Mechanism of folding chamber closure in a group II chaperonin (original) (raw)

• Bukau, B. & Horwich, A. L. The Hsp70 and Hsp60 chaperone machines. Cell 92, 351–366 (1998)
  Article CAS Google Scholar
• Frydman, J. Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu. Rev. Biochem. 70, 603–647 (2001)
  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 CAS ADS Google Scholar
• Ditzel, L. et al. Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Cell 93, 125–138 (1998)
  Article CAS Google Scholar
• Reissmann, S., Parnot, C., Booth, C. R., Chiu, W. & Frydman, J. Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins. Nature Struct. Mol. Biol. 14, 432–440 (2007)
  Article CAS Google Scholar
• Meyer, A. S. et al. Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis. Cell 113, 369–381 (2003)
  Article CAS Google Scholar
• Kusmierczyk, A. R. & Martin, J. Nucleotide-dependent protein folding in the type II chaperonin from the mesophilic archaeon Methanococcus maripaludis. Biochem. J. 371, 669–673 (2003)
  Article CAS Google Scholar
• Dobson, C. M. Principles of protein folding, misfolding and aggregation. Semin. Cell Dev. Biol. 15, 3–16 (2004)
  Article CAS Google Scholar
• Balch, W. E., Morimoto, R. I., Dillin, A. & Kelly, J. W. Adapting proteostasis for disease intervention. Science 319, 916–919 (2008)
  Article CAS ADS Google Scholar
• Yam, A. Y. et al. Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nature Struct. Mol. Biol. 15, 1255–1262 (2008)
  Article CAS Google Scholar
• Tam, S., Geller, R., Spiess, C. & Frydman, J. The chaperonin TRiC controls polyglutamine aggregation and toxicity through subunit-specific interactions. Nature Cell Biol. 8, 1155–1162 (2006)
  Article CAS Google Scholar
• Kitamura, A. et al. Cytosolic chaperonin prevents polyglutamine toxicity with altering the aggregation state. Nature Cell Biol. 8, 1163–1169 (2006)
  Article CAS Google Scholar
• Braig, K. et al. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 371, 578–586 (1994)
  Article CAS ADS Google Scholar
• Saibil, H. R. et al. ATP induces large quaternary rearrangements in a cage-like chaperonin structure. Curr. Biol. 3, 265–273 (1993)
  Article CAS Google Scholar
• Booth, C. R. et al. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nature Struct. Mol. Biol. 15, 746–753 (2008)
  Article CAS Google Scholar
• Kusmierczyk, A. R. & Martin, J. Nested cooperativity and salt dependence of the ATPase activity of the archaeal chaperonin Mm-cpn. FEBS Lett. 547, 201–204 (2003)
  Article CAS Google Scholar
• Clare, D. K. et al. Multiple states of a nucleotide-bound group 2 chaperonin. Structure 16, 528–534 (2008)
  Article CAS Google Scholar
• Blow, D. Outline of Crystallography for Biologists (Oxford Univ. Press, 2002)
  Google Scholar
• Ludtke, S. J. et al. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16, 441–448 (2008)
  Article CAS Google Scholar
• Jiang, W. et al. Backbone structure of the infectious ε15 virus capsid revealed by electron cryomicroscopy. Nature 451, 1130–1134 (2008)
  Article CAS ADS Google Scholar
• Zhang, X. et al. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl Acad. Sci. USA 105, 1867–1872 (2008)
  Article CAS ADS Google Scholar
• Yu, X., Jin, L. & Zhou, Z. H. 3.88 Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Nature 453, 415–419 (2008)
  Article CAS ADS Google Scholar
• Braig, K., Adams, P. D. & Brünger, A. T. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution. Nature Struct. Biol. 2, 1083–1094 (1995)
  Article CAS Google Scholar
• Schoehn, G., Hayes, M., Cliff, M., Clarke, A. R. & Saibil, H. R. Domain rotations between open, closed and bullet-shaped forms of the thermosome, an archaeal chaperonin. J. Mol. Biol. 301, 323–332 (2000)
  Article CAS Google Scholar
• Schröder, G. F., Brunger, A. T. & Levitt, M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 15, 1630–1641 (2007)
  Article Google Scholar
• Xu, Z., Horwich, A. L. & Sigler, P. B. The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex. Nature 388, 741–750 (1997)
  Article CAS ADS Google Scholar
• Boisvert, D. C., Wang, J., Otwinowski, Z., Horwich, A. L. & Sigler, P. B. The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATPγS. Nature Struct. Biol. 3, 170–177 (1996)
  Article CAS Google Scholar
• Tang, Y. C. et al. Structural features of the GroEL-GroES nano-cage required for rapid folding of encapsulated protein. Cell 125, 903–914 (2006)
  Article CAS Google Scholar
• Suzuki, M. et al. Effect of the C-terminal truncation on the functional cycle of chaperonin GroEL: implication that the C-terminal region facilitates the transition from the folding-arrested to the folding-competent state. J. Biol. Chem. 283, 23931–23939 (2008)
  Article CAS Google Scholar
• Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999)
  Article CAS Google Scholar
• Yang, C. et al. Estimating contrast transfer function and associated parameters by constrained nonlinear optimization. J. Microsc. 233, 391–403 (2009)
  Article MathSciNet CAS Google Scholar
• Ludtke, S. J., Jakana, J., Song, J.-L., Chuang, D. & Chiu, W. A 11.5 Å single particle reconstruction of GroEL using EMAN. J. Mol. Biol. 314, 253–262 (2001)
  Article CAS Google Scholar
• Harauz, G. & van Heel, M. Exact filters for general geometry three dimensional reconstruction. Optik 73, 146–156 (1986)
  Google Scholar
• Fernández, J. J., Luque, D., Caston, J. R. & Carrascosa, J. L. Sharpening high resolution information in single particle electron cryomicroscopy. J. Struct. Biol. 164, 170–175 (2008)
  Article Google Scholar
• Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003)
  Article CAS Google Scholar
• Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)
  Article CAS Google Scholar
• Arnold, K., Bordoli, L., Kopp, J. & Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22, 195–201 (2006)
  Article CAS Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
  Article Google Scholar
• Lovell, S. C. et al. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50, 437–450 (2003)
  Article CAS Google Scholar