title: Sliding and target location of DNA-binding proteins: an NMR view of the lac repressor system.
abstract: In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10(-12) cm(2)/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process.
authors.affiliation: Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Karine
authors.initials: K
authors.lastname: Loth
authors.forename: Manuel
authors.initials: M
authors.lastname: Gnida
authors.forename: Julija
authors.initials: J
authors.lastname: Romanuka
authors.forename: Robert
authors.initials: R
authors.lastname: Kaptein
authors.forename: Rolf
authors.initials: R
authors.lastname: Boelens
mesh_terms: D001665:Binding Sites / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D007763:Lac Operon / Q000235:genetics; D056968:Lac Repressors / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D025941:Protein Interaction Mapping; D013379:Substrate Specificity
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D056968:Lac Repressors; D046911:Macromolecular Substances