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Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays

Abstract

Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed self-assembly of proteins has largely been inaccessible because of the chemical and structural heterogeneity of protein surfaces. To circumvent the challenge of programming extensive non-covalent interactions to control protein self-assembly, we have previously exploited the directionality and strength of metal coordination interactions to guide the formation of closed, homoligomeric protein assemblies. Here, we extend this strategy to the generation of periodic protein arrays. We show that a monomeric protein with properly oriented coordination motifs on its surface can arrange, on metal binding, into one-dimensional nanotubes and two- or three-dimensional crystalline arrays with dimensions that collectively span nearly the entire nano- and micrometre scale. The assembly of these arrays is tuned predictably by external stimuli, such as metal concentration and pH.

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Figure 1: Design and initial crystallographic characterization of RIDC3.
Figure 2: Zn-induced RIDC3 self-assembly in solution characterized by light and electron microscopy.
Figure 3: Model for RIDC3 self-assembly.
Figure 4: Structural basis of Zn-mediated RIDC3 assembly.
Figure 5: RIDC3 nanotube structure and assembly.
Figure 6: Rhodamine-directed stacking of 2D RIDC3 arrays.

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References

  1. Mann, S. Life as a nanoscale phenomenon. Angew. Chem. Int. Ed. 47, 5306–5320 (2008).

    Article  CAS  Google Scholar 

  2. Nguyen, S. T., Gin, D. L., Hupp, J. T. & Zhang, X. Supramolecular chemistry: functional structures on the mesoscale. Proc. Natl Acad. Sci. USA 98, 11849–11850 (2001).

    Article  CAS  Google Scholar 

  3. Seeman, N. C. & Belcher, A. M. Emulating biology: building nanostructures from the bottom up. Proc. Natl Acad. Sci. USA 99, 6451–6455 (2002).

    Article  CAS  Google Scholar 

  4. Shenton, W., Pum, D., Sleytr, U. B. & Mann, S. Synthesis of cadmium sulphide superlattices using self-assembled bacterial S-layers. Nature 389, 585–587 (1997).

    Article  CAS  Google Scholar 

  5. McMillan, R. A. et al. Ordered nanoparticle arrays formed on engineered chaperonin protein templates. Nature Mater. 1, 247–252 (2002).

    Article  CAS  Google Scholar 

  6. Lee, Y. J. et al. Fabricating genetically engineered high-power lithium-ion batteries using multiple virus genes. Science 324, 1051–1055 (2009).

    CAS  PubMed  Google Scholar 

  7. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article  CAS  Google Scholar 

  8. Zheng, J. P. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009).

    Article  CAS  Google Scholar 

  9. Delebecque, C. J., Lindner, A. B., Silver, P. A. & Aldaye, F. A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470–474 (2011).

    Article  CAS  Google Scholar 

  10. Chworos, A. et al. Building programmable jigsaw puzzles with RNA. Science 306, 2068–2072 2004.

    Article  CAS  Google Scholar 

  11. Aggeli, A. et al. Responsive gels formed by the spontaneous self-assembly of peptides into polymeric beta-sheet tapes. Nature 386, 259–262 (1997).

    Article  CAS  Google Scholar 

  12. Banwell, E. F. et al. Rational design and application of responsive [alpha]-helical peptide hydrogels. Nature Mater. 8, 596–600 (2009).

    Article  CAS  Google Scholar 

  13. Kortemme, T. & Baker, D. Computational design of protein–protein interactions. Curr. Opin. Chem. Biol. 8, 91–97 (2004).

    Article  CAS  Google Scholar 

  14. Dotan, N., Arad, D., Frolow, F. & Freeman, A. Self-assembly of a tetrahedral lectin into predesigned diamond-like protein crystals. Angew. Chem. Int. Ed. 38, 2363–2366 (1999).

    Article  CAS  Google Scholar 

  15. Ringler, P. & Schulz, G. E. Self-assembly of proteins into designed networks. Science 302, 106–109 (2003).

    Article  CAS  Google Scholar 

  16. Ballister, E. R., Lai, A. H., Zuckermann, R. N., Cheng, Y. & Mougous, J. D. In vitro self-assembly from a simple protein of tailorable nanotubes building block. Proc. Natl Acad. Sci. USA 105, 3733–3738 (2008).

    Article  CAS  Google Scholar 

  17. Padilla, J. E., Colovos, C. & Yeates, T. O. Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc. Natl Acad. Sci. USA 98, 2217–2221 (2001).

    Article  CAS  Google Scholar 

  18. Sinclair, J. C., Davies, K. M., Venien-Bryan, C. & Noble, M. E. M. Generation of protein lattices by fusing proteins with matching rotational symmetry. Nature Nanotech. 6, 558–562 (2011).

    Article  CAS  Google Scholar 

  19. Caulder, D. L. & Raymond, K. N. Supermolecules by design. Acc. Chem. Res. 32, 975–982 (1999).

    Article  CAS  Google Scholar 

  20. Leininger, S., Olenyuk, B. & Stang, P. J. Self-assembly of discrete cyclic nanostructures mediated by transition metals. Chem. Rev. 100, 853–907 (2000).

    Article  CAS  Google Scholar 

  21. Holliday, B. J. & Mirkin, C. A. Strategies for the construction of supramolecular compounds through coordination chemistry. Angew. Chem. Int. Ed. 40, 2022–2043 (2001).

    Article  CAS  Google Scholar 

  22. Salgado, E. N., Radford, R. J. & Tezcan, F. A. Metal-directed protein self-assembly. Acc. Chem. Res. 43, 661–672 (2010).

    Article  CAS  Google Scholar 

  23. Radford, R. J., Brodin, J. D., Salgado, E. N. & Tezcan, F. A. Expanding the utility of proteins as platforms for coordination chemistry. Coord. Chem. Rev. 255, 790–803 (2011).

    Article  CAS  Google Scholar 

  24. Salgado, E. N., Faraone-Mennella, J. & Tezcan, F. A. Controlling protein–protein interactions through metal coordination: assembly of a 16-helix bundle protein. J. Am. Chem. Soc. 129, 13374–13375 (2007).

    Article  CAS  Google Scholar 

  25. Salgado, E. N., Lewis, R. A., Mossin, S., Rheingold, A. L. & Tezcan, F. A. Control of protein oligomerization symmetry by metal coordination: C2 and C3 symmetrical assemblies through CuII and NiII coordination. Inorg. Chem. 48, 2726–2728 (2009).

    Article  CAS  Google Scholar 

  26. Liu, Y. & Kuhlman, B. RosettaDesign server for protein design. Nucl. Acids Res. 34, W235–238 (2006).

    Article  CAS  Google Scholar 

  27. Jones, S. & Thornton, J. M. Principles of protein–protein interactions. Proc. Natl Acad. Sci. USA 93, 13–20 (1996).

    Article  CAS  Google Scholar 

  28. Polyakov, A., Severinova, E. & Darst, S. A. Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83, 365–373 (1995).

    Article  CAS  Google Scholar 

  29. Scheller, K. H. et al. Metal ion/buffer interactions. Eur. J. Biochem. 107, 455–466 (1980).

    Article  CAS  Google Scholar 

  30. Parent, K. N. et al. Cryo-reconstructions of P22 polyheads suggest that phage assembly is nucleated by trimeric interactions among coat proteins. Phys. Biol. 7, 045004 (2010).

    Article  Google Scholar 

  31. Hamman, B. D. et al. Tetramethylrhodamine dimer formation as a spectroscopic probe of the conformation of Escherichia coli ribosomal protein L7/L12 dimers. J. Biol. Chem. 271, 7568–7573 (1996).

    Article  CAS  Google Scholar 

  32. Chambers, R. W., Kajiwara, T. & Kearns, D. R. Effect of dimer formation of electronic absorption and emission-spectra of ionic dyes – rhodamines and other common dyes. J. Phys. Chem. 78, 380–387 (1974).

    Article  CAS  Google Scholar 

  33. Li, H. L., DeRosier, D. J., Nicholson, W. V., Nogales, E. & Downing, K. H. Microtubule structure at 8 Ångstrom resolution. Structure 10, 1317–1328 (2002).

    Article  CAS  Google Scholar 

  34. Glucksman, M. J., Bhattacharjee, S. & Makowski, L. Three-dimensional structure of a cloning vector: X-ray diffraction studies of filamentous bacteriophage M13 at 7 Å resolution. J. Mol. Biol. 226, 455–470 (1992).

    Article  CAS  Google Scholar 

  35. Sara, M. & Sleytr, U. B. S-layer proteins. J. Bacteriol. 182, 859–868 (2000).

    Article  CAS  Google Scholar 

  36. Ge, P. & Zhou, Z. H. Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches. Proc. Natl Acad. Sci. USA 108, 9637–9642 (2011).

    Article  CAS  Google Scholar 

  37. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Cryst. D 67, 235–242 (2011).

    Article  CAS  Google Scholar 

  38. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  Google Scholar 

  39. Murshudov, G., Vagin, A. & Dodson, E. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D 53, 240–255 (1996).

    Article  Google Scholar 

  40. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Cryst. D 60, 2126–2132 (2004).

    Article  Google Scholar 

  41. DeLano, W. L. The PYMOL molecular graphics system (DeLano Scientific, San Carlos, California (http://www.pymol.org), 2003).

  42. Stahlberg, H., Gipson, B., Zeng, X. & Zhang, Z. Y. 2dx – User-friendly image processing for 2D crystals. J. Struct. Biol. 157, 64–72 (2007).

    Article  Google Scholar 

  43. 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 

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Acknowledgements

This work was primarily supported by the US Department of Energy (DOE) (Division of Materials Sciences, Office of Basic Energy Sciences, Award DE-FG02-10ER46677 to F.A.T.). Additional support was provided by the Agouron Foundation, Beckman Foundation, Sloan Foundation, National Science Foundation (CHE-0908115 to F.A.T., protein design), National Institutes of Health (EM characterization, R37GM-033050 and 1S10 RR.020016 to T.S.B. and F32 AI078624 to K.N.P.) and the University of California, San Diego. Portions of this research were carried out at Stanford Synchrotron Radiation Lightsource, operated by Stanford University on behalf of the DOE.

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Contributions

J.D.B. designed and performed most of the experiments and data analysis, and co-wrote the paper. X.I.A. performed computational interface design calculations. C.T. and K.N.P. provided guidance and assistance with EM data collection and analysis. T.S.B. guided EM data analysis and co-wrote the paper. F.A.T. initiated and directed the project, analysed data and co-wrote the paper.

Corresponding author

Correspondence to F. Akif Tezcan.

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The authors declare no competing financial interests.

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Brodin, J., Ambroggio, X., Tang, C. et al. Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nature Chem 4, 375–382 (2012). https://doi.org/10.1038/nchem.1290

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