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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
Following evolutionary paths to protein-protein interactions with high affinity and selectivity
Kalia Bernath Levin1, Orly Dym, Shira Albeck
1Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
Nature Structural & Molecular Biology
|September 15, 2009
Summary
Researchers evolved a colicin-immunity protein interaction, increasing its affinity and selectivity for a new target. This study reveals how protein interfaces evolve by uncovering latent interactions and utilizing generalist intermediates.
Area of Science:
- Molecular Biology
- Protein Evolution
- Biochemistry
Background:
- Protein-protein interactions are crucial for biological functions.
- Understanding the evolution of these interactions, particularly multi-residue features like binding interfaces, is key to deciphering protein adaptation.
- Colicin-immunity proteins provide a model system to study interface evolution due to their specific binding functions.
Purpose of the Study:
- To investigate the evolutionary mechanisms of protein-protein interfaces.
- To engineer a colicin-immunity binding interaction for enhanced affinity and selectivity towards a new target.
- To elucidate the role of intermediate binding configurations in driving functional divergence.
Main Methods:
- Directed evolution involving iterative rounds of random mutagenesis and selection.
- Engineering of the Im9 colicin-immunity protein towards improved binding of ColE7 while maintaining selectivity against ColE9.
- Affinity and selectivity measurements using dissociation constant (Kd) and inhibition assays.
Main Results:
- Achieved an approximately 10(5)-fold increase in binding affinity for the new target (ColE7).
- Engineered an approximately 10(8)-fold increase in selectivity, reducing inhibition of the original target (ColE9).
- Identified intermediate variants that revealed latent interactions and alternative binding configurations, facilitating rapid functional divergence.
Conclusions:
- Protein-protein interfaces exhibit evolvability similar to enzymes, utilizing promiscuous interactions and generalist intermediates.
- Compensatory stabilizing mutations play a critical role in facilitating the divergence of new functions in protein interfaces.
- The study provides insights into the stepwise evolution of complex molecular recognition systems.
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