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Allosteric signaling of ATP hydrolysis in GroEL–GroES complexes

Nature Structural & Molecular Biology volume 13, pages 147–152 (2006)Cite this article

Abstract

The double-ring chaperonin GroEL and its lid-like cochaperonin GroES form asymmetric complexes that, in the ATP-bound state, mediate productive folding in a hydrophilic, GroES-encapsulated chamber, the so-called cis cavity. Upon ATP hydrolysis within the cis ring, the asymmetric complex becomes able to accept non-native polypeptides and ATP in the open, trans ring. Here we have examined the structural basis for this allosteric switch in activity by cryo-EM and single-particle image processing. ATP hydrolysis does not change the conformation of the cis ring, but its effects are transmitted through an inter-ring contact and cause domain rotations in the mobile trans ring. These rigid-body movements in the trans ring lead to disruption of its intra-ring contacts, expansion of the entire ring and opening of both the nucleotide pocket and the substrate-binding domains, admitting ATP and new substrate protein.

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Figure 1: Distribution of protein complexes found in the ATP and ADP samples.
Figure 2: Solution structures of GroEL–ATP7–GroES and GroEL–ADP7–GroES.
Figure 3: Quality of EM maps and atomic structure fitting.
Figure 4: Disruption of intra-ring contacts between the equatorial domains of the trans ring.
Figure 5: ATP hydrolysis in cis causes radial expansion of the trans ring.
Figure 6: Movements of key structural elements in the GroEL ATPase cycle.

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References

  1. Sigler, P.B. et al. Structure and function in GroEL-mediated protein folding. Annu. Rev. Biochem. 67, 581–608 (1998).

    Article  CAS  Google Scholar 

  2. Saibil, H.R. & Ranson, N.A. The chaperonin folding machine. Trends Biochem. Sci. 27, 627–632 (2002).

    Article  CAS  Google Scholar 

  3. Hartl, F.U. & Hayer-Hartl, F.U. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295, 1852–1858 (2002).

    Article  CAS  Google Scholar 

  4. Fenton, W.A. & Horwich, A.L. Chaperone-mediated protein folding: fate of substrate polypeptide. Q. Rev. Biophys. 36, 229–256 (2003).

    Article  CAS  Google Scholar 

  5. Yifrach, O. & Horovitz, A. Two lines of allosteric communication in the oligomeric chaperonin GroEL are revealed by the single mutation Arg196->Ala. J. Mol. Biol. 243, 397–401 (1994).

    Article  CAS  Google Scholar 

  6. Yifrach, O. & Horovitz, A. Nested co-operativity in the ATPase activity of the oligomeric chaperonin GroEL. Biochemistry 34, 5303–5308 (1995).

    Article  CAS  Google Scholar 

  7. Ranson, N.A. et al. ATP bound states of GroEL captured by cryo-electron microscopy. Cell 107, 869–879 (2001).

    Article  CAS  Google Scholar 

  8. Roseman, A.M., Chen, S., White, H., Braig, K. & Saibil, H.R. The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell 87, 241–251 (1996).

    Article  CAS  Google Scholar 

  9. 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  Google Scholar 

  10. Weissman, J.S., Rye, H.S., Fenton, W.A., Beecham, J.M. & Horwich, A.L. Characterisation of the active folding intermediate of a GroEL-GroES-mediated protein folding reaction. Cell 84, 481–490 (1996).

    Article  CAS  Google Scholar 

  11. Rye, H.S. et al. Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL. Nature 388, 792–798 (1997).

    Article  CAS  Google Scholar 

  12. Rye, H.S. et al. GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding active rings. Cell 97, 325–338 (1999).

    Article  CAS  Google Scholar 

  13. Chaudhry, C. et al. Role of the γ-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. EMBO J. 22, 4877–4887 (2003).

    Article  CAS  Google Scholar 

  14. Navaza, J., Lepault, J., Rey, F.A., Álvarez-Rúa, C. & Borge, J. On the fitting of model electron densities in EM reconstructions: a reciprocal space formulation. Acta Crystallogr. D Biol. Crystallogr. 58, 1820–1825 (2002).

    Article  CAS  Google Scholar 

  15. Horovitz, A., Bochkareva, E.S., Yifrach, O. & Girshovich, A.S. Prediction of an inter-residue interaction in the chaperonin GroEL from multiple sequence alignment is confirmed by double-mutant cycle analysis. J. Mol. Biol. 238, 133–138 (1994).

    Article  CAS  Google Scholar 

  16. Braig, K. et al. The crystal structure of the bacterial chaperonin GroEL at 2.8Å resolution. Nature 371, 578–586 (1994).

    Article  CAS  Google Scholar 

  17. White, H.E. et al. Structural basis for allosteric changes in the GroEL mutant Arg197 → Ala. Nat. Struct. Biol. 4, 690–694 (1997).

    Article  CAS  Google Scholar 

  18. Vale, R.D. & Milligan, R.A. The way things move: looking under the hood of molecular motor proteins. Science 288, 88–95 (2000).

    Article  CAS  Google Scholar 

  19. Dubochet, J. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129–228 (1988).

    Article  CAS  Google Scholar 

  20. Mindell, J.A. & Grigorieff, N. Accurate determination of microscope defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003).

    Article  Google Scholar 

  21. Smith, J.M. Ximdisp – A visualization tool to aid structure determination from electron microscope images. J. Struct. Biol. 125, 223–228 (1999).

    Article  CAS  Google Scholar 

  22. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996).

    Article  CAS  Google Scholar 

  23. Frigo, M. & Johnson, S.G. FFTW: an adaptive software architecture for the FFT. ICASSP Conference Proceedings 3, 1381–1384 (1998).

    Google Scholar 

  24. van Heel, M., Harauz, G., Orlova, E.V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17–24 (1996).

    Article  CAS  Google Scholar 

  25. Roseman, A.M., Ranson, N.A., Gowen, B., Fuller, S.D. & Saibil, H.R. The ATP-bound state of the E. coli chaperonin GroEL studied by cryo-electron microscopy. J. Struct. Biol. 135, 115–125 (2001).

    Article  CAS  Google Scholar 

  26. Case, D.A. et al. The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668–1688 (2005).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank R. Westlake and S. Killen for computer support and E. Orlova, W. Fenton and A. Horovitz for discussion. This work was supported by a Wellcome Trust Programme Grant to H.R.S., a Leeds University Research Fellowship to N.A.R. and Howard Hughes Medical Institute support to A.L.H.

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Authors and Affiliations

  1. Astbury Centre for Structural Molecular Biology and Institute of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK

    Neil A Ranson

  2. School of Crystallography and Institute for Structural Molecular Biology, Birkbeck College London, Malet Street, London, WC1E 7HX, UK

    Neil A Ranson, Daniel K Clare, David Houldershaw & Helen R Saibil

  3. Department of Genetics and Howard Hughes Medical Institute, Yale School of Medicine, New Haven, 06510, Connecticut, USA

    George W Farr & Arthur L Horwich

  4. The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Arthur L Horwich

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  1. Neil A Ranson
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  5. Arthur L Horwich
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Correspondence to Helen R Saibil.

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Supplementary information

Supplementary Figure 1

Resolution tests for GroEL-GroES complexes (PDF 321 kb)

Supplementary Figure 2

Effect of crystal packing on the GroEL-ADP7-GroES structure (PDF 1696 kb)

Supplementary Figure 3

The relay helix (PDF 961 kb)

Supplementary Video 1

Side view movie alternating between ATP bound and ADP bound state (GIF 136 kb)

Supplementary Video 2

End view movie alternating between ATP and ADP bound state (GIF 112 kb)

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Ranson, N., Clare, D., Farr, G. et al. Allosteric signaling of ATP hydrolysis in GroEL–GroES complexes. Nat Struct Mol Biol 13, 147–152 (2006). https://doi.org/10.1038/nsmb1046

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