title: Rational design of a ligand-controlled protein conformational switch.
abstract: 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.
authors.affiliation: Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Onur
authors.initials: O
authors.lastname: Dagliyan
authors.forename: David
authors.initials: D
authors.lastname: Shirvanyants
authors.forename: Andrei V
authors.initials: AV
authors.lastname: Karginov
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.forename: Lanette
authors.initials: L
authors.lastname: Fee
authors.forename: Srinivas N
authors.initials: SN
authors.lastname: Chandrasekaran
authors.forename: Christina M
authors.initials: CM
authors.lastname: Freisinger
authors.forename: Gromoslaw A
authors.initials: GA
authors.lastname: Smolen
authors.forename: Anna
authors.initials: A
authors.lastname: Huttenlocher
authors.forename: Klaus M
authors.initials: KM
authors.lastname: Hahn
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D004789:Enzyme Activation / Q000502:physiology*; D058750:Epithelial-Mesenchymal Transition / Q000502:physiology*; D006367:HeLa Cells; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D015027:Zebrafish; D019061:src-Family Kinases / Q000378:metabolism
chemical_list: D008024:Ligands; D011506:Proteins; D019061:src-Family Kinases