title: A designed conformational shift to control protein binding specificity.
abstract: In a conformational selection scenario, manipulating the populations of binding-competent states should be expected to affect protein binding. We demonstrate how in silico designed point mutations within the core of ubiquitin, remote from the binding interface, change the binding specificity by shifting the conformational equilibrium of the ground-state ensemble between open and closed substates that have a similar population in the wild-type protein. Binding affinities determined by NMR titration experiments agree with the predictions, thereby showing that, indeed, a shift in the conformational equilibrium enables us to alter ubiquitin's binding specificity and hence its function. Thus, we present a novel route towards designing specific binding by a conformational shift through exploiting the fact that conformational selection depends on the concentration of binding-competent substates.
authors.affiliation: Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen (Germany) http://www.mpibpc.mpg.de/groups/de_groot/
authors.forename: Servaas
authors.initials: S
authors.lastname: Michielssens
authors.forename: Jan Henning
authors.initials: JH
authors.lastname: Peters
authors.forename: David
authors.initials: D
authors.lastname: Ban
authors.forename: Supriya
authors.initials: S
authors.lastname: Pratihar
authors.forename: Daniel
authors.initials: D
authors.lastname: Seeliger
authors.forename: Monika
authors.initials: M
authors.lastname: Sharma
authors.forename: Karin
authors.initials: K
authors.lastname: Giller
authors.forename: Thomas Michael
authors.initials: TM
authors.lastname: Sabo
authors.forename: Stefan
authors.initials: S
authors.lastname: Becker
authors.forename: Donghan
authors.initials: D
authors.lastname: Lee
authors.forename: Christian
authors.initials: C
authors.lastname: Griesinger
authors.forename: Bert L
authors.initials: BL
authors.lastname: de Groot
mesh_terms: D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D017354:Point Mutation; D011485:Protein Binding; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D025801:Ubiquitin
keywords: molecular dynamics; protein design; protein-protein interactions; ubiquitin