly of the yeast prion Ure2p into protein fibrils-thermodynamic and kinetic characterization. J. Biol. Chem. 278 (2003) 30199-30205
17. Bhattacharyya A.M., Thakur A.K., and Wetzel R. Polyglutamine aggregation nucleation: thermodynamics of a highly unfavorable protein folding reaction. Proc. Natl Acad. Sci. USA 102 (2005) 15400-15405
18. de la Paz M.L., Goldie K., Zurdo J., Lacroix E., Dobson C.M., Hoenger A., and Serrano L. De novo designed peptide-based amyloid fibrils. Proc. Natl Acad. Sci. USA 99 (2002) 16052-16057
19. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D. J., Swaminathan S., and Karplus M. Charmm-a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4 (1983) 187-217
20. Im W.P., Lee M.S., and Brooks C.L. Generalized born model with a simple smoothing function. J. Comput. Chem. 24 (2003) 1691-1702
21. Ma B.Y., and Nussinov R. Stabilities and conformations of Alzheimer's beta-amyloid peptide oligomers (A beta(16-22′) A beta(16-35′) and A beta(10-35)): sequence effects. Proc. Natl Acad. Sci. USA 99 (2002) 14126-14131
22. Zanuy D., Ma B.Y., and Nussinov R. Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys. J. 84 (2003) 1884-1894
23. Tenidis K., Waldner M., Bernhagen J., Fischle W., Bergmann M., Weber M., et al. Identification of a penta- and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties. J. Mol. Biol. 295 (2000) 1055-1071
24. Zanuy D., and Nussinov R. The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. J. Mol. Biol. 329 (2003) 565-584
25. Zhao Y.L., and Wu Y.D. A theoretical study of beta-sheet models: is the formation of hydrogen-bond networks cooperative?. J. Am. Chem. Soc. 124 (2002) 1570-1571
26. Dill K.A., Fiebig K.M., and Chan H.S. Cooperativity in protein-folding kinetics. Proc. Natl Acad. Sci. USA 90 (1993) 1942-1946
27. MacKerell A.D., Bashford D., Bellott M., Dunbrack R. L., Evanseck J.D., Field M.J., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
28. Mackerell A.D., Feig M., and Brooks C.L. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25 (2004) 1400-1415
29. MacKerell A.D., Feig M., and Brooks C.L. Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 126 (2004) 698-699
30. Nina M., Beglov D., and Roux B. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. J. Phys. Chem. ser. B 101 (1997) 5239-5248
31. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J. Comput. Phys. 23 (1977) 327-341
32. Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Letters 314 (1999) 141-151
33. Feig M., Karanicolas J., and Brooks C.L. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J. Mol. Graph. 22 (2004) 377-395
34. Yang A.S., and Honig B. Free-energy determinants of secondary structure formation. 2. Antiparallel beta-sheets. J. Mol. Biol. 252 (1995) 366-376
35. Fandrich M. Absolute correlation between lag time and growth rate in the spontaneous formation of several amyloid-like aggregates and fibrils. J. Mol. Biol. 365 (2007) 1266-1270
36. Fawzi N.L., Okabe Y., Yap E.H., and Head-Gordon T. Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide. J. Mol. Biol. 365 (2007) 535-550
37. Krebs M.R., Devlin G.L., and Donald A.M. Protein particulates: another generic form of protein aggregation?. Biophys. J. 92 (2007) 1336-1342