The construct and recombinant adenovirus for expressing cytosol-specific roGFP in cells were generated in the laboratory of Paul T. Schumacker, PhD, Freiberg School of Medicine, Northwestern University, and ViraQuest Inc., respectively. This study was supported by the Center for Studies of Host Response to Cancer Therapy grant P20GM109005 through the NIH National Institute of General Medical Sciences Centers of Biomedical Research Excellence (COBRE NIGMS), National Institute of General Medical Sciences Systems Pharmacology and Toxicology Training Program grant T32 GM106999, UAMS Foundation/Medical Research Endowment Award AWD00053956, UAMS Year-End Chancellor&#8217;s Awards AWD00053484. The flow cytometry core facility was supported in part by the Center for Microbial Pathogenesis and Host Inflammatory Responses grant P20GM103625 through the COBRE NIGMS. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. ATA was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) 2214-A scholarship.

NOTE: This protocol was optimized for 70%&#8211;80% confluent MDA-MB-231 cells. For other cell lines, the number of cells and multiplicity of infection (MOI) should be reoptimized.
1. Preparation of cells (day 1)
<ol>
	<li>Maintain MDA-MB-231 cell line in 75 cm2 flasks with 10 mL of Dulbecco&#8217;s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37 &#176;C in a 5% CO2 humidified atmosphere. 
	NOTE: DMEM supplemented with 10% FBS, 37 &#176;C, and a 5% CO2 humidified atmosphere are used for all attachment and treatment incubations throughout the entire protocol.</li>
	<li>Prepare the MDA-MB-231 cells for experiment.
	<ol>
		<li>Aspirate the medium within the flask, detach the cells with 2 mL of 0.25% trypsin-EDTA solution for 2 min, and inactivate the trypsin activity with 6 mL of complete medium (DMEM with 10% FBS). Centrifuge the cells at 150 x g for 5 min. Aspirate the supernatant and suspend the cells in 5 mL of complete medium.</li>
		<li>Mix an equal volume cell suspension and 0.4% trypan blue. Take 10 &#181;L of this mixture and count the cells with the automated cell counter. 
		NOTE: A Coulter counter or a hemocytometer can also be used for cell counting.</li>
		<li>Seed the cells into a 6 well plate for flow cytometry analyses and seed 150,000 cells in 1 mL of medium per well. Wait 16 h for cell attachment.</li>
		<li>Seed the cells into a 4 well chamber slide for fluorescent imaging and seed 25,000 cells in 0.5 mL of medium per well. Wait 16 h for cell attachment. 
		NOTE: Seed control wells in addition to treatment wells. Use one of the control wells to determine cell number (optional: if the attachment period for the cells is shorter than the doubling time, cell number can be assumed to be the same as the seeding density) and the other for a noninfected control (0 MOI).</li>
	</ol>
	</li>
</ol>
2. Adenoviral roGFP transduction (day 2 and 3)
CAUTION: Adenoviruses can cause diseases. While transducing the cells, use filtered tips and decontaminate tips, Pasteur pipettes, and microcentrifuge tubes with 10% bleach.
NOTE: This protocol was demonstrated with cytosol-specific roGFP, but other cellular compartments (e.g., mitochondria or mitochondrial intermembrane space) can be targeted with this same protocol.
<ol>
	<li>Generate a dose-response curve for the MOI to obtain the highest transduction efficiency by calculating the volume of adenovirus (mL) required for each MOI value for MDA-MB-231 cell line (Table 1): 
	<img alt="Equation 1" src="/files/ftp_upload/61229/61229equ01.jpg" /> 
	NOTE: Functional titer of each batch of adenoviral stock, which is expressed as plaque forming unit (PFU) per mL, is provided by the company. The optimum MOI for transduction differs between cell types. For most mammalian cells, the optimum MOI range is between 10 and 300. According to the cellular response, MOI values should be recalculated (e.g., MOI range should be reduced if cells have cytotoxic response, or range should be increased if cells have low transduction efficiency).</li>
	<li>Make 1:100 dilution of 6 x 1010 PFU/mL adenoviral roGFP solution with cell culture medium (DMEM with 10% FBS) for reliable pipetting.</li>
	<li>Pipette and add 0.0125 mL (12.5 &#181;L), 0.025 mL (25 &#181;L), 0.05 mL (50 &#181;L) of adenoviral roGFP dilution into each well of the 6 well plate in order to transduce the 150,000 cells with 50, 100, and 200 MOI respectively for flow cytometry analysis (Table 1).</li>
	<li>Pipette and add 0.0042 mL (4.2 &#181;L) of adenoviral roGFP dilution in the 4-chamber slide wells to transduce 25,000 cells with 100 MOI for fluorescence imaging (Table 1). 
	NOTE: A minimal amount of medium should be used in the wells to ensure the highest interaction between the adenoviral roGFP construct and cells. The serum content of the culture medium may need to be decreased for different cell lines because high levels of serum can negatively affect transduction efficiency in some cell types.</li>
	<li>Incubate cells for 16&#8211;24 h under the cell maintenance conditions. The next day (day 3), change the medium to cell culture medium (DMEM with 10% FBS) to allow cell recovery for an additional 24 h. Visualize cells under a microscope to assess their morphology; cells can express roGFP even if they have morphological changes. 
	NOTE: On day 3, cells should start to express roGFP; therefore, transduction efficiency can be monitored using fluorescence microscopy (filters with ex. 488/em. 525). To obtain consistent assay results, be aware of and document the morphological changes under the phase contrast microscope and observe morphology while evaluating transduction efficiency.</li>
	<li>Construct a dose response curve using the 50, 100 and 200 MOI samples prepared in step 2.3 and their transduction efficiency results obtained from flow cytometry analysis (steps 3.1 and 4.1). Assess optimal transduction efficiency with documentation of morphological changes (step 2.5) and the dose-response curve of MOI. 
	NOTE: Although more than 98% of the cell population at 100 MOI and 200 MOI express roGFP (see representative results), 200 MOI group showed substantial changes in cell morphology of MDA-MB-231 cells. Consequently, the most efficacious MOI for MDA-MB-231 cells was determined to be 100 MOI.</li>
	<li>After optimal MOI (here, 100 MOI) was chosen for MDA-MB-231 cell line, conduct experiment with test materials (10 &#181;M H2O2 and its vehicle 0.1% deionized water).
	<ol>
		<li>Prepare and seed the cells according to section 1. Using the adenoviral transduction volume for 100 MOI calculated in step 2.1, repeat steps 2.2&#8722;2.4 for 100 MOI adenoviral transduction of cells. Then incubate the plate and chamber slides according to step 2.5.</li>
	</ol>
	</li>
</ol>
3. Acquisition of CyS/CySS balance
<ol>
	<li>Flow cytometry (day 4)
	<ol>
		<li>On day 4, incubate cells from step 2.7.1 with 10 &#181;M H2O2 for 1 h. 
		NOTE: 10 &#181;M H2O2 was used as the test substance and 0.1% deionized water was used as vehicle treatment in this protocol. Other oxidizing agents can be used as positive controls here.</li>
		<li>Aspirate media from the 6 well plate, replace with 750 &#181;L of 0.25% trypsin-EDTA solution and wait for 2 min for cells to detach. Inactivate trypsin with 2 mL of complete medium (DMEM with 10% FBS) and collect the volume into 15 mL conical tubes.</li>
		<li>Centrifuge the tubes at 150 x g for 5 min at 4&#186;C. Discard supernatant and suspend the cells in 500 &#181;L of phosphate-buffered saline (PBS).</li>
		<li>Repeat step 3.1.3</li>
		<li>Filter the cell suspensions into flow cytometry-compatible tubes using 40 &#181;m mesh. Keep the tubes on ice and away from the light and follow step 4.1 for data analysis.</li>
	</ol>
	</li>
	<li>Microscopic imaging (day 4)
	<ol>
		<li>On day 4, treat cells with 10 &#181;M H2O2, acquire images immediately (time point 0) and 1 h after treatment and follow step 4.2 for data analysis.</li>
	</ol>
	</li>
</ol>
4. Data analysis
<ol>
	<li>Flow cytometry quantification
	<ol>
		<li>Set flow cytometry method for 3 different analyses via sample aquisition software (see Table of Materials): forward scatter (FCS) on x-axis and side scatter (SSC) on y-axis to assess cell size and complexity of cells (SSC can be used for rough identification of dead and live cells); ex. 488 nm/em. 525 nm (fluorescein isothiocyanate [FITC]) bandpass filter on x-axis and SSC on y-axis to assess CyS-roGFP; ex. 405 nm/em. 525 nm (Brilliant Violet 510 [BV510]) bandpass filter on x-axis and SSC on y-axis to assess CySS-roGFP.</li>
		<li>Acquire 0 MOI control&#160;and visualize cells with sample acquisition software. Repeat this step for remaining samples (50, 100, 200 MOI groups and later on 10 &#181;M H2O2 treated cells and vehicle treated cells). Save the files for data analysis.</li>
		<li>Open data analysis software (see Table of Materials) and open 0 MOI sample file. Assess cell population of interest (Gate 1). Set up the following gatings to minimize background fluorescence for ex. 488 nm/em. 525 nm (Gate 2) and ex. 405 nm/em. 525 nm (Gate 3) bandpass filters with the noninfected (0 MOI) control cells.</li>
		<li>Open 50, 100, and 200 MOI sample files within data analysis software to assess the dose-response curve. Analyze mean fluorescence intensities with Gates 2 and 3 for each sample. Repeat this step for test samples (10 &#181;M H2O2 treated cells and vehicle treated cells).</li>
		<li>Calculate the mean fluorescent intensity ratio between oxidized versus reduced forms of roGFP with the following equation.</li>
	</ol>
	</li>
</ol>
<img alt="Equation 2" src="/files/ftp_upload/61229/61229equ02.jpg" />
<ol start="2">
	<li>Image assessment
	<ol>
		<li>Use a microscope that contains fluorescence filters for CyS-roGFP and CySS-roGFP (ex. 488 nm/em. 525 nm and ex. 405 nm/em. 525 nm filters, respectively).</li>
		<li>In each well of the chamber slide, pick 4 random areas to acquire images, using the 4x objective to visualize larger areas. 
		NOTE: 20x objective can also be used for image displays.</li>
		<li>Open the image with ImageJ software11. Apply Analyze | Measure commands for each image and use the equation in step 4.1.5 to quantify the data. 
		NOTE: Quantification of the images is ratiometric; therefore, the protocol does not include subtraction of background. However, to be able to compare images, brightness, contrast, and saturation must be the same for each image. Statistical significance was assessed with one-way analysis of variance (ANOVA) and Tukey&#8217;s post hoc test.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Sies, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oxidative+stress:+A+concept+in+redox+biology+and+medicine.">Oxidative stress: A concept in redox biology and medicine.</a> Redox Biology. 4, 180-183 (2015).</li><li>Jones, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Redefining+Oxidative+Stress.">Redefining Oxidative Stress.</a> Antioxidants &amp; Redox Signalling. 8 (9-10), (2006).</li><li>Pizzino, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Oxidative+Stress:+Harms+and+Benefits+for+Human+Health.">Oxidative Stress: Harms and Benefits for Human Health.</a> Oxidative Medicine and Cellular Longevity. 20117, 8416763 (2017).</li><li>Go, Y. M., Jones, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thiol/disulfide+redox+states+in+signaling+and+sensing.">Thiol/disulfide redox states in signaling and sensing.</a> Critical Reviews in Biochemistry and Molecular Biology. 48 (2), 173-191 (2013).</li><li>Hansen, J. M., Go, Y., Jones, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+and+Mitochondrial+Compartmentation+of+Oxidative+Stress+and+Redox+Signaling.">Nuclear and Mitochondrial Compartmentation of Oxidative Stress and Redox Signaling.</a> Annual Review of Pharmacology and Toxicology. 46 (1), 215-234 (2006).</li><li>Meyer, A. J., Dick, T. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescent+protein-based+redox+probes.">Fluorescent protein-based redox probes.</a> Antioxidants and Redox Signaling. 13 (5), 621-650 (2010).</li><li>Dooley, C. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imaging+dynamic+redox+changes+in+mammalian+cells+with+green+fluorescent+protein+indicators.">Imaging dynamic redox changes in mammalian cells with green fluorescent protein indicators.</a> Journal of Biological Chemistry. 279 (21), 22284-22293 (2004).</li><li>Bj&#246;rnberg, O., &#216;stergaard, H., Winther, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+intracellular+redox+conditions+using+GFP-based+sensors.">Measuring intracellular redox conditions using GFP-based sensors.</a> Antioxidants and Redox Signaling. 8 (3-4), 354-361 (2006).</li><li>Bhaskar, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reengineering+Redox+Sensitive+GFP+to+Measure+Mycothiol+Redox+Potential+of+Mycobacterium+tuberculosis+during+Infection.">Reengineering Redox Sensitive GFP to Measure Mycothiol Redox Potential of Mycobacterium tuberculosis during Infection.</a> PLoS Pathogens. 10 (1), 1003902 (2014).</li><li>Loor, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitochondrial+oxidant+stress+triggers+cell+death+in+simulated+ischemia-reperfusion.">Mitochondrial oxidant stress triggers cell death in simulated ischemia-reperfusion.</a> Biochimica et Biophysica Acta - Molecular Cell Research. 1813 (7), 1382-1394 (2011).</li><li>Schneider, C. A., Rasband, W. S., Eliceiri, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NIH+Image+to+ImageJ:+25+years+of+image+analysis.">NIH Image to ImageJ: 25 years of image analysis.</a> Nature Methods. 9 (7), 671-675 (2012).</li><li>Loor, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Menadione+triggers+cell+death+through+ROS-dependent+mechanisms+involving+PARP+activation+without+requiring+apoptosis.">Menadione triggers cell death through ROS-dependent mechanisms involving PARP activation without requiring apoptosis.</a> Free Radical Biology and Medicine. 49 (12), 1925-1936 (2010).</li><li>Esposito, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Redox-sensitive+GFP+to+monitor+oxidative+stress+in+neurodegenerative+diseases.">Redox-sensitive GFP to monitor oxidative stress in neurodegenerative diseases.</a> Reviews in the Neurosciences. 28 (2), 133-144 (2017).</li><li>Meyer, A. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Redox-sensitive+GFP+in+Arabidopsis+thaliana+is+a+quantitative+biosensor+for+the+redox+potential+of+the+cellular+glutathione+redox+buffer.">Redox-sensitive GFP in Arabidopsis thaliana is a quantitative biosensor for the redox potential of the cellular glutathione redox buffer.</a> Plant Journal. 52 (5), 973-986 (2007).</li><li>Galvan, D. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+in+vivo+mitochondrial+redox+assessment+confirms+enhanced+mitochondrial+reactive+oxygen+species+in+diabetic+nephropathy.">Real-time in vivo mitochondrial redox assessment confirms enhanced mitochondrial reactive oxygen species in diabetic nephropathy.</a> Kidney International. 92 (5), 1282-1287 (2017).</li><li>Swain, L., Nanadikar, M. S., Borowik, S., Zieseniss, A., Katschinski, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transgenic+organisms+meet+redox+bioimaging:+One+step+closer+to+physiology.">Transgenic organisms meet redox bioimaging: One step closer to physiology.</a> Antioxidants and Redox Signaling. 29 (6), 603-612 (2018).</li><li>Gutscher, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proximity-based+protein+thiol+oxidation+by+H2O2-scavenging+peroxidases.">Proximity-based protein thiol oxidation by H2O2-scavenging peroxidases.</a> Journal of Biological Chemistry. 284 (46), 31532-31540 (2009).</li><li>Morgan, B., Sobotta, M. C., Dick, T. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+EGSH+and+H2O2+with+roGFP2-based+redox+probes.">Measuring EGSH and H2O2 with roGFP2-based redox probes.</a> Free Radical Biology and Medicine. 51 (11), 1943-1951 (2011).</li><li>Dey, S., Sidor, A., O'Rourke, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartment-specific+control+of+reactive+oxygen+species+scavenging+by+antioxidant+pathway+enzymes.">Compartment-specific control of reactive oxygen species scavenging by antioxidant pathway enzymes.</a> Journal of Biological Chemistry. 291 (21), 11185-11197 (2016).</li></ol>

The authors have nothing to disclose.

The thiol/disulfide balance in an organism reflects the redox status of cells. Living organisms have glutathione, cysteine, protein thiols, and low-molecular-weight thiols, all of which are affected by the level of oxidation and echo the redox status of cells4. Engineered roGFPs allow the non-disruptive quantification of the thiol/disulfide balance via their CyS residues7. The ratiometric property of roGFP provides reliable redox measurements for mammalian cells. roGFP can ...

Oxidative stress was defined in 1985 by Helmut Sies as &#8220;a disturbance in prooxidant&#8211;antioxidant balance in favor of the former&#8221;1, and a plethora of research has been conducted to obtain disease-, nutrition-, and aging-specific redox status of organisms1,2,3. Since then, the understanding of oxidative stress has become broader. Testing the hypotheses of using antioxidants against diseases and/or aging has shown that oxidative stress not only causes harm but also has other roles in cells. Furthermore, scientists have shown that free radicals play an important role for signal transduction2. All of these studies strengthen the importance of determining the changes in reduction-oxidation (redox) ratio of macromolecules. Enzyme activity, antioxidants and/or oxidants, and oxidation products can be assessed with various methods. Among these, methods that determine thiol oxidation are arguably the most used because they report on the balance between antioxidants and prooxidants in cells, as well as organisms4. Specifically, ratios between glutathione (GSH)/glutathione disulfide (GSSG) and/or cysteine (CyS)/cystine (CySS) are used as biomarkers for monitoring the redox status of organisms2.
Methods used for assaying the balance between prooxidants and antioxidants rely mainly on the levels of reduced/oxidized proteins or small molecules within cells. Western blots and mass spectrometry are used to broadly assess the ratios of reduced/oxidized macromolecules (protein, lipids etc.), and GSH/GSSG ratios can be assessed with spectrophotometry5. A common feature of these methods is the physical perturbation of the system by cell lysis and/or tissue homogenization. These analyses also become challenging when it is necessary to measure the oxidation status of different cellular compartments. All of these perturbations cause artifacts in the assay environment.
Redox-sensitive fluorescent proteins opened an advantageous era for evaluating the redox balance without causing a disturbance in the cells6. They can target different intracellular compartments, allowing the quantification of compartment-specific activities (e.g., assaying the redox state of mitochondria and the cytosol) to investigate crosstalk between cellular organelles. Yellow fluorescent protein (YFP), green fluorescent protein (GFP), and HyPeR proteins are reviewed by Meyer and colleagues6. Among these proteins, redox-sensitive GFP (roGFP) is unique due to different fluorescent readouts of its CyS (ex. 488 nm/em. 525 nm) and CySS (ex. 405 nm/525 nm) residues, which permits ratiometric analysis, unlike other redox-sensitive proteins such as YFP7,8. Ratiometric output is valuable because it counterbalances the differences between expression levels, detection sensitivities, and photobleaching8. Subcellular compartments of cells (cytosol, mitochondria, nucleus) or different organisms (bacteria as well as mammalian cells) can be targeted by modifying roGFP7,9,10.
roGFP assays are conducted using fluorescent imaging techniques, especially for real-time visualization experiments. Flow cytometric analyses of roGFPs are also possible for experiments with predetermined time points. The current article describes both the use of fluorescent microscopy and flow cytometry to perform a ratiometric assessment of redox status in mammalian cells overexpressing roGFP (targeted to cytosol) via adenoviral transduction.

<table>
	<tbody>
		<tr>
			<td>0.25% Trypsin-EDTA</td>
			<td>Gibco by Life Sciences</td>
			<td>25200-056</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>4-well chamber slide</td>
			<td>Thermo Scientific</td>
			<td>154526</td>
			<td>Cell seeding material for fluorescent imaging</td>
		</tr>
		<tr>
			<td>5 ml tubes with cell strainer cap</td>
			<td>Falcon</td>
			<td>352235</td>
			<td>Single cell suspension tube for flow cytometry analysis</td>
		</tr>
		<tr>
			<td>6-well plate</td>
			<td>Corning</td>
			<td>353046</td>
			<td>Cell seeding material for flow cytometry analysis</td>
		</tr>
		<tr>
			<td>15 ml conical tubes</td>
			<td>MidSci</td>
			<td>C15B</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>75 cm2 ventilated cap tissue culture flasks</td>
			<td>Corning</td>
			<td>4306414</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Adenoviral cytosol specific roGFP</td>
			<td>ViraQuest</td>
			<td>VQAd roGFP</td>
			<td>roGFP construct kindly provided by Dr. Schumaker</td>
		</tr>
		<tr>
			<td>Class II, Type A2 Safety Hood Cabinet</td>
			<td>Thermo Scientific</td>
			<td>1300 Series A2</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Countess automated cell counter</td>
			<td>Invitrogen</td>
			<td>C10227</td>
			<td>Cell counting</td>
		</tr>
		<tr>
			<td>Countess cell counter chamber slides</td>
			<td>Invitrogen</td>
			<td>C10283</td>
			<td>Cell counting</td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Gibco by Life Sciences</td>
			<td>11995-065</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>Atlanta Biologicals</td>
			<td>S11150</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Filtered pipette tips, sterile, 20 &#181;l</td>
			<td>Fisherbrand</td>
			<td>02-717-161</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Filtered pipette tips, sterile, 1000 &#181;l</td>
			<td>Fisherbrand</td>
			<td>02-717-166</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Flow Cytometer</td>
			<td>BD Biosciences</td>
			<td>LSRFortessa</td>
			<td>Instrument equipped with FITC and BV510 bandpass filters for flow cytometry analyses</td>
		</tr>
		<tr>
			<td>Fluorescent Microscope</td>
			<td>Advanced Microscopy Group (AMG)</td>
			<td>Evos FL</td>
			<td>Fluorescent imaging</td>
		</tr>
		<tr>
			<td>Hydrogen Peroxide 30%</td>
			<td>Fisher Scientific</td>
			<td>H325-100</td>
			<td>Positive control</td>
		</tr>
		<tr>
			<td>Light Cube, Custom</td>
			<td>Life Sciences</td>
			<td>CUB0037</td>
			<td>Fluorescent imaging of roGFP expressing cells (ex 405 nm)</td>
		</tr>
		<tr>
			<td>Light Cube, GFP</td>
			<td>Thermo Scientific</td>
			<td>AMEP4651</td>
			<td>Fluorescent imaging of roGFP expressing cells (ex 488 nm)</td>
		</tr>
		<tr>
			<td>MDA-MB-231</td>
			<td>American Tissue Culture Collection</td>
			<td>HTB-26</td>
			<td>Human epithelial breast cancer cell line</td>
		</tr>
		<tr>
			<td>Microcentrifuge tubes, 2 ml</td>
			<td>Grenier Bio-One</td>
			<td>623201</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Gibco by Life Sciences</td>
			<td>10010-023</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Pipet controller</td>
			<td>Drummond</td>
			<td>Hood Mate Model 360</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Serologycal pipet, 1 ml</td>
			<td>Fisherbrand</td>
			<td>13-678-11B</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Serologycal pipet, 5 ml</td>
			<td>Fisherbrand</td>
			<td>13-678-11D</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Serologycal pipet, 10 ml</td>
			<td>Fisherbrand</td>
			<td>13-678-11E</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Tissue Culture Incubator</td>
			<td>Thermo Scientific</td>
			<td>HERACell 150i</td>
			<td>CO2 incubator for cell culture</td>
		</tr>
		<tr>
			<td>Trypan blue stain 0.4%</td>
			<td>Invitrogen</td>
			<td>T10282</td>
			<td>Cell counting</td>
		</tr>
	</tbody>
</table>

assessment of cellular oxidation using a subcellular compartment-specific redox-sensitive green fluorescent protein

Measuring the intracellular oxidation/reduction balance provides an overview of the physiological and/or pathophysiological redox status of an organism. Thiols are especially important for illuminating the redox status of cells via their reduced dithiol and oxidized disulfide ratios. Engineered cysteine-containing fluorescent proteins open a new era for redox-sensitive biosensors. One of them, redox-sensitive green fluorescent protein (roGFP), can easily be introduced into cells with adenoviral transduction, allowing the redox status of subcellular compartments to be evaluated without disrupting cellular processes. Reduced cysteines and oxidized cystines of roGFP have excitation maxima at 488 nm and 405 nm, respectively, with emission at 525 nm. Assessing the ratios of these reduced and oxidized forms allows the convenient calculation of redox balance within the cell. In this method article, immortalized human triple-negative breast cancer cells (MDA-MB-231) were used to assess redox status within the living cell. The protocol steps include MDA-MB-231 cell line transduction with adenovirus to express cytosolic roGFP, treatment with H2O2, and assessment of cysteine and cystine ratio with both flow cytometry and fluorescence microscopy.

The redox state of CyS/CySS is easily assayed with transduced roGFPs. The fluorescent probe quantifies the ratio between the reduced and oxidized forms (excitation wavelengths 488 nm and 405 nm, respectively). Fluorescence data can be obtained by both flow cytometry and microscopy.
A large number of cells can consistently and conveniently be acquired using flow cytometry. The analysis consists of 3 main steps: 1) select the cell population of interest with the FSC area filter (<strong class="x...

Watch this Scientific Journal Video about Assessment of Cellular Oxidation using a Subcellular Compartment-Specific Redox-Sensitive Green Fluorescent Protein at JoVE.com

Assessment of Cellular Oxidation using a Subcellular Compartment-Specific Redox-Sensitive Green Fluorescent Protein

This protocol describes the assessment of subcellular compartment-specific redox status within the cell. A redox-sensitive fluorescent probe allows convenient ratiometric analysis in intact cells.

Measuring the intracellular oxidation/reduction balance provides an overview of the physiological and/or pathophysiological redox status of an organism. ...

assessment-cellular-oxidation-using-subcellular-compartment-specific

Research

JoVE Journal

Biochemistry

7.2K Views.  University of Arkansas for Medical Sciences. This protocol describes the assessment of subcellular compartment-specific redox status within the cell. A redox-sensitive fluorescent probe allows convenient ratiometric analysis in intact cells.

Video: Assessment of Cellular Oxidation using a Subcellular Compartment-Specific Redox-Sensitive Green Fluorescent Protein

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating these studies, reincorporation of detergent-solubilized membrane proteins into liposomes is a stochastic process where protein topology is impossible to enforce. This paper offers an alternative method to these challenging techniques that utilizes a liposome-based scaffold. Protein solubility is enhanced by deletion of the transmembrane domain, and these amino acids are replaced with a tethering moiety, such as a His-tag. This tether interacts with an anchoring group (Ni2+ coordinated by nitrilotriacetic acid (NTA(Ni2+)) for His-tagged proteins), which enforces a uniform protein topology at the surface of the liposome. An example is presented wherein the interaction between Dynamin-related protein 1 (Drp1) with an integral membrane protein, Mitochondrial Fission Factor (Mff), was investigated using this scaffold liposome method. In this work, we have demonstrated the ability of Mff to efficiently recruit soluble Drp1 to the surface of liposomes, which stimulated its GTPase activity. Moreover, Drp1 was able to tubulate the Mff-decorated lipid template in the presence of specific lipids. This example demonstrates the effectiveness of scaffold liposomes using structural and functional assays and highlights the role of Mff in regulating Drp1 activity.

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

This paper describes a method for assessing the interactions and assemblies of integral membrane proteins in vitro with various partner factors in a lipid-proximal environment.

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating ...

Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase

Understanding the chemistry of redox proteins demands methods that provide precise control over redox centers within the protein. The technique of protein film electrochemistry, in which a protein is immobilized on an electrode surface such that the electrode replaces physiological electron donors or acceptors, has provided functional insight into the redox reactions of a range of different proteins. Full chemical understanding requires electrochemical control to be combined with other techniques that can add additional structural and mechanistic insight. Here we demonstrate a technique, protein film infrared electrochemistry, which combines protein film electrochemistry with infrared spectroscopic sampling of redox proteins. The technique uses a multiple-reflection attenuated total reflectance geometry to probe a redox protein immobilized on a high surface area carbon black electrode. Incorporation of this electrode into a flow cell allows solution pH or solute concentrations to be changed during measurements. This is particularly powerful in addressing redox enzymes, where rapid catalytic turnover can be sustained and controlled at the electrode allowing spectroscopic observation of long-lived intermediate species in the catalytic mechanism. We demonstrate the technique with experiments on E. coli hydrogenase 1 under turnover (H2 oxidation) and non-turnover conditions.

Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase

Here, we describe a technique, protein film infrared electrochemistry, which allows immobilized redox proteins to be studied spectroscopically under direct electrochemical control at a carbon electrode. Infrared spectra of a single protein sample can be recorded at a range of applied potentials and under a variety of solution conditions.

Understanding the chemistry of redox proteins demands methods that provide precise control over redox centers within the protein. The technique of protein ...

Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software

Number and brightness is a calibration-free fluorescence fluctuation spectroscopy (FFS) technique for detecting protein homo-oligomerization. It can be employed using a conventional confocal microscope equipped with digital detectors. A protocol for the use of the technique in vitro is shown by means of a use case where number and brightness can be seen to accurately quantify the oligomeric state of mVenus-labelled FKBP12F36V before and after the addition of the dimerizing drug AP20187. The importance of using the correct microscope acquisition parameters and the correct data preprocessing and analysis methods are discussed. In particular, the importance of the choice of photobleaching correction is stressed. This inexpensive method can be employed to study protein-protein interactions in many biological contexts.

Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software

This protocol describes a calibration-free approach for quantifying protein homo-oligomerization in vitro based on fluorescence fluctuation spectroscopy using commercial light scanning microscopy. The correct acquisition settings and analysis methods are shown.

Number and brightness is a calibration-free fluorescence fluctuation spectroscopy (FFS) technique for detecting protein homo-oligomerization. It can be ...

Structure Solution of the Fluorescent Protein Cerulean Using MeshAndCollect

X-ray crystallography is the major technique used to obtain high resolution information concerning the 3-dimensional structures of biological macromolecules. Until recently, a major requirement has been the availability of relatively large, well diffracting crystals, which are often challenging to obtain. However, the advent of serial crystallography and a renaissance in multi-crystal data collection methods has meant that the availability of large crystals need no longer be a limiting factor. Here, we illustrate the use of the automated MeshAndCollect protocol, which first identifies the positions of many small crystals mounted on the same sample holder and then directs the collection from the crystals of a series of partial diffraction data sets for subsequent merging and use in structure determination. MeshAndCollect can be applied to any type of micro-crystals, even if weakly diffracting. As an example, we present here the use of the technique to solve the crystal structure of the Cyan Fluorescent Protein (CFP) Cerulean.

We present the use of the MeshAndCollect protocol to obtain a complete diffraction data set, for use in subsequent structure determination, composed of partial diffraction data sets collected from many small crystals of the fluorescent protein Cerulean.

X-ray crystallography is the major technique used to obtain high resolution information concerning the 3-dimensional structures of biological ...

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing approaches suffer from significant limitations, we have developed a new method for determining TF-DNA binding affinities with high sensitivity on a large scale. The assay relies on the established fluorescence anisotropy (FA) principle but introduces important technical improvements. First, we measure a full FA competitive titration curve in a single well by incorporating TF and a fluorescently labeled reference DNA in a porous agarose gel matrix. Unlabeled DNA oligomer is loaded on the top as a competitor and, through diffusion, forms a spatio-temporal gradient. The resulting FA gradient is then read out using a customized epifluorescence microscope setup. This improved setup greatly increases the sensitivity of FA signal detection, allowing both weak and strong binding to be reliably quantified, even for molecules of similar molecular weights. In this fashion, we can measure one titration curve per well of a multi-well plate, and through a fitting procedure, we can extract both the absolute dissociation constant (KD) and active protein concentration. By testing all single-point mutation variants of a given consensus binding sequence, we can survey the entire binding specificity landscape of a TF, typically on a single plate. The resulting position weight matrices (PWMs) outperform those derived from other methods in predicting in vivo TF occupancy. Here, we present a detailed guide for implementing HiP-FA on a conventional automated fluorescent microscope and the data analysis pipeline.

Here we present a novel method for determining binding affinities at equilibrium and in solution with high sensitivity on a large scale. This improves the quantitative analysis of transcription factor-DNA binding. The method is based on automated fluorescence anisotropy measurements in a controlled delivery system.

Accurate quantification of transcription factor (TF)-DNA interactions is essential for understanding the regulation of gene expression. Since existing ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

Real-Time, Semi-Automated Fluorescent Measurement of the Airway Surface Liquid pH of Primary Human Airway Epithelial Cells

In recent years, the importance of mucosal surface pH in the airways has been highlighted by its ability to regulate airway surface liquid (ASL) hydration, mucus viscosity and activity of antimicrobial peptides, key parameters involved in innate defense of the lungs. This is of primary relevance in the field of chronic respiratory diseases such as cystic fibrosis (CF) where these parameters are dysregulated. While different groups have studied ASL pH both in vivo and in vitro, their methods report a relatively wide range of ASL pH values and even contradictory findings regarding any pH differences between non-CF and CF cells. Furthermore, their protocols do not always provide enough details in order to ensure reproducibility, most are low throughput and require expensive equipment or specialized knowledge to implement, making them difficult to establish in most labs. Here we describe a semi-automated fluorescent plate reader assay that enables the real-time measurement of ASL pH under thin film conditions that more closely resemble the in vivo situation. This technique allows for stable measurements for many hours from multiple airway cultures simultaneously and, importantly, dynamic changes in ASL pH in response to agonists and inhibitors can be monitored. To achieve this, the ASL of fully differentiated primary human airway epithelial cells (hAECs) are stained overnight with a pH-sensitive dye in order to allow for the reabsorption of the excess fluid to ensure thin film conditions. After fluorescence is monitored in the presence or absence of agonists, pH calibration is performed in situ to correct for volume and dye concentration. The method described provides the required controls to make stable and reproducible ASL pH measurements, which ultimately could be used as a drug discovery platform for personalized medicine, as well as adapted to other epithelial tissues and experimental conditions, such as inflammatory and/or host-pathogen models.

We present a protocol to make dynamic measurements of the airway surface liquid pH under thin film conditions using a plate-reader.

In recent years, the importance of mucosal surface pH in the airways has been highlighted by its ability to regulate airway surface liquid (ASL) ...

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the dissection and manipulation of biological pathways. Currently, only a limited number of chemically induced dimerization (CID) systems exist and engineering new ones with desired sensitivity and selectivity for specific small-molecule ligands remains a challenge in the field of protein engineering. We here describe a high throughput screening method, combinatorial binders-enabled selection of CID (COMBINES-CID), for the de novo engineering of CID systems applicable to a large variety of ligands. This method uses the two-step selection of a phage-displayed combinatorial nanobody library to obtain 1) &#34;anchor binders&#34; that first bind to a ligand of interest and then 2) &#34;dimerization binders&#34; that only bind to anchor binder-ligand complexes. To select anchor binders, a combinatorial library of over 109 complementarity-determining region (CDR)-randomized nanobodies is screened with a biotinylated ligand and hits are validated with the unlabeled ligand by bio-layer interferometry (BLI). To obtain dimerization binders, the nanobody library is screened with anchor binder-ligand complexes as targets for positive screening and the unbound anchor binders for negative screening. COMBINES-CID is broadly applicable to select CID binders with other immunoglobulin, non-immunoglobulin, or computationally designed scaffolds to create biosensors for in vitro and in vivo detection of drugs, metabolites, signaling molecules, etc.

Creating chemically induced protein dimerization systems with desired affinity and specificity for any given small molecule ligand would have many biological sensing and actuation applications. Here, we describe an efficient, generalizable method for de novo engineering of chemically induced dimerization systems via the stepwise selection of a phage-displayed combinatorial single-domain antibody library.

Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the ...

Characterizing Cellular Proteins with In-cell Fast Photochemical Oxidation of Proteins

Fast photochemical oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting method used to characterize protein structure and interactions. FPOP uses a 248 nm excimer laser to photolyze hydrogen peroxide producing hydroxyl radicals. These radicals oxidatively modify solvent exposed side chains of 19 of the 20 amino acids. Recently, this method has been used in live cells (IC-FPOP) to study protein interactions in their native environment. The study of proteins in cells accounts for intermolecular crowding and various protein interactions that are disrupted for in vitro studies. A custom single cell flow system was designed to reduce cell aggregation and clogging during IC-FPOP. This flow system focuses the cells past the excimer laser individually, thus ensuring consistent irradiation. By comparing the extent of oxidation produced from FPOP to the protein&#39;s solvent accessibility calculated from a crystal structure, IC-FPOP can accurately probe the solvent accessible side chains of proteins.

Here, we characterize protein structure and interaction sites in living cells using a protein footprinting technique termed in-cell fast photochemical oxidation of proteins (IC-FPOP).

Fast photochemical oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting method used to characterize protein structure and interactions. ...

Resin-Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation

Reversible oxidative modifications on protein thiols have recently emerged as important mediators of cellular function. Herein we describe the detailed procedure of a quantitative redox proteomics method that utilizes resin-assisted capture (RAC) in combination with tandem mass tag (TMT) isobaric labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to allow multiplexed stochiometric quantification of oxidized protein thiols at the proteome level. The site-specific quantitative information on oxidized cysteine residues provides additional insight into the functional impacts of such modifications. 
The workflow is adaptable across many sample types, including cultured cells (e.g., mammalian, prokaryotic) and whole tissues (e.g., heart, lung, muscle), which are initially lysed/homogenized and with free thiols being alkylated to prevent artificial oxidation. The oxidized protein thiols are then reduced and captured by a thiol-affinity resin, which streamlines and simplifies the workflow steps by allowing the proceeding digestion, labeling, and washing procedures to be performed without additional transfer of proteins/peptides. Finally, the labeled peptides are eluted and analyzed by LC-MS/MS to reveal comprehensive stoichiometric changes related to thiol oxidation across the entire proteome. This method greatly improves the understanding of the role of redox-dependent regulation under physiological and pathophysiological states related to protein thiol oxidation.

Protein thiol oxidation has significant implications under normal physiological and pathophysiological conditions. We describe the details of a quantitative redox proteomics method, which utilizes resin-assisted capture, isobaric labeling, and mass spectrometry, enabling site-specific identification and quantification of reversibly oxidized cysteine residues of proteins.

Reversible oxidative modifications on protein thiols have recently emerged as important mediators of cellular function. Herein we describe the detailed ...