This work was supported by NIH grants ARRA RO3 AI078145 and 1SC3GM113743 to RZ.

1. Cell Extract Preparation
<ol>
	<li>Grow the Leishmania cells in a sterile plastic bottle sealed with air tight cap at 26 &#186;C in a medium made of 1x M199 supplemented with 20 mM HEPES pH7.4, 100 U/ml penicillin, 100 &#181;g/ml streptomycin, 5 &#181;g/ml heme, 0.35 g/L NaCO2H, 0.1 mM adenine, and 2 &#181;g/ml biopterin without shaking. Harvest the cells by centrifugation at 1,500 g for 5 min at 4 &#186;C when they reach a cell density of 1-2 x 107/ml.</li>
	<li>Discard the supernatant with a pipette and wash the cells by resuspending the cell pellet with a serological pipet in half of the culture&#39;s volume of cold phosphate buffered saline (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, pH7.4). Dispose cell supernatants according to BL2 safety guidelines.</li>
	<li>Centrifuge cells again at 1,500 g for 5 min at 4 &#186;C. Discard the supernatant with a pipette. Proceed to the next step or snap freeze the cell pellet in liquid nitrogen for long term storage at -80 &#186;C (up to three months).</li>
	<li>Prepare 2x lysis buffer (0.5 M sucrose, 0.1 M TrisHCl, pH7.5, 2 mM EDTA, and 2x protease inhibitor cocktail) and keep it at 4 &#186;C on ice.</li>
	<li>Resuspend the cell pellet (fresh or frozen) in equal volume of 2x lysis buffer. Add 1x volume of glass beads. Vortex vigorously at 4 &#186;C for 10 min.</li>
	<li>Add 2 volumes of 1x lysis buffer and mix. Centrifuge cell extracts at 1,500 x g at 4 &#186;C for 10 min to pellet unbroken cells and nuclei.</li>
	<li>Transfer the supernatant with a pipet into a fresh cool centrifuge tube and keep cell extracts on ice until completion of the experiment.</li>
</ol>
2. Determine the Protein Concentration of the Cell Extract Using Protein Estimation Kit Such as Bicinchoninic Acid Assay
<ol>
	<li>Prepare the bicinchoninic acid (BCA) solution (1 ml/tube) by mixing the BCA and copper (II) sulfate in a ratio of 49:1 (v/v).</li>
	<li>Prepare the protein standards of 0, 10, 20, 30, 40, 50, and 60 &#181;g/ml by diluting a 10 mg/ml bovine serum albumin (BSA) stock solution into 1 ml aliquots of the BCA solution.</li>
	<li>Add 2 &#181;l of cells extracts in 1 ml of BCA solution in duplicates. Incubate standards and protein samples for 10 min in a pre-warmed 60 &#176;C water bath.</li>
	<li>Transfer samples to ice for 3 min. Measure the absorbance of the standards and the protein samples with a spectrophotometer at a wavelength of 562 nm.</li>
	<li>Calculate the protein concentration of the cell extracts using the BSA standard as a reference as described in the manufacturer&#39;s protocol. Dilute cell extracts to a protein concentration of 10 mg/ml with 1x lysis buffer.</li>
</ol>
3. Enzymatic Assay in 200 &#956;l per Tube
NOTE: Carry the following steps in a chemical hood.
<ol>
	<li>Test each sample in duplicate in a 15 ml conical tube. Prepare 20 &#956;l 1 M TrisHCl pH 7.5 per tube and keep it on ice. Prepare 2 ml of chloroform/methanol (1:1 (v/v); stopping solution) at RT for each tube.</li>
	<li>Pipet 20 &#956;l of 1 M TrisHCl pH 7.5 in each 15 ml conical tube on ice.</li>
	<li>Follow radiation safety guidelines from here on. Add the equivalent of 0.06 &#956;M (0.2 &#956;Ci) S-[Methyl-3H]adenosyl-L-methionine and 50 &#956;M cold SAM per tube for a total of 50.06 &#956;M of SAM. Add x &#956;l of cold water where x = 200-(20 (for buffer) + 20 (for cell extracts) + volume of cold and radioactive SAM) per tube.</li>
	<li>Transfer each conical tube to a pre-warmed 30 &#186;C water bath. Add to each tube 20 &#956;l of cell extracts (equivalent of 200 &#956;g of protein) to start the reaction. Incubate for the desired time (0 to 45 min).</li>
	<li>Stop the reaction by adding 2 ml of chloroform/methanol (1:1; v/v; stopping solution) to each tube. Transfer the conical tube to RT (20-25 &#186;C).</li>
</ol>
4. Lipid Extraction
NOTE: Carry the following steps in a chemical hood.
<ol>
	<li>Add 700 &#956;l of water to each tube containing the enzymatic reaction sample. Vortex vigorously for 30 sec. Centrifuge at 1,500 x g for 5 min at RT to separate the organic from the water phase.</li>
	<li>Transfer the lower organic phase into a new 15 ml conical tube with a pipette. Add 1 ml of water to each &#34;lower phase&#34; containing tube and vortex vigorously for 30 sec. Centrifuge again at 1,500 x g for 5 min to separate the organic from the water phase.</li>
	<li>Transfer the lower organic phase into a scintillation tube with a pipette. Dry samples under a stream of N2. Dispose the water phases containing the non-incorporated radioactive SAM and the radioactive conical tubes as per radiation guidelines.</li>
	<li>Add 2 ml/tube of scintillation liquid. Measure the incorporated radioactivity with a scintillation counter according to the manufacturers&#39; protocol and instrument&#39;s use.</li>
	<li>Calculate the enzymatic activity in nmol/mg protein using the following general equation: 
	cpm value x 103 x [total (radioactive and cold) concentration of SAM (mM)] x 5 specific activity of radioactive SAM (Ci/mmol) x [concentration of radioactive SAM (mM)] 
	NOTE: the above protocol can be altered for a SAM concentration dependent or a protein dependent PEMT assay. For SAM concentration dependent enzymatic assay, time is kept constant (15 min, which is in the linear range) and various amounts of cold SAM are added to the assay while for protein dependent PEMT assay, SAM concentration (we chose 0.05 mM) and time are kept constant (15 min). Also the pH of the buffer can be changed as needed if some PEMT enzymes have a different optimal pH value.</li>
</ol>

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No conflict of interest declared

This simple, quick PEMT assay allows the quantification of methylated forms of PE that results from the transfer of radioactive methyl groups from SAM onto PE using whole cell extract as a protein source. It is fast, sensitive, reproducible, and also suitable for purified enzymes 17. Monomethyl- or dimethyl-PE can be added to the assay if the methyltransferase of interest is specific to these substrates rather than to PE 12,13,18,19. If purified PEMT enzyme is used, PE can be added to the assay. A l...

Phosphatidylethanolamine methyltransferase (PEMT) enzymes catalyze the covalent attachment of one or more methyl groups using S-adenosylmethionine (SAM) as the methyl group donor onto PE, monomethyl-PE or dimethyl-PE to give monomethyl-PE, dimethyl-PE and/or phosphatidylcholine (PC). These enzymes are almost ubiquitous in animal cells and fungi. They can also be found in some plants 1 and approximately 10% of bacteria, particularly those that interact with eukaryotes 2.
PEMTs are relevant to the biology of the cell not only by contributing to the production of PC, which is the main lipid class in animal cells, but also by fulfilling other important cellular functions. In mammals, PEMTs are mainly expressed in the liver where they are required for normal secretion of very low-density lipoprotein and they also contribute to diet-induced obesity 3, atherosclerosis 4, and insulin resistance 5. Additionally, mammalian PEMT are also expressed in adipocytes, although to lower levels, and participate in fat deposition 6,7. PEMT role in cancer development 8, apoptosis 9, and cell growth 10 have also been demonstrated. In bacteria, PEMT enzymes have been shown to be important for normal cell growth 2, virulence 2, and symbiosis with the host plant 11.
The goal and rationale of the present protocol is to measure PEMT activity from whole cell extracts without the need to purify the enzyme. Two distinct protocols have been developed to measure PEMT activity. The first and most common one measures the transfer of tritiated methyl group from radioactive SAM onto PE, which is the topic of this article. This protocol has been originally developed to measure PEMT activity from yeast 12 and mammalian cells (liver) 13 to gain an understanding of PC biosynthesis in these cells as well as to determine the specificity of these enzymes. Later, this technique has been applied to other cell types such as bacteria 2 (using a basic pH value for the assay though 15) and protozoan parasites 14. This technique can be used with whole cell extracts as well as purified enzyme, and can potentially be applied to any cell extract system. A non radioactive assay has also been designed that relies on the enzymatic quantification of S-adenosylhomocysteine, the transmethylation product of SAM 16. The latter assay may be more convenient as it does not involve radioactivity but it is only suitable for purified enzymes.

<table><tbody><tr><td>S-[Methyl-&lt;sup&gt;3&lt;/sup&gt;H]adenosyl-L-methionine (specific activity of 5-15 Ci/mMole)</td><td>Perkin Elmer</td><td>NET155050UC</td><td>Aliquot the reagent and freeze at -20 &amp;deg;C; follow radiation safety guidelines while using this reagent</td></tr><tr><td>Protease inhibitor cocktail</td><td>Roche Life Sciences</td><td>11836170001</td><td>dilute it fresh&amp;nbsp;</td></tr><tr><td>Glass beads, acid washed, 425-600 mm</td><td>Sigma Aldrich</td><td>G8772</td><td></td></tr><tr><td>Bicinchoninic acid solution</td><td>Sigma Aldrich</td><td>B9643</td><td></td></tr><tr><td>Copper (II) sulfate</td><td>Sigma Aldrich</td><td>C2284</td><td></td></tr><tr><td>Scintillation counter MicroBeta2 with 1-detector</td><td>Perkin Elmer&amp;nbsp;</td><td>2450-0010</td><td></td></tr><tr><td>Spectrophotometer Biomate 3</td><td>Thermo Scientific</td><td>840208300</td><td></td></tr><tr><td>BSA stock solution (10 mg/ml)</td><td>New England Biolabs</td><td>B9001S</td><td></td></tr><tr><td>Scintillation liquid&amp;nbsp;</td><td>Research Product International Corp</td><td>111198</td><td></td></tr><tr><td>S-(5&#039;-Adenosyl)-L-methionine chloride (hydrochloride)&amp;nbsp;</td><td>Cayman Chemicals</td><td>13956</td><td>dilute the reagent in 20 mM HCl and freeze aliquots at -80 &amp;deg;C&amp;nbsp;</td></tr></tbody></table>

in vitro assay to measure phosphatidylethanolamine methyltransferase activity

Phosphatidylethanolamine methyltransferases are biosynthetic enzymes that catalyze the transfer of one or more methyl group(s) from S-adenosyl-L-methionine onto phosphatidylethanolamine, monomethyl-phosphatidylethanolamine, or dimethyl-phosphatidylethanolamine to give either monomethyl-phosphatidylethanolamine, dimethyl-phosphatidylethanolamine or phosphatidylcholine. These enzymes are ubiquitous in animal cells, fungi, and are also found in approximately 10% of bacteria. They fulfill various important functions in cell physiology beyond their direct role in lipid metabolism such as in insulin resistance, diabetes, atherosclerosis, cell growth, or virulence. The present manuscript reports on a simple cell-free enzymatic assay that measures the transfer of tritiated methyl group(s) from S-[Methyl-3H]adenosyl-L-methionine onto phosphatidylethanolamine using whole cell extracts as an enzyme source. The resulting methylated forms of phosphatidylethanolamine are hydrophobic and thus, can be separated from water soluble S-[Methyl-3H]adenosyl-L-methionine by organic extraction. This assay can potentially be applied to any other cell types and used to test inhibitors/drugs specific to a phosphatidylethanolamine methyltransferase of interest without the need to purify the enzyme.

Figure 1 shows a time dependant PEMT assay, which was carried out with Leishmania whole cell extract as an enzyme source using endogenous PE as a substrate. The amount of radioactivity in the organic phase was quantified by scintillation counting. The resulting numbers were utilized to calculate the amount of tritiated methyl groups transferred onto PE. The PEMT activity was linear for approximately 20 min. It then reached a plateau at around 30 min, after which ...

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In Vitro Assay to Measure Phosphatidylethanolamine Methyltransferase Activity

The present report describes an in vitro enzymatic assay to measure phosphatidylethanolamine methyltransferase activity using Leishmania cell extracts. This assay is based on the transfer of a radioactive methyl group from S-[Methyl-3H]adenosyl-L-methionine onto endogenous phosphatidylethanolamine.

In Vitro Assay to Measure Phosphatidylethanolamine Methyltransferase Activity

Phosphatidylethanolamine methyltransferases are biosynthetic enzymes that catalyze the transfer of one or more methyl group(s) from ...

in-vitro-assay-to-measure-phosphatidylethanolamine-methyltransferase

Research

JoVE Journal

Biology

9.8K Views.  St John's University. The present report describes an in vitro enzymatic assay to measure phosphatidylethanolamine methyltransferase activity using Leishmania cell extracts. This assay is based on the transfer of a radioactive methyl group from S-[Methyl-3H]adenosyl-L-methionine onto endogenous phosphatidylethanolamine. 

Video: In Vitro Assay to Measure Phosphatidylethanolamine Methyltransferase Activity

Defining Substrate Specificities for Lipase and Phospholipase Candidates

Microorganisms produce a wide spectrum of (phospho)lipases that are secreted in order to make external substrates available for the organism. Alternatively, other (phospho)lipases may be physically associated with the producing organism causing a turnover of intrinsic lipids and frequently giving rise to a remodeling of the cellular membranes. Although potential (phospho)lipases can be predicted with a number of algorithms when the gene/protein sequence is available, experimental proof of the enzyme activities, substrate specificities, and potential physiological functions has frequently not been obtained. This manuscript describes the optimization of assay conditions for prospective (phospho)lipases with unknown substrate specificities and how to employ these optimized conditions in the search for the natural substrate of a respective (phospho)lipase. Using artificial chromogenic substrates, such as p-nitrophenyl derivatives, may help to detect a minor enzymatic activity for a predicted (phospho)lipase under standard conditions. Having encountered such a minor enzymatic activity, the distinct parameters of an enzyme assay can be varied in order to obtain a more efficient hydrolysis of the artificial substrate. After having determined the conditions under which an enzyme works well, a variety of potential natural substrates should be assayed for their degradation, a process that can be followed employing distinct chromatographic methods. The definition of substrate specificities for new enzymes, often provides hypotheses for a potential physiological role of these enzymes, which then can be tested experimentally. Following these guidelines, we were able to identify a phospholipase C (SMc00171) that degrades phosphatidylcholine to phosphocholine and diacylglycerol, in a crucial step for the remodeling of membranes in the bacterium Sinorhizobium meliloti upon phosphorus-limiting conditions of growth. For two predicted patatin-like phospholipases (SMc00930 and SMc01003) of the same organism, we could redefine their substrate specificities and clarify that SMc01003 is a diacylglycerol lipase.

Many predicted (phospho)lipases are poorly characterized with regard to their substrate specificities and physiological functions. Here we provide a protocol to optimize enzyme activities, search for natural substrates, and propose physiological functions for these enzymes.

Microorganisms produce a wide spectrum of (phospho)lipases that are secreted in order to make external substrates available for the organism. ...

Biochemistry

In vitro tRNA Methylation Assay with the Entamoeba histolytica DNA and tRNA Methyltransferase Dnmt2 (Ehmeth) Enzyme

Protozoan parasites are among the most devastating infectious agents of humans responsible for a variety of diseases including amebiasis, which is one of the three most common causes of death from parasitic disease. The agent of amebiasis is the amoeba parasite Entamoeba histolytica that exists under two stages: the infective cyst found in food or water and the invasive trophozoite living in the intestine. The clinical manifestations of amebiasis range from being asymptomatic to colitis, dysentery or liver abscesses. E. histolytica is one of the rare unicellular parasite with 5-methylcytosine (5mC) in its genome. 1, 2 It contains a single DNA methyltransferase, Ehmeth, that belongs to the Dnmt2 family. 2 A role for Dnmt2 in the control of repetitive elements has been established in E. histolytica, 3 Dictyostelium discoideum 4,5 and Drosophila. 6 Our recent work has shown that Ehmeth methylates tRNAAsp, and this finding indicates that this enzyme has a dual DNA/tRNAAsp methyltransferase activity. 7 This observation is in agreement with the dual activity that has been reported for D. discoideum and D. melanogaster. 8 The functional significance of the DNA/tRNA specificity of Dnmt2 enzymes is still unknown. To address this question, a method to determine the tRNA methyltransferase activity of Dnmt2 proteins was established. In this video, we describe a straightforward approach to prepare an adequate tRNA substrate for Dnmt2 and a method to measure its tRNA methyltransferase activity.

In vitro tRNA Methylation Assay with the Entamoeba histolytica DNA and tRNA Methyltransferase Dnmt2 Ehmeth Enzyme

This protocol describes the preparation of a synthetic tRNA substrate for the Entamoeba histolytica DNA/tRNA methyltransferase 2 (Dnmt2) homolog Ehmeth and the measure of its methyltransferase activity. This experimental approach can be used for investigating the activity of other Dnmt2 proteins.

Protozoan parasites are among the most devastating infectious agents of humans responsible for a variety of diseases including amebiasis, which is one of ...

Immunology and Infection

Antibody-Free Assay for RNA Methyltransferase Activity Analysis

There are more than 100 chemically distinct modifications of RNA, two thirds of which consist of methylations. Interest in RNA modifications, and especially methylations, has re-emerged due to the important roles played by the enzymes that write and erase them in biological processes relevant to disease and cancer. Here, a sensitive in vitro assay for accurate analysis of RNA methylation writer activity on synthetic or in vitro transcribed RNAs is provided. This assay uses a tritiated form of S-adenosyl-methionine, resulting in direct labeling of methylated RNA with tritium. The low energy of tritium radiation makes the method safe, and pre-existing methods of tritium signal amplification, make it possible to quantify and to visualize the methylated RNA without the use of antibodies, which are commonly prone to artifacts. While this method is written for RNA methylation, few tweaks make it applicable to the study of other RNA modifications that can be radioactively labeled, such as RNA acetylation with 14C acetyl coenzyme A. Overall, this assay allows to quickly assess RNA methylation conditions, inhibition with small molecule inhibitors, or the effect of RNA or enzyme mutants, and provides a powerful tool to validate and expand results obtained in cells.

Here, an antibody-free in vitro assay for direct analysis of methyltransferase activity on synthetic or in vitro transcribed RNA is described.

There are more than 100 chemically distinct modifications of RNA, two thirds of which consist of methylations. Interest in RNA modifications, and ...

Genetics

Acyl-PEGyl Exchange Gel Shift Assay for Quantitative Determination of Palmitoylation of Brain Membrane Proteins

Activity-dependent alterations in the levels of synaptic AMPA receptors (AMPARs) within the postsynaptic density (PSD) is thought to represent a cellular mechanism for learning and memory. Palmitoylation regulates localization and function of many synaptic proteins including AMPA-Rs, auxiliary factors and synaptic scaffolds in an activity-dependent manner. We identified the synapse differentiation induced gene (SynDIG) family of four genes (SynDIG1-4) encoding brain-specific transmembrane proteins that associate with AMPARs and regulate synapse strength. SynDIG1 is palmitoylated at two cysteine residues located at positions 191 and 192 in the juxta-transmembrane region important for activity-dependent excitatory synapse development. Here, we describe an innovative biochemical approach, the acyl-PEGyl exchange gel shift (APEGS) assay, to investigate the palmitoylation state of any protein of interest and demonstrate its utility with the SynDIG family of proteins in mouse brain lysates.

Palmitoylation entails the incorporation of a 16-carbon palmitate moiety to cysteine residues of target proteins in a reversible manner. Here, we describe a biochemical approach, the acyl-PEGyl exchange gel shift (APEGS) assay, to investigate the palmitoylation state of any protein of interest in mouse brain lysates.

Activity-dependent alterations in the levels of synaptic AMPA receptors (AMPARs) within the postsynaptic density (PSD) is thought to represent a cellular ...

Click-Chemistry Based Fluorometric Assay for Apolipoprotein N-acyltransferase from Enzyme Characterization to High-Throughput Screening

Lipoproteins from proteobacteria are posttranslationally modified by fatty acids derived from membrane phospholipids by the action of three integral membrane enzymes, resulting in triacylated proteins. The first step in the lipoprotein modification pathway involves the transfer of a diacylglyceryl group from phosphatidylglycerol onto the prolipoprotein, resulting in diacylglyceryl prolipoprotein. In the second step, the signal peptide of prolipoprotein is cleaved, forming an apolipoprotein, which in turn is modified by a third fatty acid derived from a phospholipid. This last step is catalyzed by apolipoprotein N-acyltransferase (Lnt). The lipoprotein modification pathway is essential in most &#947;-proteobacteria, making it a potential target for the development of novel antibacterial agents. Described here is a sensitive assay for Lnt that is compatible with high-throughput screening of small inhibitory molecules. The enzyme and substrates are membrane-embedded molecules; therefore, the development of an in vitro test is not straightforward. This includes the purification of the active enzyme in the presence of detergent, the availability of alkyne-phospholipids and diacylglyceryl peptide substrates, and the reaction conditions in mixed micelles. Furthermore, in order to use the activity test in a high-throughput screening (HTS) setup, direct readout of the reaction product is preferred over coupled enzymatic reactions. In this fluorometric enzyme assay, the alkyne-triacylated peptide product is rendered fluorescent through a click-chemistry reaction and detected in a multiwell plate format. This method is applicable to other acyltransferases that use fatty acid-containing substrates, including phospholipids and acyl-CoA.

Presented here is a sensitive fluorescence assay to monitor apolipoprotein N-acyltransferase activity using diacylglyceryl peptide and alkyne-phospholipids as substrates with click-chemistry.

Lipoproteins from proteobacteria are posttranslationally modified by fatty acids derived from membrane phospholipids by the action of three integral ...

Continuous Fluorescence-Based Endonuclease-Coupled DNA Methylation Assay to Screen for DNA Methyltransferase Inhibitors

DNA methylation, a form of epigenetic gene regulation, is important for normal cellular function. In cells, proteins called DNA methyltransferases (DNMTs) establish and maintain the DNA methylation pattern. Changes to the normal DNA methylation pattern are linked to cancer development and progression, making DNMTs potential cancer drug targets. Thus, identifying and characterizing novel small molecule inhibitors of these enzymes is of great importance. This paper presents a protocol that can be used to screen for DNA methyltransferase inhibitors. The continuous coupled kinetics assay allows for initial velocities of DNA methylation to be determined in the presence and absence of potential small molecule inhibitors. The assay uses the methyl-sensitive endonuclease Gla I to couple methylation of a hemimethylated DNA substrate to fluorescence generation.
This continuous assay allows for enzyme activity to be monitored in real time. Conducting the assay in small volumes in microtiter plates reduces the cost of reagents. Using this assay, a small example screen was conducted for inhibitors of DNMT1, the most abundant DNMT isozyme in humans. The highly substituted anthraquinone natural product, laccaic acid A, is a potent, DNA-competitive inhibitor of DNMT1. Here, we examine three potential small molecule inhibitors &#8212; anthraquinones or anthraquinone-like molecules with one to three substituents &#8212; at two concentrations to describe the assay protocol. Initial velocities are used to calculate the percent activity observed in the presence of each molecule. One of three compounds examined exhibits concentration-dependent inhibition of DNMT1 activity, indicating that it is a potential inhibitor of DNMT1.

DNA methyltransferases are potential cancer drug targets. Here, a protocol is presented to assess small molecules for DNA methyltransferase inhibition. This assay utilizes an endonuclease to couple DNA methylation to fluorescence generation and allows for enzyme activity to be monitored in real time.&#160;

DNA methylation, a form of epigenetic gene regulation, is important for normal cellular function. In cells, proteins called DNA methyltransferases (DNMTs) ...

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to measure protein phosphorylation cannot preserve the heterogeneity in phosphorylation across individual proteins. The single-molecule pull-down (SiMPull) assay was developed to investigate the composition of macromolecular complexes via immunoprecipitation of proteins on a glass coverslip followed by single-molecule imaging. The current technique is an adaptation of SiMPull that provides robust quantification of the phosphorylation state of full-length membrane receptors at the single-molecule level. Imaging thousands of individual receptors in this way allows for quantifying protein phosphorylation patterns. The present protocol details the optimized SiMPull procedure, from sample preparation to imaging. Optimization of glass preparation and antibody fixation protocols further enhances data quality. The current protocol provides code for the single-molecule data analysis that calculates the fraction of receptors phosphorylated within a sample. While this work focuses on phosphorylation of the epidermal growth factor receptor (EGFR), the protocol can be generalized to other membrane receptors and cytosolic signaling molecules.

The present protocol describes sample preparation and data analysis to quantify protein phosphorylation using an improved single-molecule pull-down (SiMPull) assay.

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to ...

A Purification and In Vitro Activity Assay for a (p)ppGpp Synthetase from Clostridium difficile

Kinase and pyrophosphokinase enzymes transfer the gamma phosphate or the beta-gamma pyrophosphate moiety from nucleotide triphosphate precursors to substrates to create phosphorylated products. The use of &#947;-32-P labeled NTP precursors allows simultaneous monitoring of substrate utilization and product formation by radiography. Thin layer chromatography (TLC) on cellulose plates allows rapid separation and sensitive quantification of substrate and product. We present a method for utilizing the thin-layer chromatography to assay the pyrophosphokinase activity of a purified (p)ppGpp synthetase. This method has previously been used to characterize the activity of cyclic nucleotide and dinucleotide synthetases and is broadly suitable for characterizing the activity of any enzyme that hydrolyzes a nucleotide triphosphate bond or transfers a terminal phosphate from a phosphate donor to another molecule.

A Purification and In Vitro Activity Assay for a pppGpp Synthetase from Clostridium difficile

Here, we describe a method for purifying histidine-tagged pyrophosphokinase enzymes and utilizing thin layer chromatography of radiolabelled substrates and products to assay for the enzymatic activity in vitro. The enzyme activity assay is broadly applicable to any kinase, nucleotide cyclase, or phosphor-transfer reaction whose mechanism includes nucleotide triphosphate hydrolysis.

Kinase and pyrophosphokinase enzymes transfer the gamma phosphate or the beta-gamma pyrophosphate moiety from nucleotide triphosphate precursors to ...

Measuring In Vitro ATPase Activity for Enzymatic Characterization

Adenosine triphosphate-hydrolyzing enzymes, or ATPases, play a critical role in a diverse array of cellular functions. These dynamic proteins can generate energy for mechanical work, such as protein trafficking and degradation, solute transport, and cellular movements. The protocol described here is a basic assay for measuring the in vitro activity of purified ATPases for functional characterization. Proteins hydrolyze ATP in a reaction that results in inorganic phosphate release, and the amount of phosphate liberated is then quantitated using a colorimetric assay. This highly adaptable protocol can be adjusted to measure ATPase activity in kinetic or endpoint assays. A representative protocol is provided here based on the activity and requirements of EpsE, the AAA+ ATPase involved in Type II Secretion in the bacterium Vibrio cholerae. The amount of purified protein needed to measure activity, length of the assay and the timing and number of sampling intervals, buffer and salt composition, temperature, co-factors, stimulants (if any), etc. may vary from those described here, and thus some optimization may be necessary. This protocol provides a basic framework for characterizing ATPases and can be performed quickly and easily adjusted as necessary.

Measuring In Vitro ATPase Activity for Enzymatic Characterization

We describe a basic protocol for quantitating in vitro ATPase activity. This protocol can be optimized based on the level of activity and requirements for a given purified ATPase.

Adenosine triphosphate-hydrolyzing enzymes, or ATPases, play a critical role in a diverse array of cellular functions. These dynamic proteins can generate ...

Phospholipase Activity Assay: A Gel Diffusion Assay to Determine Phospholipase Activity in Crude Venom Extract from Anthopleura dowii

Source: Ram&#237;rez-Carreto, S., et al., <a href="https://www.jove.com/v/63630">Identification of Hemolytic and Phospholipase Activity in Crude Extracts from Sea Anemones by Straightforward Bioassays.</a> J. Vis. Exp. (2022)
In this video, we demonstrate an assay to establish the presence of phospholipase in the crude venom extract from Anthopleura dowii&#8212;a marine sea anemone. The assay utilizes an agarose gel diffusion technique, in which the enzyme phospholipase diffuses and breaks down phospholipids incorporated in the solid media in a radial manner.

Source: Ram&#237;rez-Carreto, S., et al., Identification of Hemolytic and Phospholipase Activity in Crude Extracts from Sea Anemones by Straightforward ...

In Vitro Assay to Measure Phosphatidylethanolamine Methyltransferase Activity

Summary

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Chapters in this video

Defining Substrate Specificities for Lipase and Phospholipase Candidates

In vitro tRNA Methylation Assay with the Entamoeba histolytica DNA and tRNA Methyltransferase Dnmt2 (Ehmeth) Enzyme

Antibody-Free Assay for RNA Methyltransferase Activity Analysis

Acyl-PEGyl Exchange Gel Shift Assay for Quantitative Determination of Palmitoylation of Brain Membrane Proteins

Click-Chemistry Based Fluorometric Assay for Apolipoprotein N-acyltransferase from Enzyme Characterization to High-Throughput Screening

Continuous Fluorescence-Based Endonuclease-Coupled DNA Methylation Assay to Screen for DNA Methyltransferase Inhibitors

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

A Purification and In Vitro Activity Assay for a (p)ppGpp Synthetase from Clostridium difficile

Measuring In Vitro ATPase Activity for Enzymatic Characterization

Phospholipase Activity Assay: A Gel Diffusion Assay to Determine Phospholipase Activity in Crude Venom Extract from Anthopleura dowii