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Reprogramming an ATP-driven protein machine into a light-gated nanocage

Nature Nanotechnology volume 8, pages 928–932 (2013)Cite this article

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Abstract

Natural protein assemblies have many sophisticated architectures and functions, creating nanoscale storage containers, motors and pumps1,2,3. Inspired by these systems, protein monomers have been engineered to self-assemble into supramolecular architectures4 including symmetrical5,6, metal-templated7,8 and cage-like structures8,9,10. The complexity of protein machines, however, has made it difficult to create assemblies with both defined structures and controllable functions. Here we report protein assemblies that have been engineered to function as light-controlled nanocontainers. We show that an adenosine-5′-triphosphate-driven group II chaperonin11,12, which resembles a barrel with a built-in lid, can be reprogrammed to open and close on illumination with different wavelengths of light. By engineering photoswitchable azobenzene-based molecules into the structure, light-triggered changes in interatomic distances in the azobenzene moiety are able to drive large-scale conformational changes of the protein assembly. The different states of the assembly can be visualized with single-particle cryo-electron microscopy, and the nanocages can be used to capture and release non-native cargos. Similar strategies that switch atomic distances with light could be used to build other controllable nanoscale machines.

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Figure 1: Design strategy to control the shape transition of Mm-cpn with light by reversibly switching interatomic distances in the assembly.
Figure 2: xMm-cpn switches reversibly between the closed and open conformations when illuminated with blue and near-ultraviolet light, respectively.
Figure 3: xMm-cpn is a protease-resistant nanocage and can be used for light-triggered release of non-native cargos.

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References

  1. Tanaka, S. et al. Atomic-level models of the bacterial carboxysome shell. Science 319, 1083–1086 (2008).

    Article  Google Scholar 

  2. Vale, R. D. The molecular motor toolbox for intracellular transport. Cell 112, 467–480 (2003).

    Article  Google Scholar 

  3. Forgac, M. Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology. Nature Rev. Mol. Cell Biol. 8, 917–929 (2007).

    Article  Google Scholar 

  4. Yeates, T. O. & Padilla, J. E. Designing supramolecular protein assemblies. Curr. Opin. Struct. Biol. 12, 464–470 (2002).

    Article  Google Scholar 

  5. King, N. P. et al. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336, 1171–1174 (2012).

    Article  Google Scholar 

  6. Gradisar, H. et al. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nature Chem. Biol. 9, 362–366 (2013).

    Article  Google Scholar 

  7. Brodin, J. D. et al. Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nature Chem. 4, 375–382 (2012).

    Article  Google Scholar 

  8. Huard, D. J., Kane, K. M. & Tezcan, F. A. Re-engineering protein interfaces yields copper-inducible ferritin cage assembly. Nature Chem. Biol. 9, 169–176 (2013).

    Article  Google Scholar 

  9. Fletcher, J. M. et al. Self-assembling cages from coiled-coil peptide modules. Science 340, 595–599 (2013).

    Article  Google Scholar 

  10. Lai, Y. T., Cascio, D. & Yeates, T. O. Structure of a 16-nm cage designed by using protein oligomers. Science 336, 1129 (2012).

    Article  Google Scholar 

  11. 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  Google Scholar 

  12. Zhang, J. et al. Mechanism of folding chamber closure in a group II chaperonin. Nature 463, 379–383 (2010).

    Article  Google Scholar 

  13. Pereira, J. H. et al. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J. Biol. Chem. 285, 27958–27966 (2010).

    Article  Google Scholar 

  14. Kumita, J. R., Smart, O. S. & Woolley, G. A. Photo-control of helix content in a short peptide. Proc. Natl Acad. Sci. USA 97, 3803–3808 (2000).

    Article  Google Scholar 

  15. Schierling, B. et al. Controlling the enzymatic activity of a restriction enzyme by light. Proc. Natl Acad. Sci. USA 107, 1361–1366 (2010).

    Article  Google Scholar 

  16. Banghart, M., Borges, K., Isacoff, E., Trauner, D. & Kramer, R. H. Light-activated ion channels for remote control of neuronal firing. Nature Neurosci. 7, 1381–1386 (2004).

    Article  Google Scholar 

  17. Muramatsu, S., Kinbara, K., Taguchi, H., Ishii, N. & Aida, T. Semibiological molecular machine with an implemented ‘AND’ logic gate for regulation of protein folding. J. Am. Chem. Soc. 128, 3764–3769 (2006).

    Article  Google Scholar 

  18. Umeki, N. et al. Incorporation of an azobenzene derivative into the energy transducing site of skeletal muscle myosin results in photo-induced conformational changes. J. Biochem. 136, 839–846 (2004).

    Article  Google Scholar 

  19. Beharry, A. A. et al. Quantitative analysis of the effects of photoswitchable distance constraints on the structure of a globular protein. Biochemistry 51, 6421–6431 (2012).

    Article  Google Scholar 

  20. Douglas, N. R. et al. Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber. Cell 144, 240–252 (2011).

    Article  Google Scholar 

  21. Jiang, Y. et al. Sensing cooperativity in ATP hydrolysis for single multisubunit enzymes in solution. Proc. Natl Acad. Sci. USA 108, 16962–16967 (2011).

    Article  Google Scholar 

  22. Behrendt, R. et al. Photomodulation of the conformation of cyclic peptides with azobenzene moieties in the peptide backbone. Angew. Chem. Int. Ed. 38, 2771–2774 (1999).

    Article  Google Scholar 

  23. Reissmann, S. et al. A gradient of ATP affinities generates an asymmetric power stroke driving the chaperonin TRIC/CCT folding cycle. Cell Rep. 2, 866–877 (2012).

    Article  Google Scholar 

  24. Ishii, D. et al. Chaperonin-mediated stabilization and ATP-triggered release of semiconductor nanoparticles. Nature 423, 628–632 (2003).

    Article  Google Scholar 

  25. Biswas, S. et al. Biomolecular robotics for chemomechanically driven guest delivery fuelled by intracellular ATP. Nature Chem. 5, 613–620 (2013).

    Article  Google Scholar 

  26. Dimaio, F., Zhang, J., Chiu, W. & Baker, D. Cryo-EM model validation using independent map reconstructions. Protein Sci. 22, 865–868 (2013).

    Article  Google Scholar 

  27. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9, 671–675 (2012).

    Article  Google Scholar 

  28. Ludtke, S. J., Nason, L., Tu, H., Peng, L. & Chiu, W. Object oriented database and electronic notebook for transmission electron microscopy. Microsc. Microanal. 9, 556–565 (2003).

    Article  Google Scholar 

  29. Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).

    Article  Google Scholar 

  30. Chen, D. H., Song, J. L., Chuang, D. T., Chiu, W. & Ludtke, S. J. An expanded conformation of single-ring GroEL–GroES complex encapsulates an 86 kDa substrate. Structure 14, 1711–1722 (2006).

    Article  Google Scholar 

  31. Scheres, S. H. W. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nature Methods 9, 853–854 (2012).

    Article  Google Scholar 

  32. 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  Google Scholar 

  33. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  Google Scholar 

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Acknowledgements

The authors thank J. Frydman and N. Douglas for discussions and advice throughout this work and for sharing the Mm-cpn plasmid, A. Woolley for discussions and a gift of ABDM, S.J. Ludtke for advice on image processing and J. Fraser for comments on the manuscript. This research was supported by grants from the Program for Breakthrough Biomedical Research and the Sandler Family Foundation (to T.K.), the National Institutes of Health (PN2EY016525 and P41GM103832 to W.C.), the National Science Foundation (NSF CBET-1134127 to T.K.) and a Deutsche Forschungsgemeinschaft postdoctoral fellowship (HO 4429/2-1 to D.H.).

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Authors and Affiliations

  1. Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biomedical Research, University of California, 1700 4th Street, Byers Hall 308E, San Francisco, 94158, California, USA

    Daniel Hoersch & Tanja Kortemme

  2. Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, 77030, Texas, USA

    Soung-Hun Roh & Wah Chiu

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  1. Daniel Hoersch
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Contributions

T.K. and D.H. designed the research. D.H. performed the computational design, biochemical experiments and model building. S-H.R. performed the cryo-electron microscopy experiments. S-H.R. and W.C. analysed the cryo-electron microscopy data. All authors wrote the manuscript.

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Correspondence to Tanja Kortemme.

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Hoersch, D., Roh, SH., Chiu, W. et al. Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nature Nanotech 8, 928–932 (2013). https://doi.org/10.1038/nnano.2013.242

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