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37 results for “usp5”
USP5 ZnF-UBD Co-Crystal Structure with Compound UBTR012574a
<p>Objective: To grow well-diffracting co-crystals of USP5 zinc finger ubiquitin binding domain (ZnF-UBD) to solve the co-crystal structures to determine ligand interactions in the binding pocket and to determine if the predicted binding pose is similar to the experimental binding pose.</p>
SEC-MALS: USP5 and Ubiquitin
<p>Determination of the stoichiometry of binding of monoubiquitin (Ubq) to the <a href="https://zenodo.org/record/1495189#.XnS84ohKjIV">full-length wildtype</a> USP5 and <a>R221A mutant</a> protein by size exclusion chromatography-multiple angle light scattering (SEC-MALS) to elucidate the binding properties of native Ubq for future cell-based and activity studies.</p>
USP5 zinc-finger ubiquitin binding domain with L-cysteine(residue195)-glutathione disulfide structure solution
<p>USP5 zinc-finger ubiquitin binding domain with L-cysteine(residue195)-glutathione disulfide structure solution to 1.6 Å resolution</p>
USP5 Zf-UBD Co-Crystal Structure with Compound XSR00035795a & Testing Selectivity
<p>Growth of well-diffracting co-crystals of USP5 zinc finger ubiquitin binding domain (Zf-UBD) and compound XSR00035795a to solve the structure to determine ligand interactions in the binding pocket. A surface plasmon resonance assay was used to determine if methyl group on carboxylic chain of compound XSR00035795a confers selectivity to USP5 versus HDAC6. </p>
Testing Selectivity of USP5 Zf-UBD Analogues with SPR Assay
<p>A surface plasmon resonance (SPR) assay is used to determine binding affinities of commercial compound analogues against the zinc finger ubiquitin binding domain (Zf-UBD) of USP5 and test for selectivity against HDAC6 Zf-UBD </p>
Prioritizing Commercial Analogues of Previous USP5 ZnF-UBD Hits
<p>Expansion of the chemical series of <a href="https://openlabnotebooks.org/co-crystal-structures-of-usp5-zf-ubd-and-weak-binding-compounds/">previous hits of USP5 zinc finger ubiquitin binding domain</a> (ZnF-UBD) by docking commercially available chemical analogs and prioritizing chemical analogues to exploit new interactions in the binding pocket of USP5 ZnF-UBD</p>
Testing USP5 ZnF-UBD analogues with a Displacement Assay and SPR
<p>20 <a href="https://zenodo.org/record/3356885#.XcwPD1dKjIV">commercial analogues</a> from the Enamine REAL database were screened against the USP5 zinc finger ubiquitin-binding domain (ZnF-UBD) using a <a href="https://zenodo.org/record/3403804#.XcwPjFdKjIV">displacement assay</a> and the binding potency of best displacing compounds was assessed with a surface plasmon resonance (SPR) assay</p>
Development and Optimization of an IQF USP5 Activity Assay
<p>Development and optimization of a fluorescence based deubiquitinase (DUB) activity assay for USP5 with internally quenched fluorophore pair (IQF) substrates: di-ubiquitin lysine linked K48 and K63 (Ub2K48, Ub2K63). The inhibitory capability of USP5 zinc-finger ubiquitin binding domain (ZnF-UBD) ligands was investigated. </p>
USP5 Zf-UBD Purification & Fluorescence Polarization Displacement Assay Development
<p>USP5 zinc-finger ubiquitin binding domain (Zf-UBD) expression and purification from <em>E. coli, </em>and screening conditions for a fluorescence polarization (FP) displacement assay with a FITC-labelled ubiquitin peptide. </p>
Crystallization of USP5 Zf-UBD
<p>Determination of crystallization conditions which allow growth of well-diffracting apo crystals of the USP5 zinc finger ubiquitin binding domain (Zf-UBD) </p>
USP5 Zf-UBD Differential Scanning Fluorimetry Assay Development
<p>Development of DSF assay for USP5 Zf-UBD to determine optimal protein screening conditions and significance of thermal shift of USP5 Zf-UBD in the presence of a ubiquitin RLRGG peptide </p>
USP5 Zf-UBD Fluorescence Polarization Displacement Assay Optimization
<p>Optimization of a fluorescence polarization (FP) assay for USP5 zinc finger ubiquitin binding domain (Zf-UBD) with an N-terminal FITC-labeled ubiquitin RLRGG peptide. </p>
USP5 Zf-UBD Differential Scanning Fluorimetry Assay Optimization
<p>Optimization of a differential scanning fluorimetry (DSF) assay for USP5 zinc finger ubiquitin binding domain (Zf-UBD) to determine if the presence of detergent in buffer conditions results in significant difference in melting temperatures of USP5 Zf-UBD and if the addition of increasing concentrations of ubiquitin RLRGG peptide results in thermal shift of USP5 Zf-UBD. </p>
Is USP5 Zf-UBD a dimer?
<p>Determination of the molar mass of USP5 zinc finger ubiquitin binding domain (Zf-UBD) using size exclusion chromatography with multiple angle light scattering (SEC-MALS). </p>
Structural Analysis of USP5 Zf-UBD
<p>Analysis of the <a href="https://zenodo.org/record/1209986#.Wr1Pqy7wapo">solved structure</a> of USP5 zinc finger ubiquitin binding domain (Zf-UBD) in crystallization conditions of 1.8 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 5.5, 1.7 mM l-glutathione reduced, l-glutathione-oxidized to determine if the ubiquitin binding pocket is accessible through solvent channels for inhibitor screening. </p>
Apo USP5 zinc-finger ubiquitin binding domain structure solution 2018/03/30
<p>USP5 zinc-finger ubiquitin binding domain structure solution to 1.55 Å resolution</p>
Crystallization of USP5 Zf-UBD #2
<p>Determination of crystallization conditions which allow growth of well diffracting apo crystals of USP5 zinc finger ubiquitin binding domain (Zf-UBD) permissible to soaking with small molecule ligands and optimization and assessment of cryo-protective conditions and DMSO tolerance of these crystals.</p>
USP5 Zf-UBD Fluorescence Polarization Displacement Assay #3
<p>Development of a fluorescence polarization (FP) assay for USP5 zinc finger ubiquitin binding domain (Zf-UBD) with different lengths of N-terminal FITC-ubiquitin peptides. </p>
5-fluoro-tryptophan USP5 Zf-UBD Growth & Purification for 19F NMR Screening
<p>The expression and purification of USP5<sup>171-290</sup> in media supplemented with 5-fluoro-tryptophan. Mass spectrometry, differential scanning fluorimetry and fluorescence polarization assays were used to verify label incorporation, protein folding and ubiquitin peptide binding respectively. Preliminary 19F NMR experiments were completed with the purified protein to determine if there are perturbations in one of the 19F resonances with a ubiquitin peptide, LRLRGG. </p> <p> </p>
Compounds of interest identified by screening a focused library against USP5 Zf-UBD with a 19F NMR assay
<p>Screening a set of commercial compounds selected from computational docking studies against USP5 zinc finger ubiquitin binding domain (Zf-UBD) using <sup>19</sup>F NMR spectroscopy. You can find details of preliminary <sup>19</sup>F NMR experiments <a href="https://zenodo.org/record/1246807#.WxV8HkgvzIV">here</a>.</p>
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