Weissman, A.M. Themes and variations on ubiquitylation. Nat. Rev. Mol. Cell. Biol.2, 169–178 (2001). ArticleCAS Google Scholar
Hochstrasser, M. & Wang, J. Unraveling the means to the end in ATP-dependent proteases. Nat. Struct. Biol.8, 294–296 (2001). ArticleCAS Google Scholar
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. Cell7, 627–637 (2001). ArticleCAS Google Scholar
Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J.M. & Gaub, H.E. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science276, 1109–1112 (1997). ArticleCAS Google Scholar
Oberhauser, A.F., Marszalek, P.E., Erickson, H.P. & Fernandez, J.M. The molecular elasticity of the extracellular matrix protein tenascin. Nature393, 181–185 (1998). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Carrion-Vazquez, M. et al. Mechanical and chemical unfolding of a single protein: a comparison. Proc. Natl. Acad. Sci. USA96, 3694–3699 (1999). ArticleCAS Google Scholar
Li, H. et al. Reverse engineering of the giant muscle protein titin. Nature418, 998–1002 (2002). ArticleCAS Google Scholar
Marszalek, P.E. et al. Mechanical unfolding intermediates in titin modules. Nature402, 100–103 (1999). ArticleCAS Google Scholar
Yang, G. et al. Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme. Proc. Natl. Acad. Sci. USA97, 139–144 (2000). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Brockwell, D.J. et al. The effect of core destabilization on the mechanical resistance of I27. Biophys. J.83, 458–472 (2002). ArticleCAS Google Scholar
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). CASPubMed Google Scholar
Khorasanizadeh, S., Peters, I.D., Butt, T.R. & Roder, H. Folding and stability of a tryptophan-containing mutant of ubiquitin. Biochemistry32, 7054–7063 (1993). ArticleCAS Google Scholar
Oesterhelt, F. et al. Unfolding pathways of individual bacteriorhodopsins. Science288, 143–146 (2000). ArticleCAS Google Scholar
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
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. USA97, 6527–6531 (2000). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Varadan, R., Walker, O., Pickart, C. & Fushman, D. Structural properties of polyubiquitin chains in solution. J. Mol. Biol.324, 637–647 (2002). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Evans, E. & Ritchie, K. Dynamic strength of molecular adhesion bonds. Biophys. J.72, 1541–1555 (1997). ArticleCAS Google Scholar
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. USA99, 12143–12148 (2002). ArticleCAS Google Scholar
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. USA98, 468–472 (2001). ArticleCAS Google Scholar
Lu, H. & Schulten, K. The key event in force-induced unfolding of Titin's immunoglobulin domains. Biophys. J.79, 51–65 (2000). ArticleCAS Google Scholar
Gao, M., Lu, H. & Schulten, K. Simulated refolding of stretched titin immunoglobulin domains. Biophys. J.81, 2268–2277 (2001). ArticleCAS Google Scholar
Beal, R.E., Toscano-Cantaffa, D., Young, P., Rechsteiner, M. & Pickart, C.M. The hydrophobic effect contributes to polyubiquitin chain recognition. Biochemistry37, 2925–2934 (1998). ArticleCAS Google Scholar
Thrower, J.S., Hoffman, L., Rechsteiner, M. & Pickart, C.M. Recognition of the polyubiquitin proteolytic signal. EMBO J.19, 94–102 (2000). ArticleCAS Google Scholar
Vale, R.D. AAA proteins. Lords of the ring. J. Cell Biol.150, F13–19 (2000). ArticleCAS Google Scholar
Brockwell, D.J. et al. Pulling geometry defines the mechanical resistance of a β-sheet protein. Struct. Biol.10, 731–737 (2003). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Shtilerman, M., Lorimer, G.H. & Englander, S.W. Chaperonin function: folding by forced unfolding. Science284, 822–825 (1999). ArticleCAS Google Scholar
Navon, A. & Goldberg, A.L. Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome. Mol. Cell8, 1339–1349 (2001). ArticleCAS Google Scholar
Horwich, A.L., Weber-Ban, E.U. & Finley, D. Chaperone rings in protein folding and degradation. Proc. Natl. Acad. Sci. USA96, 11033–11040 (1999). ArticleCAS Google Scholar
Wiborg, O. et al. The human ubiquitin multigene family: some genes contain multiple directly repeated ubiquitin coding sequences. EMBO J.4, 755–759 (1985). ArticleCAS Google Scholar
Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, New York, 2001). Google Scholar
Brooks, B. et al. CHARMM: a program for macromolecular energy, minimization and molecular dynamics calculations. J. Comp. Chem.4, 187–217 (1983). ArticleCAS Google Scholar
Nelson, M. et al. NAMD—A parallel, object-oriented molecular dynamics program. J. Supercomp. Appl.10, 251–268 (1996). Google Scholar
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph.14, 33–38, 27–38 (1996). ArticleCAS Google Scholar