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De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy

Abstract

Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here we report the design of a novel protein, PS1, that binds a highly electron-deficient non-natural porphyrin at temperatures up to 100 °C. The high-resolution structure of holo-PS1 is in sub-Å agreement with the design. The structure of apo-PS1 retains the remote core packing of the holoprotein, with a flexible binding region that is predisposed to ligand binding with the desired geometry. Our results illustrate the unification of core packing and binding-site definition as a central principle of ligand-binding protein design.

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Figure 1: The design strategy.
Figure 2: The computational design workflow for optimized core packing.
Figure 3: Biophysical characterization of apo- and holo-PS1.
Figure 4: The structure of holo-PS1 agrees closely with the design.
Figure 5: Apo- and holo-PS1 share similar folded cores and differ in the binding region.

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Acknowledgements

N.F.P., J.R. and M.J.T. acknowledge research support from the National Science Foundation (NSF) through Grant CHE-1413333. D.N.B. acknowledges the National Institutes of Health (NIH) (GM-071628 and GM-048043) for support of this work. W.F.D. acknowledges support from the NSF (CHE-1413295), the NIH (GM-054616 and GM-071628) and the Materials Research Science and Engineering Centers program of the NSF (DMR-1120901). Simulations were carried out in part with XSEDE resources through grant MCB080011.

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N.F.P. and W.F.D. designed the protein. N.F.P., Y.W., A.M.M., S.-Q.Z. and J.R. performed the experiments. T.L. performed the molecular dynamics simulations. N.F.P., Y.W., W.F.D. and S.-Q.Z. performed the data analysis. N.F.P., W.F.D., D.N.B. and M.J.T. wrote the paper.

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Correspondence to David N. Beratan, Michael J. Therien or William F. DeGrado.

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The authors declare no competing financial interests.

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Polizzi, N., Wu, Y., Lemmin, T. et al. De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy. Nature Chem 9, 1157–1164 (2017). https://doi.org/10.1038/nchem.2846

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