ArticleJournal of molecular biology2010
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.
Article in Journal of molecular biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Regulating IL-2 Immune Signaling Function Via A Core Allosteric Structural Network.Journal of molecular biology · 2025Article
- Transient exposure of a buried phosphorylation site in an autoinhibited protein.Biophysical journal · 2022Article
- Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs.Frontiers in molecular biosciences · 2021Article
- Differential proteomics study of postharvest Volvariella volvacea during storage at 4 °C.Scientific reports · 2020Article
- Recognition of Poly-Ubiquitins by the Proteasome through Protein Refolding Guided by Electrostatic and Hydrophobic Interactions.The journal of physical chemistry. B · 2016Article
- Dimeric interactions and complex formation using direct coevolutionary couplings.Scientific reports · 2015Article
- Development of inhibitors in the ubiquitination cascade.FEBS letters · 2014Review
- Bacterial expression and purification of the amyloidogenic peptide PAPf39 for multidimensional NMR spectroscopy.Protein expression and purification · 2013Article
- Expanding the proteome: disordered and alternatively folded proteins.Quarterly reviews of biophysics · 2011Article
- In silico elucidation of the recognition dynamics of ubiquitin.PLoS computational biology · 2011Article
- The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch.Protein science : a publication of the Protein Society · 2011Article
- WD40 repeat propellers define a ubiquitin-binding domain that regulates turnover of F box proteins.Molecular cell · 2010Article
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Authors and funding
5 authors.
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Abstract
Ubiquitin-interacting motifs (UIMs) are an important class of protein domains that interact with ubiquitin or ubiquitin-like proteins. These approximately 20-residue-long domains are found in a variety of ubiquitin receptor proteins and serve as recognition modules towards intracellular targets, which may be individual ubiquitin subunits or polyubiquitin chains attached to a variety of proteins. Previous structural studies of interactions between UIMs and ubiquitin have shown that UIMs adopt an extended structure of a single alpha-helix, containing a hydrophobic surface with a conserved sequence pattern that interacts with key hydrophobic residues on ubiquitin. In light of this large body of structural studies, details regarding the presence and the roles of structural dynamics and plasticity are surprisingly lacking. In order to better understand the structural basis of ubiquitin-UIM recognition, we have characterized changes in the structure and dynamics of ubiquitin upon binding of a UIM domain from the yeast Vps27 protein. The solution structure of a ubiquitin-UIM fusion protein designed to study these interactions is reported here and found to consist of a well-defined ubiquitin core and a bipartite UIM helix. Moreover, we have studied the plasticity of the docking interface, as well as global changes in ubiquitin due to UIM binding at the picoseconds-to-nanoseconds and microseconds-to-milliseconds protein motions by nuclear magnetic resonance relaxation. Changes in generalized-order parameters of amide groups show a distinct trend towards increased structural rigidity at the UIM-ubiquitin interface relative to values determined in unbound ubiquitin. Analysis of (15)N Carr-Purcell-Meiboom-Gill relaxation dispersion measurements suggests the presence of two types of motions: one directly related to the UIM-binding interface and the other induced to distal parts of the protein. This study demonstrates a case where localized interactions among protein domains have global effects on protein motions at timescales ranging from picoseconds to milliseconds.
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