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A de novo protein binding pair by computational design and directed evolution
Karanicolas, John Corn, Jacob E. Chen, Irwin Joachimiak, Lukasz A. Dym, Orly Peck, Sun H. Albeck, Shira Unger, Tamar Hu, Wenxin Liu, Gaohua
Karanicolas, John
Corn, Jacob E.
Chen, Irwin
Joachimiak, Lukasz A.
Dym, Orly
Peck, Sun H.
Albeck, Shira
Unger, Tamar
Hu, Wenxin
Liu, Gaohua
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Abstract
The de novo design of protein-protein interfaces is a stringent test of our understanding of the principles underlying protein-protein interactions and would enable new approaches to biological and medical challenges. Here we describe a novel motif-based method to computationally design protein-protein complexes with native-like interface composition and interaction density. Using this method we designed a pair of proteins, Prb and Pdar, that heterodimerize with a Kd of 130 nM, 1,000-fold tighter than any previously designed de novo protein-protein complex. Directed evolution identified two point mutations that improve affinity to 180 pM. Crystal structures of complexes containing designed and evolved proteins reveal binding is entirely through the designed interface, making use of specific designed interactions. Surprisingly, in the evolved complex one of the partners is rotated 180 degrees relative to the design model. This work demonstrates that current understanding of protein-protein interfaces is sufficient to rationally design interfaces de novo, and underscores remaining challenges.
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Date
2011-04-22
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Publisher
Elsevier
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Keywords
Computational design, Directed evolution, Protein-protein interface, Protein interaction, Hotspot, Ankyrin Repeat, Protein docking
Citation
Karanicolas, J., Corn, J. E., Chen, I., Joachimiak, L. A., Dym, O., Peck, S. H., … Baker, D. (2011). A de novo protein binding pair by computational design and directed evolution. Molecular Cell, 42(2), 250–260. http://doi.org/10.1016/j.molcel.2011.03.010