Dagliyan, O., Shirvanyants, D., Karginov, A.V., Ding, F., Fee, L., Chandrasekaran, S.N., Freisinger, C.M., Smolen, G.A., Huttenlocher, A., Hahn, K.M., and Dokholyan, N.V. (2013) Rational design of a ligand-controlled protein conformational switch. Proceedings of the National Academy of Sciences of the United States of America. 110(17):6800-4.
Design of a regulatable multistate protein is a challenge for protein engineering. Here we design a protein with a unique
topology, called uniRapR, whose conformation is controlled by the binding of a small molecule. We confirm switching and control
ability of uniRapR in silico, in vitro, and in vivo. As a proof of concept, uniRapR is used as an artificial regulatory domain to control activity of
kinases. By activating Src kinase using uniRapR in single cells and whole organism, we observe two unique phenotypes consistent
with its role in metastasis. Activation of Src kinase leads to rapid induction of protrusion with polarized spreading in HeLa
cells, and morphological changes with loss of cell–cell contacts in the epidermal tissue of zebrafish. The rational creation
of uniRapR exemplifies the strength of computational protein design, and offers a powerful means for targeted activation of
many pathways to study signaling in living organisms.
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