Article

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

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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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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.

Author information

Affiliations

  1. Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA

    • Nicholas F. Polizzi
    •  & David N. Beratan
  2. Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA

    • Nicholas F. Polizzi
    • , Yibing Wu
    • , Thomas Lemmin
    • , Alison M. Maxwell
    • , Shao-Qing Zhang
    • , David N. Beratan
    •  & William F. DeGrado
  3. Department of Chemistry, Duke University, Durham, North Carolina 27708, USA

    • Jeff Rawson
    •  & Michael J. Therien
  4. Department of Physics, Duke University, Durham, North Carolina 27708, USA

    • David N. Beratan

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Contributions

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.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

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

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