A de novo protein binding pair by computational design and directed evolution

By John Karanicolas, J. Corn, Irwin Chen, L. Joachimiak, Orly Dym, Sun H. Peck, Shira Albeck, T. Unger, Wenxin Hu, Gaohua Liu and 5 more. 2011

169 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging

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Citations in the corpus

Computational design of a protein-based enzyme inhibitor. (2013, unknown): “…generated protein pairs that have been shown to interact experimentally, though the structures of the complexes either have not been solved [4] or have been found to be different from the original design conception [5], highlighting the challenges to designing specific and accurate interactions.”
AbDesign: an algorithm for combinatorial backbone design guided by natural conformations and sequences (2015, background): “b-sheets); (2) Interactions with the ligand are largely mediated by hydrophobic amino acid sidechains; and (3) The buried surface area upon binding is at or smaller than the average for naturally occurring protein–protein interactions (1600 Å(2)).”
Computational design of a symmetric homodimer using β-strand assembly (2011, background): “Some previous attempts at computational protein interface design have been plagued by problems controlling binding orientation, including a complete 180° rotation from the design model (39) or existence of multiple low-energy binding conformations (9).”
The Protein Structure Initiative: achievements and visions for the future (2012, background): “PSI Centers are also involved in collaborative projects aimed at accelerating the field of protein NMR structure analysis [22-28] and computational protein design [29-31].”
Emerging themes in the computational design of novel enzymes and protein–protein interfaces (2013, methodology): “In cases where these routes were not taken, some ﬂexibility at the sidechain level caused altered binding, either through minor sidechain rearrangements [30] or large binding mode differences [46].”
Protein Engineering by Combined Computational and In Vitro Evolution Approaches. (2016, background): “Concluding Remarks and Future Directions In this review, we have demonstrated how computational and combinatorial techniques are not mutually exclusive and how their combination can solve PPI engineering problems that would be difficult to solve by either of the approaches alone [22,23].”
Achievements and Challenges in Computational Protein Design. (2017, methodology): “In 2011 the Baker lab applied a motif-based method to computationally design protein–protein complexes with native-like interface composition and interaction density as exemplified on the Prb-Pdar heterodimer [87].”