Protein folding and misfolding (original) (raw)

• Vendruscolo, M., Zurdo, J., MacPhee, C. E. & Dobson, C. M. Protein folding and misfolding: a paradigm of self-assembly and regulation in complex biological systems. Phil. Trans. R. Soc. Lond. 361, 1205–1222 (2003).
  Article ADS MathSciNet CAS Google Scholar
• Radford, S. E. & Dobson, C. M. From computer simulations to human disease: emerging themes in protein folding. Cell 97, 291–298 (1999).
  Article CAS Google Scholar
• Dobson, C. M., Sali, A. & Karplus, M. Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. Eng. 37, 868–893 (1998).
  Article Google Scholar
• Wolynes, P. G., Onuchic, J. N. & Thirumalai, D. Navigating the folding routes. Science 267, 1619–1620 (1995).
  Article ADS CAS Google Scholar
• Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10–19 (1997).
  Article CAS Google Scholar
• Dinner, A. R., Sali, A., Smith, L. J., Dobson, C. M. & Karplus, M. Understanding protein folding via free energy surfaces from theory and experiment. Trends Biochem. Sci. 25, 331–339 (2000).
  Article CAS Google Scholar
• Baldwin, R. L. Protein folding: matching speed and stability. Nature 369, 183–184 (1994).
  Article ADS CAS Google Scholar
• Eaton, W. A., Munoz, V., Thompson, P. A., Henry, E. R. & Hofrichter, J. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Acc. Chem. Res. 31, 745–753 (1998).
  Article CAS Google Scholar
• Snow, C. D., Nguyen, H., Pande, V. S. & Gruebele, M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420, 102–106 (2002).
  Article ADS CAS Google Scholar
• Yang, W. Y. & Gruebele, M. Folding at the speed limit. Nature 423, 193–197 (2003).
  Article ADS CAS Google Scholar
• Mayor, U. et al. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421, 863–867 (2003).
  Article ADS CAS Google Scholar
• Plaxco, K. W., Simons, K. T. & Baker, D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985–994 (1998).
  Article CAS Google Scholar
• Schuler, B., Lipman, E. A. & Eaton, W. A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419, 743–747 (2002).
  Article ADS CAS Google Scholar
• Fersht, A. R. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (W.H. Freeman, New York, 1999).
  Google Scholar
• Fersht, A. R. Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl Acad. Sci. USA 97, 1525–1529 (2000).
  Article ADS CAS Google Scholar
• Shea, J. E. & Brooks, C. L. From folding surfaces to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52, 499–535 (2001).
  Article ADS CAS Google Scholar
• Fersht, A. R. & Daggett, V. Protein folding and unfolding at atomic resolution. Cell 108, 573–582 (2002).
  Article CAS Google Scholar
• Vendruscolo, M., Paci, E., Dobson, C. M. & Karplus, M. Three key residues form a critical contact network in a transition state for protein folding. Nature 409, 641–646 (2001).
  Article ADS CAS Google Scholar
• Makarov, D. E. & Plaxco, K. W. The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci. 12, 17–26 (2003).
  Article CAS Google Scholar
• Baker, D. A surprising simplicity to protein folding. Nature 405, 39–42 (2000).
  Article ADS CAS Google Scholar
• Roder, H. & Colon, W. Kinetic role of early intermediates in protein folding. Curr. Opin. Struct. Biol. 7, 15–28 (1997).
  Article CAS Google Scholar
• Sanchez, I. E. & Kiefhaber, T. Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325, 367–376 (2003).
  Article CAS Google Scholar
• Khan, F., Chuang, J. I., Gianni, S. & Fersht, A. R. The kinetic pathway of folding of barnase. J. Mol. Biol. 333, 169–186 (2003).
  Article CAS Google Scholar
• Vendruscolo, M., Paci, E., Karplus, M. & Dobson, C. M. Structures and relative free energies of partially folded states of proteins. Proc. Natl Acad. Sci. USA 100, 14817–14821 (2003).
  Article ADS CAS Google Scholar
• Cheung, M. S., Garcia, A. E. & Onuchic, J. N. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl Acad. Sci. USA 99, 685–690 (2002).
  Article ADS CAS Google Scholar
• Hardesty, B. & Kramer, G. Folding of a nascent peptide on the ribosome. Prog. Nucleic Acid Res. Mol. Biol. 66, 41–66 (2001).
  Article CAS Google Scholar
• Bukau, B. & Horwich, A. L. The Hsp70 and Hsp60 chaperone machines. Cell 92, 351–366 (1998).
  Article CAS Google Scholar
• Hartl, F. U. & Hayer-Hartl, M. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295, 1852–1858 (2002).
  Article ADS CAS Google Scholar
• Ellis, R. J. Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr. Opin. Struct. Biol. 11, 114–119 (2001).
  Article CAS Google Scholar
• Schiene, C. & Fischer, G. Enzymes that catalyse the restructuring of proteins. Curr. Opin. Struct. Biol. 10, 40–45 (2000).
  Article CAS Google Scholar
• Hammon, C. & Helenius, A. Quality control in the secretory pathway. Curr. Opin. Cell. Biol. 7, 523–529 (1995).
  Article Google Scholar
• Kaufman, R. J. et al. The unfolded protein response in nutrient sensing and differentiation. Nature Rev. Mol. Cell Biol. 3, 411–421 (2002).
  Article CAS Google Scholar
• Wilson, M. R. & Easterbrook Smith, S. B. Clusterin is a secreted mammalian chaperone. Trends Biochem. Sci. 25, 95–98 (2000).
  Article CAS Google Scholar
• Schubert, U. et al. Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature 404, 770–774 (2000).
  Article ADS CAS Google Scholar
• Bence, N. F., Sampat, R. M. & Kopito, R. R. Impairment of the ubiquitin–proteasome system by protein aggregation. Science 292, 1552–1555 (2001).
  Article ADS CAS Google Scholar
• Thomas, P. J., Qu, B. H. & Pedersen, P. L. Defective protein folding as a basis of human disease. Trends Biochem. Sci. 20, 456–459 (1995).
  Article CAS Google Scholar
• Dobson, C. M. The structural basis of protein folding and its links with human disease. Phil. Trans. R. Soc. Lond. B 356, 133–145 (2001).
  Article CAS Google Scholar
• Horwich, A. Protein aggregation in disease: a role for folding intermediates forming specific multimeric interactions. J. Clin. Invest. 110, 1221–1232 (2002).
  Article CAS Google Scholar
• Bullock, A. N. & Fersht, A. R. Rescuing the functions of mutant p53. Nature Rev. Cancer 1, 68–76 (2001).
  Article CAS Google Scholar
• Tan, S. Y. & Pepys, M. B. Amyloidosis. Histopathology 25, 403–414 (1994).
  Article CAS Google Scholar
• Kelly, J. W. Alternative conformation of amyloidogenic proteins and their multi-step assembly pathways. Curr. Opin. Struct. Biol. 8, 101–106 (1998).
  Article CAS Google Scholar
• Sunde, M. & Blake, C. C. F. The structure of amyloid fibrils by electron microscopy and X-ray diffraction. Adv. Protein Chem. 50, 123–159 (1997).
  Article CAS Google Scholar
• Dobson, C. M. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24, 329–332 (1999).
  Article CAS Google Scholar
• Fändrich, M. & Dobson, C. M. The behaviour of polyamino acids reveals an inverse side-chain effect in amyloid structure formation. EMBO J. 21, 5682–5690 (2002).
  Article Google Scholar
• Jiménez, J. L. et al. Cryo-electron microscopy of an SH3 amyloid fibril and model of the molecular packing. EMBO J. 18, 815–821 (1999).
  Article Google Scholar
• Petkova, A. T. et al. A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl Acad. Sci. USA 99, 16742–16747 (2002).
  Article ADS CAS Google Scholar
• Chiti, F., Stefani, M., Taddei, N., Ramponi, G. & Dobson, C. M. Rationalization of mutational effects on protein aggregation rates. Nature 424, 805–808 (2003).
  Article ADS CAS Google Scholar
• Caughey, B. & Lansbury, P. T. Jr. 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
• Bitan, G. et al. Amyloid β-protein (Aβ) assembly: Aβ40 and Aβ42 oligomerize through distinct pathways. Proc. Natl Acad. Sci. USA 100, 330–335 (2003).
  Article ADS CAS Google Scholar
• Nilsson, M. R., Driscoll, M. & Raleigh, D. P. Low levels of asparagine deamidation can have a dramatic effect on aggregation of amyloidogenic peptides: implications for the study of amyloid formation. Protein Sci. 11, 342–349 (2002).
  Article CAS Google Scholar
• Schlunegger, M. P., Bennett, M. J. & Eisenberg, D. Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Adv. Protein Chem. 50, 61–122 (1997).
  Article CAS Google Scholar
• Bucciantini, M. et al. Inherent cytotoxicity of aggregates implies a common origin for protein misfolding diseases. Nature 416, 507–511 (2002).
  Article ADS CAS Google Scholar
• Lashuel, H. A., Hartley, D., Petre, B. M., Walz, T. & Lansbury, P. T. Jr. Neurodegenerative disease: amyloid pores from pathogenic mutations. Nature 418, 291 (2002).
  Article ADS CAS Google Scholar
• Dobson, C. M. Protein folding and disease: a view from the First Horizon Symposium. Nature Rev. Drug Discov. 2, 154–160 (2003).
  Article CAS Google Scholar
• True, H. L. & Lindquist, S. L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477–483 (2000).
  Article ADS CAS Google Scholar
• Chapman, M. R. et al. Role of Escherichia coli curli operons in directing amyloid fiber formation. Science 295, 851–855 (2002).
  Article ADS CAS Google Scholar
• Kelly, J. W. & Balch, W. E. Amyloid as a natural product. J. Cell Biol. 161, 461–462 (2003).
  Article CAS Google Scholar
• Broome, B. M. & Hecht, M. H. Nature disfavours sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J. Mol. Biol. 296, 961–968 (2000).
  Article CAS Google Scholar
• Chiti, F. et al. Kinetic partitioning of protein folding and aggregation. Nature Struct. Biol. 9, 137–143 (2002).
  Article CAS Google Scholar
• Macario, A. J. L. & Macario, E. C. Sick chaperones and ageing: a perspective. Ageing Res. Rev. 1, 295–311 (2002).
  Article CAS Google Scholar
• Ramirez-Alvarado, M., Merkel, J. S. & Regan, L. A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro. Proc. Natl Acad. Sci. USA 97, 8979–8984 (2000).
  Article ADS CAS Google Scholar
• Dumoulin, M. et al. A camelid antibody fragment inhibits amyloid fibril formation by human lysozyme. Nature 424, 783–788 (2003).
  Article ADS CAS Google Scholar
• Prusiner, S. B. Prion diseases and the BSE crisis. Science 278, 245–251 (1997).
  Article CAS Google Scholar
• Taylor, J. P., Hardy, J. & Fischbeck, K. H. Toxic proteins in neurodegenerative disease. Science 296, 1991–1995 (2002).
  Article ADS CAS Google Scholar
• Walsh, D. M. et al. Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo. Nature 416, 535–539 (2002).
  Article ADS CAS Google Scholar
• Kayed, R. et al. Common structure of soluble amyloid oligomers implies common mechanisms of pathogenesis. Science 300, 486–489 (2003).
  Article ADS CAS Google Scholar
• Stefani, M. & Dobson, C. M. Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J. Mol. Med. 81, 678–699 (2003).
  Article CAS Google Scholar
• Sherman, M. Y. & Goldberg, A. L. Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases. Neuron 29, 15–32 (2001).
  Article CAS Google Scholar
• Muchowski, P. J. et al. Hsp70 and Hsp40 chaperones can inhibit self-assembly of polyglutamine proteins into amyloid-like fibrils. Proc. Natl Acad. Sci. USA 97, 7841–7846 (2000).
  Article ADS CAS Google Scholar
• Csermely, P. Chaperone overload is a possible contributor to 'civilization diseases'. Trends Genet. 17, 701–704 (2001).
  Article CAS Google Scholar
• Dobson, C. M. Getting out of shape—protein misfolding diseases. Nature 418, 729–730 (2002).
  Article ADS CAS Google Scholar