Understanding amyloid aggregation by statistical analysis of atomic force microscopy images (original) (raw)

References

  1. Caughey, B. & Lansbury, P. T. Protofibrils, pores, fibrils and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annu. Rev. Neurosci. 26, 267–298 (2003).
    Article CAS Google Scholar
  2. Stradner, A. et al. Equilibrium cluster formation in concentrated protein solutions and colloids. Nature 432, 492–495 (2004).
    Article CAS Google Scholar
  3. Mezzenga, R., Schurtenberger, P., Burbidge, A. & Michel, M. Understanding foods as soft materials. Nature Mater. 4, 729–740 (2005).
    Article CAS Google Scholar
  4. Selkoe, D. J. Folding proteins in fatal ways. Nature 426, 900–904 (2003).
    Article CAS Google Scholar
  5. Chiti, F. & Dobson, C. M. Amyloid formation by globular proteins under native conditions. Nature Chem. Biol. 5, 15–22 (2009).
    Article CAS Google Scholar
  6. Knowles, T. P. et al. Role of intermolecular forces in defining material properties of protein nanofibrils. Science 318, 1900–1903 (2007).
    Article CAS Google Scholar
  7. Nelson, R. et al. Structure of the cross-beta spine of amyloid-like fibrils. Nature 435, 773–778 (2005).
    Article CAS Google Scholar
  8. Chiti, F. & Dobson, C. M. Protein misfolding, functional amyloid and human disease. Annu. Rev. Biochem. 75, 333–366 (2006).
    Article CAS Google Scholar
  9. Dobson, C. M. Protein folding and misfolding. Nature 426, 884–890 (2003).
    Article CAS Google Scholar
  10. Graumann, P. L. Cytoskeletal elements in bacteria. Annu. Rev. Microbiol. 61, 589–618 (2007).
    Article CAS Google Scholar
  11. Kueh, H. Y. & Mitchison, T. J. Structural plasticity in actin and tubulin polymer dynamics. Science 325, 960–963 (2009).
    Article CAS Google Scholar
  12. Pearce, F. G., Mackintosh, S. H. & Gerrard, J. A. Formation of amyloid-like fibrils by ovalbumin and related proteins under conditions relevant to food processing. J. Agric. Food Chem. 55, 318–322 (2007).
    Article CAS Google Scholar
  13. Kavanagh, G. M., Clark, A. H. & Ross-Murphy, S. B. Heat-induced gelation of globular proteins: part 3. Molecular studies on low pH beta-lactoglobulin gels. Int. J. Biol. Macromol. 28, 41–50 (2000).
    Article CAS Google Scholar
  14. Bolder, S. G., Sagis, L. M., Venema, P. & van der Linden, E. Effect of stirring and seeding on whey protein fibril formation. J. Agric. Food Chem. 55, 5661–5669 (2007).
    Article CAS Google Scholar
  15. Gosal, W. S., Clark, A. H. & Ross-Murphy, S. B. Fibrillar beta-lactoglobulin gels: Part 1. Fibril formation and structure. Biomacromolecules 5, 2408–2419 (2004).
    Article CAS Google Scholar
  16. Jung, J. M., Savin, G., Pouzot, M., Schmitt, C. & Mezzenga, R. Structure of heat-induced beta-lactoglobulin aggregates and their complexes with sodium-dodecyl sulfate. Biomacromolecules 9, 2477–2486 (2008).
    Article CAS Google Scholar
  17. Gosal, W. S., Clark, A. H., Pudney, P. D. A. & Ross-Murphy, S. B. Novel amyloid fibrillar networks derived from a globular protein: beta-lactoglobulin. Langmuir 18, 7174–7181 (2002).
    Article CAS Google Scholar
  18. Veerman, C., Ruis, H., Sagis, L. M. & van der Linden, E. Effect of electrostatic interactions on the percolation concentration of fibrillar beta-lactoglobulin gels. Biomacromolecules 3, 869–873 (2002).
    Article CAS Google Scholar
  19. Arnaudov, L. N., de Vries, R., Ippel, H. & van Mierlo, C. P. Multiple steps during the formation of beta-lactoglobulin fibrils. Biomacromolecules 4, 1614–1622 (2003).
    Article CAS Google Scholar
  20. Bromley, E. H., Krebs, M. R. & Donald, A. M. Aggregation across the length-scales in beta-lactoglobulin. Faraday Discuss. 128, 13–27 (2005).
    Article CAS Google Scholar
  21. Sagis, L. M., Veerman, C. & van der Linden, E. Mesoscopic properties of semiflexible amyloid fibrils. Langmuir 20, 924–927 (2004).
    Article CAS Google Scholar
  22. Arnaudov, L. N. & de Vries, R. Strong impact of ionic strength on the kinetics of fibrilar aggregation of bovine beta-lactoglobulin. Biomacromolecules 7, 3490–3498 (2006).
    Article CAS Google Scholar
  23. Nilsson, M. R. Techniques to study amyloid fibril formation in vitro. Methods 34, 151–160 (2004).
    Article CAS Google Scholar
  24. Lashuel, H. A. & Wall, J. S. Molecular electron microscopy approaches to elucidating the mechanisms of protein fibrillogenesis. Methods Mol. Biol. 299, 81–101 (2005).
    CAS Google Scholar
  25. Ikeda, S. & Morris, V. J. Fine-stranded and particulate aggregates of heat-denatured whey proteins visualized by atomic force microscopy. Biomacromolecules 3, 382–389 (2002).
    Article CAS Google Scholar
  26. Chamberlain, A. K. et al. Ultrastructural organization of amyloid fibrils by atomic force microscopy. Biophys. J. 79, 3282–3293 (2000).
    Article CAS Google Scholar
  27. Khurana, R. et al. A general model for amyloid fibril assembly based on morphological studies using atomic force microscopy. Biophys. J. 85, 1135–1144 (2003).
    Article CAS Google Scholar
  28. Witz, G., Rechendorff, K., Adamcik, J. & Dietler, G. Conformation of circular DNA in two dimensions. Phys. Rev. Lett. 101, 148103 (2008).
    Article Google Scholar
  29. Manning, G. S. Correlation of polymer persistence length with Euler buckling. Phys. Rev. A 34, 4467–4468 (1986).
    Article CAS Google Scholar
  30. Aggeli, A. et al. Hierarchical self-assembly of chiral rod-like molecules as a model for peptide beta-sheet tapes, ribbons, fibrils and fibers. Proc. Natl Acad. Sci. USA 98, 11857–11862 (2001).
    Article CAS Google Scholar
  31. Paravastu, A. K., Leapman, R. D., Yau, W. M. & Tycko, R. Molecular structural basis for polymorphism in Alzheimer's beta-amyloid fibrils. Proc. Natl Acad. Sci. USA 105, 18349–18354 (2008).
    Article CAS Google Scholar
  32. Jung, J. M. & Mezzenga, R. Liquid crystalline phase behavior of protein fibers in water: experiments versus theory. Langmuir 26, 504–514 (2010).
    Article CAS Google Scholar
  33. Marek, J. et al. Interactive measurement and characterization of DNA molecules by analysis of AFM images. Cytometry A 63, 87–93 (2005).
    Article CAS Google Scholar

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