title: Structural properties of polyubiquitin chains in solution.
abstract: Because polyubiquitin chain structure modulates Ub-mediated signaling, knowledge of the physiological conformations of chain signals should provide insights into specific recognition. Here, we characterized the solution conformations of K48-linked Ub(2) and Ub(4) using a combination of NMR techniques, including chemical shift mapping of the interdomain interface, domain orientation measurements on the basis of 15N relaxation and residual dipolar couplings, and the solvent accessibility studies. Our data indicate a switch in the conformation of Ub(2), from open to closed, with increasing pH. The closed conformation features a well-defined interface that is related to, but distinguishable from, that observed in the Ub(2) crystal structure. This interface is dynamic in solution, such that important hydrophobic residues (L8, I44, V70) that are sequestered at the interface in the closed conformation may be accessible for direct interactions with recognition factors. Our results suggest that the distal two units of Ub(4), which is the minimum signal for efficient proteasomal degradation, may adopt the closed Ub(2) conformation.
authors.affiliation: Department of Chemistry and Biochemistry, Center of Biomolecular Structure and Organization, University of Maryland, 115 Agriculture/Life Science Surge Building, College Park, MD 20742-3360, USA.
authors.forename: Ranjani
authors.initials: R
authors.lastname: Varadan
authors.forename: Olivier
authors.initials: O
authors.lastname: Walker
authors.forename: Cecile
authors.initials: C
authors.lastname: Pickart
authors.forename: David
authors.initials: D
authors.lastname: Fushman
mesh_terms: D000577:Amides / Q000737:chemistry; D000641:Ammonia / Q000378:metabolism; D001704:Biopolymers / Q000737:chemistry; D004058:Diffusion; D004926:Escherichia coli / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D025821:Polyubiquitin / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012399:Rotation; D012996:Solutions; D013329:Structure-Activity Relationship; D014452:Ubiquitins / Q000737:chemistry
chemical_list: D000577:Amides; D001704:Biopolymers; D009587:Nitrogen Isotopes; D012996:Solutions; D014452:Ubiquitins; D025821:Polyubiquitin; D000641:Ammonia