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Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

Nature Biotechnology volume 30, pages 190–192 (2012)Cite this article

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Abstract

Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes1,2,3,4. Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure. Players of the online game Foldit5,6 were challenged to remodel the backbone of a computationally designed bimolecular Diels-Alderase3 to enable additional interactions with substrates. Several iterations of design and characterization generated a 24-residue helix-turn-helix motif, including a 13-residue insertion, that increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems.

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Figure 1: Crystal structure of Foldit design is similar to player model.
Figure 2: Activity of designed enzymes DA_20_10, CE0, CE4 and CE6.

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Acknowledgements

We would like to acknowledge the members of the Foldit team for their help designing and developing the game and all the Foldit players who volunteered to make this work possible. We would also like to thank J. Thompson for useful scripts, as well as B. Siegel and M. Eiben for helpful comments on the manuscript. This work was supported by the Center for Game Science at the University of Washington, US Defense Advanced Research Projects Agency (DARPA) grant N00173-08-1-G025, the DARPA PDP program, the Howard Hughes Medical Institute (D.B.), a National Science Foundation graduate research fellowship to J.B.B. (grant no. DGE-0718124), and a National Science Foundation grant for F.K. (grant no. 0906026).

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Author notes

  1. Christopher B Eiben and Justin B Siegel: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry, University of Washington, Seattle, Washington, USA

    Christopher B Eiben, Justin B Siegel, Jacob B Bale, Firas Khatib, Foldit Players & David Baker

  2. Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA

    Jacob B Bale

  3. Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA

    Seth Cooper & Zoran Popovic

  4. Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

    Betty W Shen & Barry L Stoddard

  5. Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA

    David Baker

Authors
  1. Christopher B Eiben
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  2. Justin B Siegel
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  6. Betty W Shen
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  7. Foldit Players
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  8. Barry L Stoddard
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  10. David Baker
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Contributions

C.B.E. analyzed community models, in addition to designing, building and testing the enzyme libraries. J.B.S. designed the experimental and computational methods, and built the initial computational models. F.K. set up the Foldit puzzles and curated the player results for analysis by C.B.E. S.C. led design and development of Foldit. B.L.S., J.B.B. and B.W.S. grew the crystals and collected X-ray diffraction data, processed X-ray data and analyzed the structure. Foldit Players designed new protein backbones and sequences. Z.P. and D.B. contributed to the writing of the manuscript.

Corresponding author

Correspondence to David Baker.

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The authors declare no competing financial interests.

Supplementary information

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Supplementary Table 1, Supplementary Libraries 1–3, Supplementary Data, Supplementary Methods and Supplementary Figures 1–9 (PDF 4381 kb)

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Eiben, C., Siegel, J., Bale, J. et al. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat Biotechnol 30, 190–192 (2012). https://doi.org/10.1038/nbt.2109

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