Following evolutionary paths to protein-protein interactions with high affinity and selectivity

Kalia Bernath Levin, Orly Dym*, Shira Albeck, Shlomo Magdassi, Anthony H. Keeble, Colin Kleanthous, Dan S. Tawfik

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

68 Scopus citations

Abstract

How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10 14 M affinity, and evolved it toward ColE7, which it inhibits promiscuously (K d 10 8 M). Iterative rounds of random mutagenesis and selection toward higher affinity for ColE7, and selectivity (against ColE9 inhibition), led to an 10 5-fold increase in affinity and a 10 8-fold increase in selectivity. Analysis of intermediates along the evolved variants revealed that changes in the binding configuration of the Im protein uncovered a latent set of interactions, thus providing the key to the rapid divergence of new Im7 variants. Overall, protein-protein interfaces seem to share the evolvability features of enzymes, that is, the exploitation of promiscuous interactions and alternative binding configurations via 'generalist' intermediates, and the key role of compensatory stabilizing mutations in facilitating the divergence of new functions.

Original languageAmerican English
Pages (from-to)1049-1055
Number of pages7
JournalNature Structural and Molecular Biology
Volume16
Issue number10
DOIs
StatePublished - Oct 2009

Bibliographical note

Funding Information:
We gratefully acknowledge financial support by the Israel Ministry of Science and Technology, the EU training network ProSA and the Sasson and Marjorie Peress Philanthropic Fund. We are grateful to G. Schreiber, O. Cohavi and M. Harel for their help in affinity measurements. C.K. acknowledges the UK Biotechnology and Biological Sciences Research Council for funding.

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