8DAB

Coevolved affibody-Z domain pair LL2.c17

Summary for 8DAB

• Entry DOI: 10.2210/pdb8dab/pdb
• Related: 8DA3 8DA4 8DA5 8DA6 8DA7 8DA8 8DA9 8DAC
• Descriptor: Immunoglobulin G-binding protein A, Affibody LL2.IVVY (3 entities in total)
• Functional Keywords: affibody, protein binding
• Biological source: Staphylococcus aureus; More
• Total number of polymer chains: 2
• Total formula weight: 15528.31

Authors

Jude, K.M.,Yang, A.,Garcia, K.C. (deposition date: 2022-06-13, release date: 2023-07-26, Last modification date: 2023-11-22)

Primary citation

Yang, A.,Jude, K.M.,Lai, B.,Minot, M.,Kocyla, A.M.,Glassman, C.R.,Nishimiya, D.,Kim, Y.S.,Reddy, S.T.,Khan, A.A.,Garcia, K.C.
Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.
Science, 381:eadh1720-eadh1720, 2023

PubMed Abstract: Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

PubMed: 37499032
DOI: 10.1126/science.adh1720

Experimental method

X-RAY DIFFRACTION (1.134 Å)