The mechanical stability of ubiquitin is linkage dependent (original) (raw)

References

  1. Pickart, C.M. Mechanisms underlying ubiquitination. Annu. Rev. Biochem. 70, 503–533 (2001).
    Article CAS Google Scholar
  2. Weissman, A.M. Themes and variations on ubiquitylation. Nat. Rev. Mol. Cell. Biol. 2, 169–178 (2001).
    Article CAS Google Scholar
  3. Hochstrasser, M. & Wang, J. Unraveling the means to the end in ATP-dependent proteases. Nat. Struct. Biol. 8, 294–296 (2001).
    Article CAS Google Scholar
  4. Lee, C., Schwartz, M.P., Prakash, S., Iwakura, M. & Matouschek, A. ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal. Mol. Cell 7, 627–637 (2001).
    Article CAS Google Scholar
  5. Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J.M. & Gaub, H.E. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276, 1109–1112 (1997).
    Article CAS Google Scholar
  6. Oberhauser, A.F., Marszalek, P.E., Erickson, H.P. & Fernandez, J.M. The molecular elasticity of the extracellular matrix protein tenascin. Nature 393, 181–185 (1998).
    Article CAS Google Scholar
  7. Lu, H., Isralewitz, B., Krammer, A., Vogel, V. & Schulten, K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys. J. 75, 662–671 (1998).
    Article CAS Google Scholar
  8. Fisher, T.E., Marszalek, P.E. & Fernandez, J.M. Stretching single molecules into novel conformations using the atomic force microscope. Nat. Struct. Biol. 7, 719–724 (2000).
    Article CAS Google Scholar
  9. Carrion-Vazquez, M. et al. Mechanical and chemical unfolding of a single protein: a comparison. Proc. Natl. Acad. Sci. USA 96, 3694–3699 (1999).
    Article CAS Google Scholar
  10. Li, H. et al. Reverse engineering of the giant muscle protein titin. Nature 418, 998–1002 (2002).
    Article CAS Google Scholar
  11. Marszalek, P.E. et al. Mechanical unfolding intermediates in titin modules. Nature 402, 100–103 (1999).
    Article CAS Google Scholar
  12. Yang, G. et al. Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme. Proc. Natl. Acad. Sci. USA 97, 139–144 (2000).
    Article CAS Google Scholar
  13. Lenne, P.F., Raae, A.J., Altmann, S.M., Saraste, M. & Horber, J.K. States and transitions during forced unfolding of a single spectrin repeat. FEBS Lett. 476, 124–128 (2000).
    Article CAS Google Scholar
  14. Best, R.B., Li, B., Steward, A., Daggett, V. & Clarke, J. Can non-mechanical proteins withstand force? Stretching barnase by atomic force microscopy and molecular dynamics simulation. Biophys. J. 81, 2344–2356 (2001).
    Article CAS Google Scholar
  15. Brockwell, D.J. et al. The effect of core destabilization on the mechanical resistance of I27. Biophys. J. 83, 458–472 (2002).
    Article CAS Google Scholar
  16. Baumeister, W., Cejka, Z., Kania, M. & Seemuller, E. The proteasome: a macromolecular assembly designed to confine proteolysis to a nanocompartment. Biol. Chem. 378, 121–130 (1997).
    CAS PubMed Google Scholar
  17. Khorasanizadeh, S., Peters, I.D., Butt, T.R. & Roder, H. Folding and stability of a tryptophan-containing mutant of ubiquitin. Biochemistry 32, 7054–7063 (1993).
    Article CAS Google Scholar
  18. Marko, J.F. & Siggia, E.D. Stretching DNA. Macromolecules 28, 8759–8770 (1995).
    Article CAS Google Scholar
  19. Oesterhelt, F. et al. Unfolding pathways of individual bacteriorhodopsins. Science 288, 143–146 (2000).
    Article CAS Google Scholar
  20. Vijay–Kumar, S., Bugg, C.E. & Cook, W.J. Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol. 194, 531–544 (1987).
    Article Google Scholar
  21. Li, H., Oberhauser, A.F., Fowler, S.B., Clarke, J. & Fernandez, J.M. Atomic force microscopy reveals the mechanical design of a modular protein. Proc. Natl. Acad. Sci. USA 97, 6527–6531 (2000).
    Article CAS Google Scholar
  22. Cook, W.J., Jeffrey, L.C., Kasperek, E. & Pickart, C.M. Structure of tetraubiquitin shows how multiubiquitin chains can be formed. J. Mol. Biol. 236, 601–609 (1994).
    Article CAS Google Scholar
  23. Varadan, R., Walker, O., Pickart, C. & Fushman, D. Structural properties of polyubiquitin chains in solution. J. Mol. Biol. 324, 637–647 (2002).
    Article CAS Google Scholar
  24. Li, H., Carrion-Vazquez, M., Oberhauser, A.F., Marszalek, P.E. & Fernandez, J.M. Point mutations alter the mechanical stability of immunoglobulin modules. Nat. Struct. Biol. 7, 1117–1120 (2000).
    Article CAS Google Scholar
  25. Evans, E. & Ritchie, K. Dynamic strength of molecular adhesion bonds. Biophys. J. 72, 1541–1555 (1997).
    Article CAS Google Scholar
  26. Best, R.B., Fowler, S.B., Toca-Herrera, J.L. & Clarke, J. A simple method for probing the mechanical unfolding pathway of proteins in detail. Proc. Natl. Acad. Sci. USA 99, 12143–12148 (2002).
    Article CAS Google Scholar
  27. Oberhauser, A.F., Hansma, P.K., Carrion-Vazquez, M. & Fernandez, J.M. Stepwise unfolding of titin under force-clamp atomic force microscopy. Proc. Natl. Acad. Sci. USA 98, 468–472 (2001).
    Article CAS Google Scholar
  28. Lu, H. & Schulten, K. The key event in force-induced unfolding of Titin's immunoglobulin domains. Biophys. J. 79, 51–65 (2000).
    Article CAS Google Scholar
  29. Gao, M., Lu, H. & Schulten, K. Simulated refolding of stretched titin immunoglobulin domains. Biophys. J. 81, 2268–2277 (2001).
    Article CAS Google Scholar
  30. Beal, R.E., Toscano-Cantaffa, D., Young, P., Rechsteiner, M. & Pickart, C.M. The hydrophobic effect contributes to polyubiquitin chain recognition. Biochemistry 37, 2925–2934 (1998).
    Article CAS Google Scholar
  31. Thrower, J.S., Hoffman, L., Rechsteiner, M. & Pickart, C.M. Recognition of the polyubiquitin proteolytic signal. EMBO J. 19, 94–102 (2000).
    Article CAS Google Scholar
  32. Vale, R.D. AAA proteins. Lords of the ring. J. Cell Biol. 150, F13–19 (2000).
    Article CAS Google Scholar
  33. Brockwell, D.J. et al. Pulling geometry defines the mechanical resistance of a β-sheet protein. Struct. Biol. 10, 731–737 (2003).
    Article CAS Google Scholar
  34. Minajeva, A., Kulke, M., Fernandez, J.M. & Linke, W.A. Unfolding of titin domains explains the viscoelastic behavior of skeletal myofibrils. Biophys. J. 80, 1442–1451 (2001).
    Article CAS Google Scholar
  35. Huang, S., Ratliff, K.S., Schwartz, M.P., Spenner, J.M. & Matouschek, A. Mitochondria unfold precursor proteins by unraveling them from their N-termini. Nat. Struct. Biol. 6, 1132–1138 (1999).
    Article CAS Google Scholar
  36. Shtilerman, M., Lorimer, G.H. & Englander, S.W. Chaperonin function: folding by forced unfolding. Science 284, 822–825 (1999).
    Article CAS Google Scholar
  37. Navon, A. & Goldberg, A.L. Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome. Mol. Cell 8, 1339–1349 (2001).
    Article CAS Google Scholar
  38. Horwich, A.L., Weber-Ban, E.U. & Finley, D. Chaperone rings in protein folding and degradation. Proc. Natl. Acad. Sci. USA 96, 11033–11040 (1999).
    Article CAS Google Scholar
  39. Wiborg, O. et al. The human ubiquitin multigene family: some genes contain multiple directly repeated ubiquitin coding sequences. EMBO J. 4, 755–759 (1985).
    Article CAS Google Scholar
  40. Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, New York, 2001).
    Google Scholar
  41. Brooks, B. et al. CHARMM: a program for macromolecular energy, minimization and molecular dynamics calculations. J. Comp. Chem. 4, 187–217 (1983).
    Article CAS Google Scholar
  42. Nelson, M. et al. NAMD—A parallel, object-oriented molecular dynamics program. J. Supercomp. Appl. 10, 251–268 (1996).
    Google Scholar
  43. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38, 27–38 (1996).
    Article CAS Google Scholar

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