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Computational redesign of protein-protein interaction specificity

Nature Structural & Molecular Biology volume 11, pages 371–379 (2004)Cite this article

Abstract

We developed a 'computational second-site suppressor' strategy to redesign specificity at a protein-protein interface and applied it to create new specifically interacting DNase-inhibitor protein pairs. We demonstrate that the designed switch in specificity holds in in vitro binding and functional assays. We also show that the designed interfaces are specific in the natural functional context in living cells, and present the first high-resolution X-ray crystallographic analysis of a computer-redesigned functional protein-protein interface with altered specificity. The approach should be applicable to the design of interacting protein pairs with novel specificities for delineating and re-engineering protein interaction networks in living cells.

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Figure 1: The DNase-immunity protein model system.
Figure 2: In vitro DNase activity assay.
Figure 3: SPR sensograms.
Figure 4: Intrinsic fluorescence.
Figure 5: In vivo cell death assay.
Figure 6: The crystal structure of the E7_C/Im7_C complex.

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Acknowledgements

We thank the members of the Baker lab for stimulating discussions, and J. Havranek for critical reading of the manuscript. This work was supported by a long-term fellowship from the Human Frontier Science Program (T.K.), a Wellcome Trust International Prize fellowship (A.N.B.), a US National Institutes of Health (NIH) training grant (L.A.J.) and a grant from the NIH (D.B.).

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Author notes

  1. Alex N Bullock

    Present address: The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK

  2. Tanja Kortemme, Lukasz A Joachimiak and Alex N Bullock: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute & Department of Biochemistry, Box 357350, University of Washington, Seattle, 98195-7350, Washington, USA

    Tanja Kortemme, Lukasz A Joachimiak, Alex N Bullock & David Baker

  2. Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A3-023, Seattle, 98109, Washington, USA

    Lukasz A Joachimiak, Aaron D Schuler & Barry L Stoddard

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  1. Tanja Kortemme
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Correspondence to David Baker.

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Kortemme, T., Joachimiak, L., Bullock, A. et al. Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 11, 371–379 (2004). https://doi.org/10.1038/nsmb749

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