This work was funded by Sanford Research startup funds to FB and the NIH grant R01CA233700 to MJS. The artwork was done by Felipe G. Serrano (www.illustrative-science.com).&#160;We thank Dr. Greg Findlay (University of&#160;Dundee) for the GST-USP27X plasmid.

The following protocol can be adapted for recombinant proteins using various affinity tags expressed in different strains of competent cells. Depending on the protein being expressed, the culturing and overnight expression conditions may require optimization of the OD600 at expression induction, expression time, expression temperature, and IPTG concentration. An overview of the protocol is illustrated in Figure 1. The details of the reagents and the equipment used in this study are listed in the Table of Materials.
1. Transformation of competent Rosetta 2 E. coli cells with the recombinant GST-USP27X expression plasmid
NOTE: To maintain the sterility of the bacterial culture, perform steps where media containers are open under a Bunsen burner flame. To allow optimal oxygen transfer, perform bacterial culture shaking in a benchtop temperature-controlled shaker with an orbit of 19 mm to 50 mm and a speed of 200 rpm29.
<ol>
	<li>Thaw 20 &#181;L of chemically competent Rosetta 2 E. coli cells on ice immediately before use. Add 1-10 ng of the pGEX6P1-USP27X expression plasmid (encoding for N-terminal Glutathione-S-transferase (GST)30 -tagged USP27X and containing Ampicillin resistance) and incubate 5 min on ice.</li>
	<li>Heat shock for 30 s at 42 &#176;C in a dry bath. Incubate on ice for 2 min.</li>
	<li>Add 80 &#181;L of room temperature (RT) SOC medium. Incubate for 60 min at 37 &#176;C with 200 rpm rotation in a 19 mm orbit benchtop temperature-controlled shaker.</li>
	<li>Plate 50 &#181;L of culture on an LB agar plate supplemented with 25 &#181;g/L Chloramphenicol and 50 &#181;g/L Ampicillin. Incubate for 20 h at 37 &#176;C lid-side down in a temperature-controlled incubator.</li>
</ol>
2. Overnight bacterial expression of recombinant protein from expression plasmid
NOTES: To maintain the sterility of the bacterial culture, perform steps where media containers are open under a Bunsen burner flame. To allow optimal oxygen transfer, perform bacterial culture shaking in a benchtop temperature-controlled shaker with an orbit of 19 mm to 50 mm and a speed of 200 rpm29. Measure culture OD600 using a spectrophotometer.
<ol>
	<li>Prepare 1 L of Terrific Broth (TB) medium by adding 47.6 g of TB Powder to 1 L of ultrapure water with 0.4% glycerol in a 2 L baffled culture flask. Autoclave medium for 30 min and cool to RT.</li>
	<li>Pick a single colony of transformed bacteria and add to 10 mL of sterile LB medium supplemented with 25 &#181;g/L Chloramphenicol and 50 &#181;g/L Ampicillin. Incubate for 20 h at 37 &#176;C with 200 rpm rotation in a 19 mm orbit benchtop temperature-controlled shaker.</li>
	<li>Add 10 mL overnight culture to 1 L of TB medium supplemented with 25 &#181;g/L Chloramphenicol and 50 &#181;g/L Ampicillin (1:100 ratio of starting culture to expression culture). Incubate at 37 &#176;C with 200 rpm rotation in a 19 mm orbit benchtop temperature-controlled shaker until the culture OD600 is between 0.5-0.6.</li>
	<li>Add 50 &#181;M of IPTG to the culture to induce expression, cool to 16 &#176;C, and incubate for 20 h at 16 &#176;C with 200 rpm rotation.</li>
	<li>Pellet cells from expression culture by centrifugation for 20 min at &#8805;3,000 x g and 4 &#176;C. Store the pellet at -80 &#176;C for at least 1 h. 
	NOTE: At this point, the experiment can be paused and restarted later (preferably the same week). The pellet can be stored for the long term at -80 &#176;C.</li>
</ol>
3. Protein purification by gravity-flow affinity column
NOTE: The resin, binding, wash, elution, and storage buffers appropriate for each purification will depend on the recombinant protein being purified. Collect samples from the cell pellet, supernatant, flow-through, wash fractions, and elution fractions in SDS-PAGE buffer. Perform SDS-PAGE and Coomassie staining for the samples to evaluate the success of the purification. Perform purification at 4 &#176;C and handle fractions on ice. Cleavage of protein tags can be performed on or off the column using the appropriate protease to target the relevant protease-specific cleavage site.
<ol>
	<li>Secure the empty gravity flow column in the retort stand and fill it with glutathione agarose resin. Use 2-3 mL of resin to purify a cell pellet collected from 1 L of expression culture.</li>
	<li>Wash the column with one resin-bed volume of 20% ethanol. Wash column 3 times with one resin-bed volume of MS500 buffer (20 mM of Tris pH 7.5, 500 mM of NaCl, 0.5 mM of TCEP). Stop the column so the resin remains covered with buffer to prevent drying while preparing the cell pellet.</li>
	<li>Thaw the cell pellet at 4 &#176;C. Add 30 mL of MS500 buffer (20 mM of Tris pH 7.5, 500 mM of NaCl, 0.5 mM of TCEP, 60 mg of lysozyme, and one protease inhibitor tablet) to the thawed pellet. Lyse for 30 min at 4 &#176;C with gentle end-over-end rotation.</li>
	<li>Sonicate lysed cells in either a 50 mL centrifuge tube or a metal beaker on ice until the lysate flows freely when dispensed from a pipette tip. Centrifuge for 30 min at 4 &#176;C and &#8805;20,000 x g to clear the supernatant. 
	NOTE: Determine sonicator settings empirically. Set the sonicator such that 120 s total time is enough to reduce the viscous lysate to a free-flowing and transparent liquid.</li>
	<li>Decant the supernatant into a beaker and load cleared lysate onto the column. Run lysate through the column by gravity flow while collecting the flow through. Load the column with the collected flow through and run it through the column.</li>
	<li>Wash the column with at least two resin-bed volumes of MS500 wash buffer (20 mM of Tris pH 7.5, 500 mM of NaCl, 0.5 mM of TCEP) 5 times. Collect the wash flow through in 5 mL fractions. Add 1 &#181;L of each fraction to 100 &#181;L of Bradford reagent to visually check for protein presence. Wash until unbound protein is no longer present in the last wash, adding additional wash steps if necessary.</li>
	<li>Recover protein by running MS500 elution buffer (MS500 buffer supplemented with 10 mM of glutathione and 10 mM of NaOH) through the column, collecting 5 mL elution fractions. Check for protein presence by adding 1 &#181;L of eluate to 100 &#181;L of Bradford reagent. Stop collecting fractions when the Bradford reagent no longer indicates proteins are present.</li>
	<li>Perform buffer exchange by precipitation and centrifugation. Precipitate protein by adding 2 volumes of 4 M of ammonium sulfate to the eluate, gently inverting until cloudy, and then centrifuging for 30 min at 4 &#176;C and &#8805;20,000 x g and again for another 5 min. Remove the supernatant after each centrifugation without disturbing the protein pellet.</li>
	<li>Re-dissolve and store protein in MS500 supplemented with 25% glycerol. Store protein pellets or protein in storage buffer at -80 &#176;C.</li>
</ol>
4. In vitro ubiquitin chain cleavage assay
NOTE: Select ubiquitin chain length and linkage types based on DUB specificity described in previous reports31 or determined empirically. If necessary, this protocol could be used to test the activity of the wild-type DUB of interest on a panel of commercially available ubiquitin chains of defined length and linkage type. A di-ubiquitin chain amount of 375-750 ng and a DUB concentration of 1-2 &#181;M can be used as starting points for the assay27.
<ol>
	<li>Prepare 10x DUB activation buffer (500 mM of Tris-HCl pH 7.5, 500 mM of NaCl, and 100 mM of TCEP).</li>
	<li>For each time point for each DUB, prepare 10 &#181;L total of 2 &#181;M of purified GST-USP27X in 1x DUB activation buffer (DUB mix). Prepare master mixes and split them into time points.</li>
	<li>Incubate the DUB mix for 10 min at RT.</li>
	<li>Add 7 &#181;L of SDS-PAGE loading buffer to time 0 before adding ubiquitin chains to prevent the deubiquitylation reaction from starting.</li>
	<li>To each time point for each DUB, add 375 ng of K-63 di-ubiquitin chains diluted in 10 &#181;L 1x DUB activation buffer. The total volume is 20 &#181;L per reaction.</li>
	<li>Incubate the tubes at 30 &#176;C, stopping each time point with 7 &#181;L of SDS-PAGE loading buffer.</li>
	<li>Perform SDS-PAGE with a 4%-12% gradient gel and immunoblot7,32 for ubiquitin and USP27X to analyze the change in mono-ubiquitin presence across selected time points.</li>
</ol>
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/67367/67367fig01v2.jpg" /> 
Figure 1: Schematic of the study design. (A) Transformation of competent E. coli cells with recombinant protein expression plasmid. (B) Overnight bacterial expression of recombinant deubiquitylase protein. (C) Protein purification of recombinant deubiquitylase using a gravity-flow affinity column. (D) In vitro ubiquitin chain cleavage assay to evaluate deubiquitylating activity. <a href="https://www.jove.com/files/ftp_upload/67367/67367fig01largev2.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Assessing DUB Variants in Neurodevelopmental Disorders Using a Cleavage Assay

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The authors declare no conflicts of interest.

This article presents a protocol for the expression and purification of recombinant USP27X DUBs and an in vitro ubiquitin chain cleavage assay to compare the deubiquitylating activity of wild-type USP27X and NDD-associated variant proteins. This assay determined that XLID105-associated variants disrupt USP27X catalytic activity7. This mechanistic insight helped us define XLID105 as a USP27X functional disruption disorder.
This protocol can be adapted to other D...

Neurodevelopmental disorders (NDDs) arise from diverse etiologies with environmental or genetic determinants that drive atypical nervous system development1. Next-generation sequencing genetic testing has linked an increasing number of variants in ubiquitin system-related genes with genetic NDDs2. The ubiquitin system catalyzes the ligation of the small protein modifier ubiquitin to primarily lysine residues in protein substrates to drive changes in cellular behavior, including localization, stability, protein-protein interactions, or activity3. Ubiquitylation is mediated by E1 activating, E2 conjugating, and E3 ligase enzymes4 and is reversible by the activity of deubiquitylating enzymes (DUBs) that catalyze the cleavage and removal of ubiquitin from protein substrates5. Ubiquitin can be ligated to the substrate as a monomer (monoubiquitylation) or polymeric chains (polyubiquitylation) that are formed on any of the seven lysine residues (K6, K11, K27, K29, K33, K48, K63) or the M1 residue of ubiquitin. These different ubiquitin chain topologies and their combinations create a cellular code that is key for signal transduction6.
DUBs such as USP27X, USP7, USP9X, USP48, STAMBP, OTUD4, OTUD6B, and OTUD5 have been associated with NDDs2,7,8,9,10,11. For most NDDs, the molecular mechanisms that drive pathogenesis remain experimentally undefined. Some of the DUBs driving recently described disorders are poorly understood and lack known cellular readouts that can be used to assess the impact of genetic variation on protein function. In vitro, ubiquitin chain cleavage assays overcome this limitation as substrate-independent DUB activity readouts that can measure the impact of gene variants on enzymatic activity12.
In vitro ubiquitin cleavage assays have been used since the 1980s. These assays using radiolabeled substrates allowed for the discovery of the first DUBs, including isopeptidase, identified for its capacity to deubiquitylate Histone H2A13, and ubiquitin carboxyl-terminal hydrolase (UCH), identified by its ability to hydrolyze ubiquitin from a variety of chemical conjugates14,15,16. Further, radiolabeled polyubiquitylated full-length proteins or peptides were used to identify isopeptidase T and several UCHs and ubiquitin-specific proteases (UBPs) from erythrocytes and skeletal muscle, respectively17,18,19,20. Ubiquitin chains of a defined length and linkage type (K48-linked tetra-ubiquitin) were first used to measure the DUB activity of Isopeptidase T21. Since then, this assay has become the gold standard to measure DUB activity in mutational analyses22,23. The refinement of this assay currently allows visualization of ubiquitin cleavage via electrophoresis and conventional gel stains such as Coomassie blue, SYPRO orange, ruby, and silver stain or fluorescent or immunoblotting-based detection12,24. Molecular aspects of DUB activity, such as minimum chain length and linkage specificity25,26,27,28, can be clarified by using ubiquitin chains of different lengths (e.g., di-, tri-, tetra-ubiquitin) and linkages (K6, K11, K27, K29, K33, K48, K63, linear) in functional assays. NDD-associated variants can drive DUB activity defects that are ubiquitin chain linkage type specific11.
A di-ubiquitin cleavage assay using purified recombinant DUB proteins can directly measure the impact of NDD variants on DUB activity. USP27X, which is mutated in the NDD X-linked intellectual disability disorder 105 (XLID105)7,28 models the process presented here. This approach allows for the determination of how DUB activity is disrupted by gene variants in existing and unknown DUB-associated NDDs.

<table><tbody><tr><td>Amersham Protran 0.45 NC 200 mm &amp;times; 200 mm 25/PK</td><td>Cytiva</td><td>10600041</td><td></td></tr><tr><td>Ammonium sulfate</td><td>Fisher Scientific</td><td>AC205872500</td><td></td></tr><tr><td>Ampicillin</td><td>Fisher Scientific</td><td>BP1760 25</td><td></td></tr><tr><td>Anti- Ubiquitin (Mouse monoclonal)</td><td>Biolegend</td><td>Cat# 646302, RRID:AB_1659269</td><td>(WB: 1:1000)</td></tr><tr><td>Anti-GST (Sheep polyclonal)</td><td>MRC-PPU Reagents and Services</td><td>Cat# S902A Third bleed</td><td>(WB: 1:1000) https://mrcppureagents.dundee.ac.uk/</td></tr><tr><td>Baffled Culture Flasks 2 L</td><td>Fisher Scientific</td><td>10-042-5N</td><td></td></tr><tr><td>Bradford Reagent</td><td>Millipore Sigma</td><td>B6916-500ML</td><td></td></tr><tr><td>Chloramphenicol</td><td>Gold Biotechnology</td><td>C-105-25</td><td></td></tr><tr><td>Complete, Protease Inhibitor tablets</td><td>Millipore Sigma</td><td>5056489001</td><td></td></tr><tr><td>Econo-Column 1.5 &amp;times; 5 cm</td><td>Bio-Rad</td><td>7371507</td><td></td></tr><tr><td>Eppendorf ThermoMixer F1.5&amp;nbsp;</td><td>Eppendorf</td><td>5384000020</td><td></td></tr><tr><td>Excel</td><td>Microsoft</td><td></td><td>https://www.microsoft.com/en-us/microsoft-365/excel</td></tr><tr><td>Glycerol</td><td>Genesee Scientific</td><td>18-205</td><td></td></tr><tr><td>Illustrator</td><td>Adobe</td><td></td><td>https://www.adobe.com/products/illustrator.html</td></tr><tr><td>Image Studio</td><td>LI-COR Biosciences</td><td></td><td>https://www.licor.com/bio/image-studio/</td></tr><tr><td>Inkscape</td><td>Inkscape</td><td></td><td>https://inkscape.org/</td></tr><tr><td>Invitrogen 4-12% NuPAGE 1mm 12 well gel</td><td>Thermo Fisher Scientific</td><td>NP0322BOX</td><td></td></tr><tr><td>IPTG (Isopropyl-b-D-Thiogalactopyranoside)</td><td>Genesee Scientific</td><td>20-109</td><td></td></tr><tr><td>IRDye 800CW Donkey anti-Goat IgG Secondary Antibody</td><td>LI-COR Biosciences</td><td>Cat# 926-32214</td><td>(WB: 1:10000)</td></tr><tr><td>IRDye 800CW Donkey anti-Mouse IgG Secondary Antibody</td><td>LI-COR Biosciences</td><td>Cat# 926-32212</td><td>(WB: 1:10000)</td></tr><tr><td>Isotemp Digital Dry Bath</td><td>Fisher Scientific</td><td>88860022</td><td></td></tr><tr><td>K63 Di-Ubiquitin</td><td>South Bay Bio LLC</td><td>SBB-UP0072</td><td></td></tr><tr><td>LB Agar</td><td>Genesee Scientific</td><td>11-119</td><td></td></tr><tr><td>LB Broth</td><td>Genesee Scientific</td><td>11-118</td><td></td></tr><tr><td>Lysozyme</td><td>Gold Biotechnology</td><td>L-040-100</td><td></td></tr><tr><td>MaxQ 4000 Benchtop Orbital Shaker</td><td>Thermo Fisher Scientific</td><td>SHKE4000-7</td><td></td></tr><tr><td>MES-SDS Running Buffer</td><td>Boston Bioproducts Inc</td><td>BP-177</td><td></td></tr><tr><td>Mini Tube Rotator</td><td>Fisher Scientific</td><td>88-861-051</td><td></td></tr><tr><td>NuPage LDS Sample buffer 4x</td><td>Thermo Fisher Scientific</td><td>NP0007</td><td></td></tr><tr><td>Odyssey&amp;nbsp;Fc Imager</td><td>LI-COR Biosciences</td><td>43214</td><td></td></tr><tr><td>PageRuler Plus Ladder</td><td>Thermo Fisher Scientific</td><td>26620</td><td></td></tr><tr><td>pGEX6P1 human USP27X</td><td>MRC-PPU Reagents and Services</td><td>DU21193</td><td>https://mrcppureagents.dundee.ac.uk/</td></tr><tr><td>pGEX6P1 human USP27X F313V</td><td>Addgene</td><td>225715</td><td>Koch et at 2024 (PMID: 38182161)</td></tr><tr><td>pGEX6P1 human USP27X S404N</td><td>Addgene</td><td>225717</td><td>Koch et at 2024 (PMID: 38182161)</td></tr><tr><td>pGEX6P1 human USP27X Y381H</td><td>Addgene</td><td>225716</td><td>Koch et at 2024 (PMID: 38182161)</td></tr><tr><td>Pierce Glutathione Agarose</td><td>Thermo Fisher Scientific</td><td>16100</td><td></td></tr><tr><td>PMSF (Phenylmethylsulfonyl fluoride)</td><td>Gold Biotechnology</td><td>P-470-10</td><td></td></tr><tr><td>Polysorbate 20 (Tween 20)</td><td>Fisher Scientific</td><td>AC233360010</td><td></td></tr><tr><td>Rosetta 2 Competent Cells</td><td>Millipore Sigma</td><td>71402-M</td><td></td></tr><tr><td>SimplyBlue SafeStain</td><td>Thermo Fisher Scientific</td><td>LC6060</td><td></td></tr><tr><td>SmartSpec 3000</td><td>Bio-Rad</td><td>170-2501</td><td></td></tr><tr><td>SOC medium</td><td>Thermo Fisher Scientific</td><td>15544034</td><td></td></tr><tr><td>Sodium chloride</td><td>Genesee Scientific</td><td>18-216</td><td></td></tr><tr><td>Sonifier 250</td><td>Branson</td><td>100-132-135</td><td></td></tr><tr><td>Sorvall RC 6 Plus Centrifuge</td><td>Thermo Fisher Scientific</td><td>46910</td><td></td></tr><tr><td>TCEP (Tris-(carboxyethyl) phosphine hydrochloride)</td><td>Gold Biotechnology</td><td>TCEP10</td><td></td></tr><tr><td>Terrific Broth Powder</td><td>Genesee Scientific</td><td>18-225</td><td></td></tr><tr><td>Tris Base</td><td>Genesee Scientific</td><td>18-146</td><td></td></tr><tr><td>XCell SureLock Mini-Cell and XCell II Blot Module&amp;nbsp;</td><td>Thermo Fisher Scientific</td><td>EI0002</td><td></td></tr></tbody></table>

measuring enzymatic activity of neurodevelopmental disorder-associated deubiquitylating enzymes via an in vitro ubiquitin chain cleavage assay

Neurodevelopmental disorders (NDDs) are associated with impairments in nervous system function but often remain poorly understood at the molecular level. Discrete disorders caused by single genes provide models to investigate mechanisms driving atypical neurodevelopment. Variants of genes encoding deubiquitylating enzyme (DUB) family proteins are associated with several NDDs, but there is a need to determine the pathogenic mechanisms of disorders driven by these gene variants. The impact of gene variants on DUB activity can be experimentally determined using a substrate-independent in vitro ubiquitin cleavage assay. This assay does not require knowledge of downstream substrates to directly measure catalytic activity. Here, the protocol for determining the impact of gene variants on enzymatic activity is modeled using the DUB Ubiquitin Specific Protease 27, X-linked (USP27X), which is mutated in X-linked intellectual disability 105 (XLID105). This experimental pipeline can be used to clarify the mechanisms underlying neurodevelopmental disorders driven by variants in DUB genes.

To determine the impact of XLID105-associated variants on USP27X catalytic activity, GST-tagged wild-type USP27X and the XLID105-associated variant F313V, Y381H, and S404N USP27X proteins were purified from bacteria. These variants are located within the USP catalytic domain of USP27X (Figure 2A). Because USP27X was previously reported to cleave K63 ubiquitin chains31, wild-type USP27X and the XLID105-associated variant F313V, Y381H, and S404N USP27X proteins were inc...

Measuring Enzymatic Activity of Neurodevelopmental Disorder-Associated Deubiquitylating Enzymes via an In Vitro Ubiquitin Chain Cleavage Assay

This protocol explains how to measure the effect of genetic variation associated with neurodevelopmental disorders on deubiquitylating enzyme activity by combining recombinant protein purification with ubiquitin chain cleavage assays.

Neurodevelopmental disorders (NDDs) are associated with impairments in nervous system function but often remain poorly understood at the molecular level. ...

measuring-enzymatic-activity-neurodevelopmental-disorder-associated

Research

JoVE Journal

Biochemistry

381 Views.  Sanford Research. This protocol explains how to measure the effect of genetic variation associated with neurodevelopmental disorders on deubiquitylating enzyme activity by combining recombinant protein purification with ubiquitin chain cleavage assays.

Video: Measuring Enzymatic Activity of Neurodevelopmental Disorder-Associated Deubiquitylating Enzymes via an In Vitro Ubiquitin Chain Cleavage Assay

High-throughput Screening of Carbohydrate-degrading Enzymes Using Novel Insoluble Chromogenic Substrate Assay Kits

Carbohydrates active enzymes (CAZymes) have multiple roles in vivo and are widely used for industrial processing in the biofuel, textile, detergent, paper and food industries. A deeper understanding of CAZymes is important from both fundamental biology and industrial standpoints. Vast numbers of CAZymes exist in nature (especially in microorganisms) and hundreds of thousands have been cataloged and described in the carbohydrate active enzyme database (CAZy). However, the rate of discovery of putative enzymes has outstripped our ability to biochemically characterize their activities. One reason for this is that advances in genome and transcriptome sequencing, together with associated bioinformatics tools allow for rapid identification of candidate CAZymes, but technology for determining an enzyme's biochemical characteristics has advanced more slowly. To address this technology gap, a novel high-throughput assay kit based on insoluble chromogenic substrates is described here. Two distinct substrate types were produced: Chromogenic Polymer Hydrogel (CPH) substrates (made from purified polysaccharides and proteins) and Insoluble Chromogenic Biomass (ICB) substrates (made from complex biomass materials). Both CPH and ICB substrates are provided in a 96-well high-throughput assay system. The CPH substrates can be made in four different colors, enabling them to be mixed together and thus increasing assay throughput. The protocol describes a 96-well plate assay and illustrates how this assay can be used for screening the activities of enzymes, enzyme cocktails, and broths.

A high-throughput assay for enzyme screening is described. This multiplexed ready-to-use assay kit comprises of pre-chosen Chromogenic Polymer Hydrogel (CPH) substrates and complex Insoluble Chromogenic Biomass (ICB) substrates. Target enzymes are polysaccharide degrading endo-enzymes and proteases.

Carbohydrates active enzymes (CAZymes) have multiple roles in vivo and are widely used for industrial processing in the biofuel, textile, detergent, paper ...

A Fluorescence-based Assay of Phospholipid Scramblase Activity

Scramblases translocate phospholipids across the membrane bilayer bidirectionally in an ATP-independent manner. The first scramblase to be identified and biochemically verified was opsin, the apoprotein of the photoreceptor rhodopsin. Rhodopsin is a G protein-coupled receptor localized in rod photoreceptor disc membranes of the retina where it is responsible for the perception of light. Rhodopsin&#39;s scramblase activity does not depend on its ligand 11-cis-retinal, i.e., the apoprotein opsin is also active as a scramblase. Although constitutive and regulated phospholipid scrambling play an important role in cell physiology, only a few phospholipid scramblases have been identified so far besides opsin. Here we describe a fluorescence-based assay of opsin&#39;s scramblase activity. Opsin is reconstituted into large unilamellar liposomes composed of phosphatidylcholine, phosphatidylglycerol and a trace quantity of fluorescent NBD-labeled PC (1-palmitoyl-2-{6-[7-nitro-2-1,3-benzoxadiazole-4-yl)amino]hexanoyl}-sn-glycero-3-phosphocholine). Scramblase activity is determined by measuring the extent to which NBD-PC molecules located in the inner leaflet of the vesicle are able to access the outer leaflet where their fluorescence is chemically eliminated by a reducing agent that cannot cross the membrane. The methods we describe have general applicability and can be used to identify and characterize scramblase activities of other membrane proteins.

We describe a fluorescence-based assay to measure phospholipid scrambling in large unilamellar liposomes reconstituted with opsin.

Scramblases translocate phospholipids across the membrane bilayer bidirectionally in an ATP-independent manner. The first scramblase to be identified and ...

In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones

Ubiquitination is a post-translational modification that plays important roles in various signaling pathways and is notably involved in the coordination of chromatin function and DNA-associated processes. This modification involves a sequential action of several enzymes including E1 ubiquitin-activating, E2 ubiquitin-conjugating and E3 ubiquitin-ligase and is reversed by deubiquitinases (DUBs). Ubiquitination induces degradation of proteins or alteration of protein function including modulation of enzymatic activity, protein-protein interaction and subcellular localization. A critical step in demonstrating protein ubiquitination or deubiquitination is to perform in vitro reactions with purified components. Effective ubiquitination and deubiquitination reactions could be greatly impacted by the different components used, enzyme co-factors, buffer conditions, and the nature of the substrate.&#160; Here, we provide step-by-step protocols for conducting ubiquitination and deubiquitination reactions. We illustrate these reactions using minimal components of the mouse Polycomb Repressive Complex 1 (PRC1), BMI1, and RING1B, an E3 ubiquitin ligase that monoubiquitinates histone H2A on lysine 119. Deubiquitination of nucleosomal H2A is performed using a minimal Polycomb Repressive Deubiquitinase (PR-DUB) complex formed by the human deubiquitinase BAP1 and the DEUBiquitinase ADaptor (DEUBAD) domain of its co-factor ASXL2. These ubiquitination/deubiquitination assays can be conducted in the context of either recombinant nucleosomes reconstituted with bacteria-purified proteins or native nucleosomes purified from mammalian cells. We highlight the intricacies that can have a significant impact on these reactions and we propose that the general principles of these protocols can be swiftly adapted to other E3 ubiquitin ligases and deubiquitinases.

Ubiquitination is a post-translational modification that plays important roles in cellular processes and is tightly coordinated by deubiquitination. Defects in both reactions underlie human pathologies. We provide protocols for conducting ubiquitination and deubiquitination reaction in vitro using purified components.

Ubiquitination is a post-translational modification that plays important roles in various signaling pathways and is notably involved in the coordination ...

Detection of Protein Ubiquitination

Ubiquitination, the covalent attachment of the polypeptide ubiquitin to target proteins, is a key posttranslational modification carried out by a set of three enzymes. They include ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, and ubiquitin ligase E3. Unlike to E1 and E2, E3 ubiquitin ligases display substrate specificity. On the other hand, numerous deubiquitylating enzymes have roles in processing polyubiquitinated proteins. Ubiquitination can result in change of protein stability, cellular localization, and biological activity. Mutations of genes involved in the ubiquitination/deubiquitination pathway or altered ubiquitin system function are associated with many different human diseases such as various types of cancer, neurodegeneration, and metabolic disorders. The detection of altered or normal ubiquitination of target proteins may provide a better understanding on the pathogenesis of these diseases. &nbsp;Here, we describe protocols to detect protein ubiquitination in cultured cells in vivo and test tubes in vitro. These protocols are also useful to detect other ubiquitin-like small molecule modification such as sumolyation and neddylation.

Ubiquitination is a key posttranslational modification carried out by a set of three enzymes. Mutations of genes involved in this modification are associated with many different human diseases. Here, we describe protocols to detect protein ubiquitination in cultured cells in vivo and test tubes in vitro.

Ubiquitination, the covalent attachment of the polypeptide ubiquitin to target proteins, is a key posttranslational modification carried out by a set of ...

Biology

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Assessment of the global profile of ubiquitin chain topologies within a proteome is of interest to answer a wide range of biological questions. The protocol outlined here takes advantage of the di-glycine (-GG) modification left after the tryptic digestion of ubiquitin incorporated in a chain. By quantifying these topology-characteristic peptides the relative abundance of each ubiquitin chain topology can be determined. The steps required to quantify these peptides by a parallel reaction monitoring experiment are reported taking into consideration the stabilization of ubiquitin chains. Preparation of heavy controls, cell lysis, and digestion are described along with the appropriate mass spectrometer setup and data analysis workflow. An example data set with perturbations in ubiquitin topology is presented, accompanied by examples of how optimization of the protocol can affect results. By following the steps outlined, a user will be able to perform a global assessment of the ubiquitin topology landscape within their biological context.

This method describes the assessment of global changes in ubiquitin chain topology. The assessment is performed by the application of a mass spectrometry-based targeted proteomics approach.

Assessment of the global profile of ubiquitin chain topologies within a proteome is of interest to answer a wide range of biological questions. The ...

Quantifying Subcellular Ubiquitin-proteasome Activity in the Rodent Brain

The ubiquitin-proteasome system is a key regulator of protein degradation and a variety of other cellular processes in eukaryotes. In the brain, increases in ubiquitin-proteasome activity are critical for synaptic plasticity and memory formation and aberrant changes in this system are associated with a variety of neurological, neurodegenerative and psychiatric disorders. One of the issues in studying ubiquitin-proteasome functioning in the brain is that it is present in all cellular compartments, in which the protein targets, functional role and mechanisms of regulation can vary widely. As a result, the ability to directly compare brain ubiquitin protein targeting and proteasome catalytic activity in different subcellular compartments within the same animal is critical for fully understanding how the UPS contributes to synaptic plasticity, memory and disease. The method described here allows collection of nuclear, cytoplasmic and crude synaptic fractions from the same rodent (rat) brain, followed by simultaneous quantification of proteasome catalytic activity (indirectly, providing activity of the proteasome core only) and linkage-specific ubiquitin protein tagging. Thus, the method can be used to directly compare subcellular changes in ubiquitin-proteasome activity in different brain regions in the same animal during synaptic plasticity, memory formation and different disease states. This method can also be used to assess the subcellular distribution and function of other proteins within the same animal.

This protocol is designed to efficiently quantify ubiquitin-proteasome system (UPS) activity in different cellular compartments of the rodent brain. Users are able to examine UPS functioning in nuclear, cytoplasmic and synaptic fractions in the same animal, reducing the amount of time and number of animals needed to perform these complex analyses.

The ubiquitin-proteasome system is a key regulator of protein degradation and a variety of other cellular processes in eukaryotes. In the brain, increases ...

Neuroscience

Method for Measuring the Activity of Deubiquitinating Enzymes in Cell Lines and Tissue Samples

The ubiquitin-proteasome system has recently been implicated in various pathologies including neurodegenerative diseases and cancer. In light of this, techniques for studying the regulatory mechanism of this system are essential to elucidating the cellular and molecular processes of the aforementioned diseases. The use of hemagglutinin derived ubiquitin probes outlined in this paper serves as a valuable tool for the study of this system. This paper details a method that enables the user to perform assays that give a direct visualization of deubiquitinating enzyme activity. Deubiquitinating enzymes control proteasomal degradation and share functional homology at their active sites, which allows the user to investigate the activity of multiple enzymes in one assay. Lysates are obtained through gentle mechanical cell disruption and incubated with active site directed probes. Functional enzymes are tagged with the probes while inactive enzymes remain unbound. By running this assay, the user obtains information on both the activity and potential expression of multiple deubiquitinating enzymes in a fast and easy manner. The current method is significantly more efficient than using individual antibodies for the predicted one hundred deubiquitinating enzymes in the human cell.

The current protocol details a method for measuring the activity of functionally homologous deubiquitinating enzymes. Specialized probes covalently modify the enzyme and allow for detection. This method holds the potential to identify new therapeutic targets.

The ubiquitin-proteasome system has recently been implicated in various pathologies including neurodegenerative diseases and cancer. In light of this, ...

A Scalable, Cell-Based Method for the Functional Assessment of Ube3a Variants

The increased use of sequencing in medicine has identified millions of coding variants in the human genome. Many of these variants occur in genes associated with neurodevelopmental disorders, but the functional significance of the vast majority of variants remains unknown. The present protocol describes the study of variants for Ube3a, a gene that encodes an E3 ubiquitin ligase linked to both autism and Angelman syndrome. Duplication or triplication of Ube3a is strongly linked to autism, whereas its deletion causes Angelman syndrome. Thus, understanding the valence of changes in UBE3A protein activity is important for clinical outcomes. Here, a rapid, cell-based method that pairs Ube3a variants with a Wnt pathway reporter is described. This simple assay is scalable and can be used to determine the valence and magnitude of activity changes in any Ube3a variant. Moreover, the facility of this method allows the generation of a wealth of structure-function information, which can be used to gain deep insights into the enzymatic mechanisms of UBE3A.

A Scalable, Cell-Based Method for the Functional Assessment of Ube3a Variants

A simple and scalable method was developed to assess the functional significance of missense variants in Ube3a, a gene whose loss and gain of function are linked to both Angelman syndrome and autism spectrum disorder.

The increased use of sequencing in medicine has identified millions of coding variants in the human genome. Many of these variants occur in genes ...

In Vitro Analysis of E3 Ubiquitin Ligase Function

The covalent attachment of ubiquitin (Ub) to internal lysine residue(s) of a substrate protein, a process termed ubiquitylation, represents one of the most important post-translational modifications in eukaryotic organisms. Ubiquitylation is mediated by a sequential cascade of three enzyme classes including ubiquitin-activating enzymes (E1 enzymes), ubiquitin-conjugating enzymes (E2 enzymes), and ubiquitin ligases (E3 enzymes), and sometimes, ubiquitin-chain elongation factors (E4 enzymes). Here, in vitro protocols for ubiquitylation assays are provided, which allow the assessment of E3 ubiquitin ligase activity, the cooperation between E2-E3 pairs, and substrate selection. Cooperating E2-E3 pairs can be screened by monitoring the generation of free poly-ubiquitin chains and/or auto-ubiquitylation of the E3 ligase. Substrate ubiquitylation is defined by selective binding of the E3 ligase and can be detected by western blotting of the in vitro reaction. Furthermore, an E2~Ub discharge assay is described, which is a useful tool for the direct assessment of functional E2-E3 cooperation. Here, the E3-dependent transfer of ubiquitin is followed from the corresponding E2 enzyme onto free lysine amino acids (mimicking substrate ubiquitylation) or internal lysines of the E3 ligase itself (auto-ubiquitylation). In conclusion, three different in vitro protocols are provided that are fast and easy to perform to address E3 ligase catalytic functionality.

In Vitro Analysis of E3 Ubiquitin Ligase Function

The present study provides detailed in vitro ubiquitylation assay protocols for the analysis of E3 ubiquitin ligase catalytic activity. Recombinant proteins were expressed using prokaryotic systems such as Escherichia coli culture.

The covalent attachment of ubiquitin (Ub) to internal lysine residue(s) of a substrate protein, a process termed ubiquitylation, represents one of the ...

Virtual Screening and Validation of UCHL3 Inhibitors Using Molecular Docking

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

Deubiquitinating enzymes&#160;(DUBs) play a pivotal role in modulating ubiquitination homeostasis, with UCHL3 being an archetypal cysteine DUB intricately involved in a myriad of physiological and pathological processes. Therefore, developing small molecule inhibitors targeting Ubiquitin C-Terminal Hydrolase L3 (UCHL3) is of great significance. This protocol aims to establish a process for virtual screening and in vitro validation of small molecule inhibitors of cysteine DUB represented by UCHL3. Firstly, potential inhibitors of UCHL3 are virtually screened using molecular docking technology, and the interaction between drugs and protein targets is visualized. Subsequently, the effectiveness of the screened drug, Danshensu, is verified through in vitro activity inhibition assays. Ubiquitin-7-amino-4-methylcoumarin (Ub-AMC) and hemagglutinin-ubiquitin-vinyl sulfone (HA-Ub-VS) are used as probes for in vitro activity testing, as they can competitively bind to DUB with small molecule inhibitors to assess the activity of UCHL3. The results indicate that Danshensu has a good binding affinity with UCHL3 in molecular docking, and it can competitively inhibit the activity of UCHL3 with HA-Ub-VS. These findings provide important references for further research and development of therapeutic drugs targeting UCHL3.

The experiment used here shows a method of molecular docking combined with probe technologies to predict and validate the interaction between small molecules of traditional Chinese medicine and protein targets.

Deubiquitinating enzymes&#160;(DUBs) play a pivotal role in modulating ubiquitination homeostasis, with UCHL3 being an archetypal cysteine DUB intricately ...

Measuring Enzymatic Activity of Neurodevelopmental Disorder-Associated Deubiquitylating Enzymes via an In Vitro Ubiquitin Chain Cleavage Assay

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High-throughput Screening of Carbohydrate-degrading Enzymes Using Novel Insoluble Chromogenic Substrate Assay Kits

A Fluorescence-based Assay of Phospholipid Scramblase Activity

In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones

Detection of Protein Ubiquitination

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Quantifying Subcellular Ubiquitin-proteasome Activity in the Rodent Brain

Method for Measuring the Activity of Deubiquitinating Enzymes in Cell Lines and Tissue Samples

A Scalable, Cell-Based Method for the Functional Assessment of Ube3a Variants

In Vitro Analysis of E3 Ubiquitin Ligase Function

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology