|Molecular Cell (2011) 42:250-60|
|Northeast Structural Genomics Consortium|
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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 unique approaches to biological and medical challenges. ...
Here we describe a 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, 1000-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 an affinity-matured complex reveal binding is entirely through the designed interface residues. Surprisingly, in the in vitro evolved complex one of the partners is rotated 180° relative to the original design model, yet still maintains the central computationally designed hotspot interaction and preserves the character of many peripheral interactions. This work demonstrates that high-affinity protein interfaces can be created by designing complementary interaction surfaces on two noninteracting partners and underscores remaining challenges.
|metabolism chemistry genetics |
|Binding Sites Models, Molecular Protein Binding Proteins Protein Conformation Mutation Molecular Weight Surface Properties Protein Interaction Mapping Chemistry Techniques, Analytical Computer-Aided Design Protein Multimerization Protein Interaction Domains and Motifs |
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