3Q9U

In silico and in vitro co-evolution of a high affinity complementary protein-protein interface

Summary for 3Q9U

• Entry DOI: 10.2210/pdb3q9u/pdb
• Related: 3Q9N 3QA9 3q98
• Descriptor: CoA binding protein, consensus ankyrin repeat, COENZYME A (3 entities in total)
• Functional Keywords: structural genomics, israel structural proteomics center, ispc, prb-binding designed ankyrin repeat, protein binding, de novo protein
• Biological source: Escherichia coli; More
• Total number of polymer chains: 4
• Total formula weight: 66707.21

Authors

Karanicolas, J.,Corn, J.E.,Chen, I.,Joachimiak, L.A.,Dym, O.,Chung, S.,Albeck, S.,Unger, T.,Hu, W.,Liu, G.,Delbecq, S.,Montelione, G.T.,Spiegel, C.,Liu, D.,Baker, D.,Israel Structural Proteomics Center (ISPC) (deposition date: 2011-01-10, release date: 2011-04-20, Last modification date: 2023-09-13)

Primary citation

Karanicolas, J.,Corn, J.E.,Chen, I.,Joachimiak, L.A.,Dym, O.,Peck, S.H.,Albeck, S.,Unger, T.,Hu, W.,Liu, G.,Delbecq, S.,Montelione, G.T.,Spiegel, C.P.,Liu, D.R.,Baker, D.
A de novo protein binding pair by computational design and directed evolution.
Mol.Cell, 42:250-260, 2011

PubMed 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 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.

PubMed: 21458342
DOI: 10.1016/j.molcel.2011.03.010

Experimental method

X-RAY DIFFRACTION (2.3 Å)