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Automated design of specificity in molecular recognition

Nature Structural Biology volume 10, pages 45–52 (2003)Cite this article

Abstract

Specific protein–protein interactions are crucial in signaling networks and for the assembly of multi-protein complexes, and represent a challenging goal for protein design. Optimizing interaction specificity requires both positive design, the stabilization of a desired interaction, and negative design, the destabilization of undesired interactions. Currently, no automated protein-design algorithms use explicit negative design to guide a sequence search. We describe a multi-state framework for engineering specificity that selects sequences maximizing the transfer free energy of a protein from a target conformation to a set of undesired competitor conformations. To test the multi-state framework, we engineered coiled-coil interfaces that direct the formation of either homodimers or heterodimers. The algorithm identified three specificity motifs that have not been observed in naturally occurring coiled coils. In all cases, experimental results confirm the predicted specificities.

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Figure 1: A GCN4-derived scaffold for coiled-coil design.
Figure 2: Positive and negative design states.
Figure 3: Results of design calculations.
Figure 4: Predicted specificity motifs.
Figure 5: Specificity of designed coiled coils.
Figure 6: Stability of designed coiled coils.

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Acknowledgements

We thank F.E. Boas, J.A. Silverman, D.R. Halpin, S.J. Wrenn and R.L. Baldwin for stimulating conversations and criticism during the course of this work and for comments on the manuscript. We also acknowledge helpful suggestions from the anonymous referees. This research was funded by a Searle scholar grant to P.B.H. from the Chicago Community Trust.

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  1. Biophysics Program, Stanford University, Stanford, 94305, California, USA

    James J. Havranek

  2. Department of Biochemistry, Stanford University, Stanford, 94305, California, USA

    Pehr B. Harbury

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  1. James J. Havranek
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  2. Pehr B. Harbury
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Correspondence to Pehr B. Harbury.

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Havranek, J., Harbury, P. Automated design of specificity in molecular recognition. Nat Struct Mol Biol 10, 45–52 (2003). https://doi.org/10.1038/nsb877

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