Control over protein activity demands control over the protein backbone structure, but the backbone has numerous degrees of freedom and design of new backbones in protein active sites has been a notoriously difficult problem. By combining information from naturally occurring structures and sequences with atomistic design calculations, we developed a new approach for backbone design in active sites. Initially, we implemented this strategy to design new antibodies, and therefore called the method AbDesign. Encouraged by the method's success in designing atomically accurate new antibodies with over 50 mutations from any naturally occurring antibody, we next applied this method for the design of high-efficiency new enzymes and a large network of interacting pairs of proteins that exhibited ultrahigh specificity binding. Thus, evolution-guided atomistic design provides exquisite control over protein structure, stability, and activity.
Recently, we extended de novo design to generate novel receptor-like transmembrane domains (Elazar eLife 2022). These designs have been integrated in CAR-T constructs and shown to have significant advantages in tuning target-cell killing while minimising undesired cytokine release.
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- Lapidoth, G.; Khersonsky, O.; Lipsh, R.; Dym, O.; Albeck, S.; Rogotner, S.; Fleishman, S. J. Highly Active Enzymes by Automated Combinatorial Backbone Assembly and Sequence Design. Nat. Commun. 2018, 9 (1), 2780.
- Netzer, R.; Listov, D.; Lipsh, R.; Dym, O.; Albeck, S.; Knop, O.; Kleanthous, C.; Fleishman, S. J. Ultrahigh Specificity in a Network of Computationally Designed Protein-Interaction Pairs. Nat. Commun. 2018, 9 (1), 5286.
- Elazar, A.; Chandler, N. J.; Davey, A. S.; Weinstein, J. Y.; Nguyen, J. V.; Trenker, R.; Cross, R. S.; Jenkins, M. R.; Call, M. J.; Call, M. E.; Fleishman, S. J. De Novo-Designed Transmembrane Domains Tune Engineered Receptor Functions. Elife 2022, 11. https://doi.org/10.7554/eLife.75660.