title: Small Molecule-Induced Domain Swapping as a Mechanism for Controlling Protein Function and Assembly.
abstract: Domain swapping is the process by which identical proteins exchange reciprocal segments to generate dimers. Here we introduce induced domain swapping (INDOS) as a mechanism for regulating protein function. INDOS employs a modular design consisting of the fusion of two proteins: a recognition protein that binds a triggering molecule, and a target protein that undergoes a domain swap in response to binding of the triggering ligand. The recognition protein (FK506 binding protein) is inserted into functionally-inactivated point mutants of two target proteins (staphylococcal nuclease and ribose binding protein). Binding of FK506 to the FKBP domain causes the target domain to first unfold, then refold via domain swap. The inactivating mutations become 'swapped out' in the dimer, increasing nuclease and ribose binding activities by 100-fold and 15-fold, respectively, restoring them to near wild-type values. INDOS is intended to convert an arbitrary protein into a functional switch, and is the first example of rational design in which a small molecule is used to trigger protein domain swapping and subsequent activation of biological function.
authors.affiliation: Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY, 13210, USA.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Karchin
authors.affiliation: Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY, 13210, USA.
authors.forename: Jeung-Hoi
authors.initials: JH
authors.lastname: Ha
authors.affiliation: Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY, 13210, USA.
authors.forename: Kevin E
authors.initials: KE
authors.lastname: Namitz
authors.affiliation: Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY, 13210, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Cosgrove
authors.affiliation: Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY, 13210, USA.
authors.forename: Stewart N
authors.initials: SN
authors.lastname: Loh
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D003001:Cloning, Molecular; D003851:Deoxyribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D005822:Genetic Vectors / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D009154:Mutation; D033902:Periplasmic Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D058570:TOR Serine-Threonine Kinases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016559:Tacrolimus / Q000737:chemistry* / Q000378:metabolism; D046968:Thermoanaerobacter / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D033902:Periplasmic Binding Proteins; D011994:Recombinant Proteins; D058570:TOR Serine-Threonine Kinases; D003851:Deoxyribonucleases; D016559:Tacrolimus