title: Distinguishing induced fit from conformational selection.
abstract: The interactions between proteins and ligands often involve a conformational change in the protein. This conformational change can occur before (conformational selection) or after (induced fit) the association with ligand. It is often very difficult to distinguish induced fit from conformational selection when hyperbolic binding kinetics are observed. In light of a recent paper in this journal (Vogt et al., Biophys. Chem., 186, 2014, 13-21) and the current interest in binding mechanisms emerging from observed sampling of distinct conformations in protein domains, as well as from the field of intrinsically disordered proteins, we here describe a kinetic method that, at least in some cases, unequivocally distinguishes induced fit from conformational selection. The method relies on measuring the observed rate constant λ for binding and varying both the protein and the ligand in separate experiments. Whereas induced fit always yields a hyperbolic dependence of increasing λ values, the conformational selection mechanism gives rise to distinct kinetics when the ligand and protein (displaying the conformational change) concentration is varied in separate experiments. We provide examples from the literature and discuss the limitations of the approach.
authors.affiliation: Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom. Electronic address: Stefano.Gianni@uniroma1.it.
authors.forename: Stefano
authors.initials: S
authors.lastname: Gianni
authors.affiliation: Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
authors.forename: Jakob
authors.initials: J
authors.lastname: Dogan
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden. Electronic address: Per.Jemth@imbim.uu.se.
authors.forename: Per
authors.initials: P
authors.lastname: Jemth
mesh_terms: D000495:Allosteric Site / Q000187:drug effects; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation / Q000187:drug effects; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D008024:Ligands; D011506:Proteins
keywords: Conformational selection; Induced fit; Kinetics; Protein–protein interactions