This work was supported by start-up funds from the University of Maryland, Baltimore and the NIH 1R01 GM 127595 awarded to LMJ. The authors thank Dr. Daniel Deredge for his help in editing the manuscript.

1. C. elegans maintenance and culture
<ol>
	<li>Grow and synchronize worms colonies to their fourth larvae (L4) stage following standard laboratory procedures8.</li>
	<li>The day of IV-FPOP experiment, wash L4 worms from bacterial lawns (OP50 E. coli) with M9 buffer (0.02 M KH2PO4, 0.08 M Na2HPO4, 0.08 M NaCl, 1 mM MgSO4).</li>
	<li>Obtain 500 &#181;L aliquots of ~10,000 worms per IV-FPOP sample.</li>
</ol>
2. Microfluidic flow system assembly
<ol>
	<li>Start the flow system assembly by cutting a 2 cm piece of fluorinated ethylene propylene (FEP) tubing (1/16 in. outer diameter (o.d.) x 0.020 in. inner diameter (i.d.)).</li>
	<li>Using a clean dissecting needle, widen the i.d. of the FEP tubing in order to make a small crater at one end only, ~50 mm in length. The crater should be big enough to fit two 360 &#181;m o.d. pieces of fused silica. 
	NOTE: Do not widen the opposite end as this end will only be used to fit the outlet capillary.</li>
	<li>With a ceramic cutter, cut two 15 cm pieces of 250 &#181;m i.d. fused silica. These two pieces will become the infusing lines of the flow system.</li>
	<li>Using self-adhesive tape, tape the two 250 &#181;m i.d. capillaries together ensuring they are parallel to each other and their ends are 100% flushed. 
	NOTE: To ensure the fused silica ends are not crushed after cutting, and are straight and 100% flushed against each other, it is recommended to examine them using a magnifying glass or under a stereo microscope.</li>
	<li>Insert the two taped capillaries into the handmade crater of the FEP tubing. Push the capillaries up to the very edge of the handmade crater. 
	CAUTION: To maintain the efficacy of the flow system, do not push past the handmade crater (Figure 1a).</li>
	<li>Place a small dot of epoxy resin on a clean surface and mix with a dissecting needle.</li>
	<li>Quickly, using the same needle, place a small drop of resin at the end of the infusing capillaries where they connect with the FEP tubing and allow the resin to dry, hanging outlet-side up, for a few minutes (Figure 1a).</li>
	<li>While the resin dries, binding the FEP tubing and two capillaries together, cut a new 250 &#181;m i.d. capillary. The new capillary will become the outlet capillary of the flow system. The desired length of the capillary can be calculated using the equation below: 
	<img alt="Equation 1" src="/files/ftp_upload/60910/60910eq1.jpg" /> 
	Where &#8467; is length of the capillary to be cut in centimeters, t is the desired reaction time in minutes, f is the flow rate in mL/min, and i.d. is the inner diameter of the capillary in centimeters. 
	NOTE: After cutting the outlet capillary, examine the ends ensuring they are straight and not crushed.</li>
	<li>Once the resin has dried, insert the new capillary through the FEP tubing outlet end. The inside ends of the outlet capillary and the two infusing capillaries should be flush against each other inside the FEP tubing, this creates the mixing-T (Figure 1b).</li>
	<li>Bind the outlet capillary and FEP tubing with fresh epoxy resin as described in steps 2.6 and 2.7.</li>
	<li>Allow the resin to dry overnight binding the flow system together. Set up the microfluidic flow system the next day (Figure 1c).</li>
</ol>
3. Microfluidic flow system for in vivo FPOP
<ol>
	<li>Insert four magnetic stirrers inside one 5 mL syringe. This syringe becomes the sample syringe. The magnetic stirrers prevent the worms from settling inside the syringe during IV-FPOP (Figure 2A).</li>
	<li>Fill the two 5 mL syringes with M9. Make sure there are no air bubbles inside each syringe as they can affect the flow rate and mixing efficiency.</li>
	<li>Connect a Luer adapter to each 5 mL syringe ensuring they are finger tight and secured in place.</li>
	<li>Attach each syringe to a single 3-2 valve. The syringe should be attached to the middle port of the valve (Figure 2B).</li>
	<li>Secure each 5 mL syringe to the dual syringe pump and adjust the mechanical stop collar to prevent over pressure to the syringe from the pusher block. Keep in mind the addition of the magnetic stirrers when setting the stop collar.</li>
	<li>Attach each infusing capillary end of the homemade microfluidic flow system to the top port of each 3-2 valve using a super flangeless nut, FEP sleeve, and super flangeless ferrule (Figure 2B).</li>
	<li>To the remaining opened port of the 3-2 valve (bottom port), attach a 10 cm 450 &#181;m i.d. capillary using a super flangeless nut, FEP sleeve, and super flangeless ferrule (Figure 2B). These capillaries become the withdrawing sample capillaries.</li>
	<li>Start the pump flow and check all connections of the microfluidic flow system for visual leaks. Flow at least three syringe volumes using the experimental flow rate. The final flow rate is dependent on the laser irradiation window, laser frequency, and a zero-exclusion fraction volume. 
	NOTE: For this protocol, a final flow rate of 375.52 &#181;L/min was calculated from a laser irradiation window of 2.55 mm, 250 &#181;m i.d. fused silica, zero exclusion fraction, and 50 Hz frequency.
	<ol>
		<li>The flow path is marked by the arrows on the 3-2 valve handle. Each syringe can be refilled manually by moving the valve handle from the expelling position to the withdrawing position. 
		NOTE: Leaks at the 3-2 valve can be fixed by re-screwing the super flangeless nut or replacing any of the valve connections (super flangeless nut, FEP sleeve, or super flangeless ferrule). Leaks at the mixing-T require a reassembly of the microfluidic flow system (steps 2.1 to 2.11).</li>
	</ol>
	</li>
	<li>Move the microfluidic flow system to the experimental bench and secure the outlet capillary to the radiating stage using a 360 &#181;m o.d. stainless steel union (Figure 2C,D).</li>
	<li>Using a long-reach lighter, burn the coating of the fused silica at the laser irradiation window. Clean the burned coating using lint-free tissue and methanol. 
	NOTE: Alternate between burning cycles and methanol cleaning cycles to avoid over-heating the capillary as excess heat can melt and/or break the capillary.</li>
	<li>Position the magnetic stirrer block above the 5 mL syringe containing the magnetic stirrers. Adjust the speed and position of the magnetic stirrer block so that the magnetic stirrers inside the 5 mL syringe are rotating slowly and constantly.</li>
</ol>
4. In vivo FPOP
<ol>
	<li>Turn on the KrF excimer laser and allow the thyratron to warm-up. 
	CAUTION: The laser emits visible and invisible radiation at 248 nm wavelength that can damage eyes. Proper eye protection should be worn before turning on the laser and opening the beam exit window.</li>
	<li>Measure the laser energy at a frequency of 50 Hz for at least 100 pulses by placing the optical sensor at the beam exit window. 
	NOTE: For this protocol, a 2.55 mm irradiation window was used with a laser energy of 150 &#177; 2.32 mJ.</li>
	<li>Obtain approximatively 10,000 worms (500 &#181;L) and manually withdraw the sample into the sample syringe.</li>
	<li>Fill the sample syringe with 2.5 mL of M9 buffer for a final sample volume of 3 mL. Make sure that no air bubbles are introduced into the sample syringe.</li>
	<li>Fill the second syringe with 3 mL of 200 mM H2O2, again ensuring no air bubbles are introduced into the syringe.</li>
	<li>At the end of the outlet capillary, place a 15 mL conical tube wrapped in aluminum foil containing 6 mL of 40 mM N&#8217;-Dimethylthiourea (DMTU), 40 mM N-tert-Butyl-&#945;-phenylnitrone (PBN), and 1% dimethyl sulfoxide to quench excess H2O2, hydroxyl radicals, and inhibit methionine sulfoxide reductase activity, respectively.</li>
	<li>Start the excimer laser from the software window, wait for the first pulse, and start the sample flow from the dual syringe. 
	NOTE: Samples should be run in biological duplicates in technical triplicates under 3 samples conditions: laser irradiation with H2O2 (sample), no laser irradiation with H2O2 and no laser irradiation no H2O2 (controls), totaling to 9 samples per biological set.</li>
	<li>Collect the entire sample in the 15 mL tube, while actively monitoring the sample flow for any visual leaks as some back pressure from the sample syringe can sometimes build-up.</li>
	<li>Following IV-FPOP, pellet worms by centrifugation at 805 x g for 2 min. Remove quench solution, add 250 &#181;L of lysis buffer (8 M urea, 0.5% SDS, 50 mM HEPES, 50 mM NaCl, 1 mM EDTA, 1 mM phenylmethylsulfonyl fluoride [PMSF]). Transfer the sample to a clean microcentrifuge tube, flash freeze, and store at -80 &#176;C until sample digestion.</li>
</ol>
5. Protein extraction, purification, and proteolysis
<ol>
	<li>Thaw frozen samples on ice and homogenize by sonication for 10 s, followed by a 60 s ice incubation. Multiple rounds of sonication may be required, homogenate can be observed under a stereomicroscope by placing a 2 &#181;L sample aliquot on a microscope slide. Sample homogenization is complete when small to no pieces of worms are seen.</li>
	<li>Centrifuge homogenized worms at 400 x g for 5 min at 4 &#176;C and collect the supernatant into a clean microcentrifuge tube.</li>
	<li>Determine sample protein concentrations using a bicinchoninic acid assay (BCA assay) using the manufacturer&#8217;s instructions. 
	NOTE: Sample concentration can be determined using any biochemical protein concentration assay of choice. Keep in mind reagent compatibility with lysis buffer (8 M urea, 0.5% SDS, 50 mM HEPES, 50 mM NaCl, 1 mM EDTA, 1 mM PMSF). Additionally, a buffer dilution may be necessary.</li>
	<li>Obtain 100 &#181;g of protein from each sample and place in clean microcentrifuge tubes.</li>
	<li>Add dithiothreitol (DTT) to a 10 mM final concentration to reduce disulfide bonds in all samples. Vortex, spin down, and incubate samples at 50 &#176;C for 45 min.</li>
	<li>Cool samples to room temperature for 10 min.</li>
	<li>Add iodoacetamide (IAA) to a 50 mM final concentration to alkylate reduced residues. Vortex, spin down, and incubate samples for 20 min at room temperature protected from light.</li>
	<li>Immediately after alkylation, precipitate the protein sample by adding 4 volumes of 100% pre-chilled acetone and incubate at -20 &#176;C overnight.</li>
	<li>The next day, pellet protein precipitate by centrifugation at 16,000 x g for 10 min. Wash sample pellet with 90% acetone, remove supernatant, and allow pellet to dry for 2&#8211;3 min.</li>
	<li>Re-suspend the protein pellet in 25 mM Tris-HCl (1 &#181;g/&#181;L). Add trypsin at a final protease to protein ratio of 1:50 (w/w) and digest samples at 37 &#176;C overnight.</li>
	<li>The next day quench the trypsin digestion reaction by adding 5% formic acid. 
	NOTE: A minimum of 0.5 &#181;g of peptides per sample is needed for LC-MS/MS analysis (steps 6.1-6.5). Determine sample peptide concentrations using a quantitative colorimetric peptide assay (see the Table of Materials) as described by the manufacturer&#8217;s protocol.</li>
</ol>
6. High performance liquid chromatography-tandem mass spectrometry (LC-MS/MS)
<ol>
	<li>Use the following LC mobile phases: water in 0.1% FA (A) and ACN in 0.1% FA (B).</li>
	<li>Load 0.5 &#181;g of peptides onto a trap column (180 &#181;m &#215; 20 mm) containing C18 (5 &#181;m, 100 &#197;) and wash sample with 99% solvent A and 1% B for 15 min at 15 &#181;L/min flow rate.</li>
	<li>Separate peptides using an in-house packed column (0.075 mm i.d. &#215; 20 mm) with C18 reverse phase material (5 &#956;m, 125 &#197;).</li>
	<li>Use the following analytical separation method: the gradient was pumped at 300 nL/min for 120 min: 0&#8722;1 min, 3% B; 2&#8722;90 min, 10&#8722;45% B; 100&#8722;105 min, 100% B; 106&#8722;120 min, 3% B.</li>
	<li>Perform data acquisition of peptides in positive ion mode nano-electrospray ionization (nESI) using a high-resolution mass spectrometer. 
	NOTE: For this protocol, an ultra-performance LC (UPLC) instrument couple to a high-resolution mass spectrometer was utilized. Data dependent acquisition was utilized. The m/z scan range for MS1 was 3750&#8211;1500 at 60,000 resolution and 60 s dynamic exclusion. Ions with charge states of +1 and &#62;6 were excluded. An automatic gain control (AGC) target of 5.5e5 was used with a maximum injection time of 50 ms and an intensity threshold of 5.5e4. Ions selected for MS2 were subjected to higher-energy collisional dissociation (HCD) fragmentation using 32% normalized collision energy. Fragment ions were detected in the spectrometer with 15,000 resolution and a 5.0e4 AGC target.</li>
</ol>
7. Data analysis
<ol>
	<li>Search tandem MS files with a bottom-up proteomics analysis software against the C. elegans database.</li>
	<li>Set the protein analysis search parameters as follow: one trypsin missed cleavage, 375&#8211;1500 m/z peptide mass range, fragment mass tolerance of 0.02, and precursor mass tolerance of 10 ppm. Carbamidomethylation is set as a static modification and all know hydroxyl radical side-chain modifications9,10 as dynamic. Peptide identification is established at 95% confidence (medium) and residue at 99% confidence (high). The false discovery rate (FDR) is set a 1%.</li>
	<li>Export data to an electronic database and summarize the extent of oxidation per peptide or residue using the equation below11: 
	<img alt="Equation 2" src="/files/ftp_upload/60910/60910eq2.jpg" /> 
	NOTE: Where EIC area modified is the extracted ion chromatographic area (EIC) of the peptide or residue with an oxidative modification, and EIC area is the total area of the same peptide or residue with and without the oxidative modification.</li>
</ol>

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This publication was written in partial fulfillment of JAE Ph.D. thesis. The authors declare no conflict of interest.

The current benchmark for the study of in vivo protein-protein interactions (PPI) is fluorescence resonance energy transfer (FRET). In its most simple form, this technique studies PPI by energy transfer between two molecules when they are in close proximity to one another15. Unlike MS techniques, FRET does not have the resolution to characterize conformational changes and interaction sites at the amino-acid level. MS based techniques have been increasingly utilized for the study of PPI16. IV-FPOP is a HRPF method that allows for the in vivo protein structural analysis in C. elegans. In order to successfully label C. elegans by IV-FPOP, it is important to properly assemble the microfluidic flow system to reduce sample loss. The 250 &#181;m i.d. capillary has shown to maximize sample recovery when compared to smaller i.d. capillaries4. Larger i.d. capillaries have not been tested, however the microfluidic flow system is designed using a capillary with the same i.d. as a commercially available flow cytometry system for the sorting of C. elegans.17 The worm sample size is also important, a sample size of less than ~10,000 per sample prior to FPOP does not yield protein concentrations high enough for LC-MS/MS analysis. Higher samples sizes (&#62;10,000 worms) can also be used by adjusting the initial starting volume (step 4.5).
Proper assembly of the microfluidic flow system is important. Leaks in the sample pathway result in an inconsistent flow of the worms or H2O2. The ferrules, sleeves, and 3-2 valves can be reused from multiple IV-FPOP experiments if properly cleaned after each experiment. However, we recommend to assemble a new microfluidic flow system for every biological replicate. If the microfluidics is properly assembled, the worms and H2O2 will mix at the mixing-T with minimal back pressure. As quality control (QC) of the microfluidic flow system, we recommend testing the mixing efficiency by using colored dyes. It is important to monitor the motion of the magnetic stirrers inside the worm syringe during IV-FPOP, improper sample mixing at the worm syringe or the mixing-T can result in back pressure causing leaks. In addition, poor mixing conditions lead to large sample losses, poor laser exposure of worms at the laser window, and clogging.
C. elegans maintenance is important in order to decrease background oxidation. We recommend growing the worms at low temperatures under low stress conditions as high temperatures can affect total background oxidation. A control sample set of worms only, no H2O2 and no laser irradiation, is recommended for all IV-FPOP experiments to account for background oxidation due to laboratory maintenance. One of the current limitations of this technique is total number of oxidatively modified peptides identified and the total number of residues oxidized per peptide in order to gain higher protein structural information. Although not recommended, an increase in oxidative modifications could be achieve by using higher concentrations of hydrogen peroxide. An increase in hydrogen peroxide could significantly alter important biological pathways as well as lead to oxidation-induced unfolding. If the hydrogen peroxide concentration for IV-FPOP is increased, it is recommended to test worm viability and background oxidation as concentrations higher than 200 mM have not been tested.
The LC-MS/MS protocol described can be optimized and modified to meet the MS QC of other laboratories. The use of 2D-chromatography techniques has been previously shown to increase the identification of oxidatively modified peptides and proteins18. Nonetheless, protein enrichment techniques that target a specific protein of interest are not recommend, including but not limited to antibody precipitation or pull-down assays. These techniques can bias towards one protein conformer if the epitope/binding site of the protein has been oxidatively modified by IV-FPOP. New developments in footprinting radical reagents, such as sulfate radical anion10 or trifluoromethylation19 could increase the versatility of IV-FPOP. Although the only labeling reagent tested in vivo thus far is hydrogen peroxide, other laser-activated radicals could be optimized. The use of other radicals should prove to be compatible with worm viability, cell permeable, and the 248 nm laser wavelength. Owing to the use of C. elegans as a model system for many human diseases, IV-FPOP has the potential to have a strong impact in studying the role of protein structure in disease pathogenesis.

Protein footprinting coupled to mass spectrometry (MS) has been used in recent years to study protein interactions and conformational changes. Hydroxyl radical protein footprinting (HRPF) methods probe protein solvent accessibility by modifying protein amino acid side chains. The HRPF method, fast photochemical oxidation of proteins (FPOP)1, has been used to probe protein structure in vitro2, in-cell (IC-FPOP)3, and most recently in vivo (IV-FPOP)4. FPOP utilizes a 248 nm wavelength excimer laser in order to rapidly generate hydroxyl radicals by photolysis of hydrogen peroxide to form hydroxyl radicals1. In turn, these radicals can label 19 out of 20 amino acids on a microsecond time scale, faster than proteins can unfold. Although, the reactivity of each amino acid with hydroxyl radicals extends 1000-fold, it is possible to normalize side chain oxidation by calculating a protection factor (PF)5.
Since FPOP can oxidatively modify proteins regardless of their size or primary sequence, it proves to be advantageous for in-cell and in vivo protein studies. IV-FPOP probes protein structure in C. elegans similarly to in vitro and in-cell studies4. C. elegans are part of the nematode family and are widely used as a model to study human diseases. The ability of the worm to uptake hydrogen peroxide by both passive and active diffusion allows for the study of protein structure in different body systems. In addition, C. elegans are suited for IV-FPOP due to their transparency at the 248 nm laser wavelength needed for FPOP6. Coupling of this method to mass spectrometry allows for the identification of multiple modified proteins using traditional bottom-up proteomics approaches.
In this protocol, we describe how to perform IV-FPOP for the analysis of protein structure in C. elegans. The experimental protocol requires the assembly and set-up of microfluidic flow system for IV-FPOP adapted from Konermann et al7. After IV-FPOP, samples are homogenized for protein extraction. Protein samples are proteolyzed and peptides are analyzed by liquid chromatograph (LC) tandem MS, followed by quantification.

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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">15mL Conical Centrifuge Tubes</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">14-959-53A</td>
			<td style="width:251px;">any brand is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">5 mL Gas Tight Syringe, Removable Luer Lock</td>
			<td style="width:179px;">SGE Analytical Science</td>
			<td style="width:161px;">008760</td>
			<td>2 minimum</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">60 Sonic Dismembrator</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">FM3279</td>
			<td>This item is no longer available. Any low-volume sonicator will be sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Acetone, HPLC Grade</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">A929-4</td>
			<td>4 L quantity is not necessary</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Acetonitrile with 0.1% Formic Acid (v/v), LC/MS Grade</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">LS120-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">ACQUITY UPLC M-Class Symmetry C18 Trap Column, 100&#197;, 5 &#181;m, 180 &#181;m x 20 mm, 2G, V/M, 1/pkg</td>
			<td style="width:179px;">Waters</td>
			<td style="width:161px;">186007496</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">ACQUITY UPLC M-Class System</td>
			<td>Waters</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Aluminum Foil</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">01-213-100</td>
			<td>any brand is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Aqua 5 &#181;m C18 125 &#197; packing material</td>
			<td style="width:179px;">Phenomenex</td>
			<td style="width:161px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Centrifuge</td>
			<td style="width:179px;">Eppendorf</td>
			<td style="width:161px;">022625501</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Delicate Task Wipers</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">06-666A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Dissecting Needle</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">50-822-525</td>
			<td>only a couple are needed</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Dithiothreiotol (DTT)</td>
			<td style="width:179px;">AmericanBio</td>
			<td style="width:161px;">AB00490-00005</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">DMSO, Anhydrous</td>
			<td style="width:179px;">Invitrogen</td>
			<td style="width:161px;">D12345</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Epoxy instant mix 5 minute</td>
			<td>Loctite</td>
			<td>1365868</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Ethylenediaminetetraacetic acid (EDTA)</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">S311-100</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">EX350 excimer laser (248 nm wavelength)</td>
			<td style="width:179px;">GAM Laser</td>
			<td style="width:161px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">FEP Tubing 1/16&#34; OD x 0.020&#34; ID</td>
			<td style="width:179px;">IDEX Health &#38; Sciene</td>
			<td style="width:161px;">1548L</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Formic Acid, LC/MS Grade</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">A117-50</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">HEPES</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">BP310-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">HV3-2 VALVE</td>
			<td style="width:179px;">Hamilton</td>
			<td>86728</td>
			<td>2 minimum</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Hydrochloric Acid</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">A144S-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Hydrogen Peroxide</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">H325-100</td>
			<td>any 30% hydrogen peroxide is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Iodoacetamide (IAA)</td>
			<td style="width:179px;">ACROS Organics</td>
			<td style="width:161px;">122270050</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Legato 101 syringe pump</td>
			<td>KD Scientific</td>
			<td>788101</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Luer Adapter Female Luer to 1/4-28 Male Polypropylene</td>
			<td style="width:179px;">IDEX Health &#38; Sciene</td>
			<td style="width:161px;">P-618L</td>
			<td>2 minimum</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Magnesium Sulfate</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">M65-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Methanol, LC/MS Grade</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">A454SK-4</td>
			<td>4 L quantity is not necessary</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Microcentrifuge</td>
			<td style="width:179px;">Thermo Scientific</td>
			<td style="width:161px;">75002436</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">N,N&#8242;-Dimethylthiourea (DMTU)</td>
			<td style="width:179px;">ACROS Organics</td>
			<td style="width:161px;">116891000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">NanoTight Sleeve Green 1/16&#34; ID x .0155&#34; ID x1.6&#34;&#39;</td>
			<td style="width:179px;">IDEX Health &#38; Sciene</td>
			<td style="width:161px;">F-242X</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">NanoTight Sleeve Yellow 1/16&#34; OD x 0.027&#34; ID x 1.6&#34;</td>
			<td style="width:179px;">IDEX Health &#38; Sciene</td>
			<td style="width:161px;">F-246</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">N-tert-Butyl-&#945;-phenylnitrone (PBN)</td>
			<td style="width:179px;">ACROS Organics</td>
			<td style="width:161px;">177350250</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">OmniPur Phenylmethyl Sulfonyl Fluoride (PMSF)</td>
			<td style="width:179px;">Sigma-Aldrich</td>
			<td style="width:161px;">7110-OP</td>
			<td>any protease inhibitor is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Orbitrap Fusion Lumos Tribrid Mass Spectrometer</td>
			<td style="width:179px;">Thermo Scientific</td>
			<td style="width:161px;"></td>
			<td>other high resolution instruments (e.g. Q exactive Orbitrap or Orbitrap Fusion) can be used</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">PE50-C pyroelectric energy meter</td>
			<td style="width:179px;">Ophir Optronics</td>
			<td style="width:161px;">7Z02936</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Pierce Quantitative Colorimetric Peptide Assay</td>
			<td style="width:179px;">Thermo Scientific</td>
			<td style="width:161px;">23275</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Pierce Rapid Gold BCA Protein Assay Kit</td>
			<td style="width:179px;">Thermo Scientific</td>
			<td style="width:161px;">A53225</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Pierce Trypsin Protease, MS Grade</td>
			<td style="width:179px;">Thermo Scientific</td>
			<td style="width:161px;">90058</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Polymicro Cleaving Stone, 1&#34; x 1&#34; x 1/32&#8221;</td>
			<td style="width:179px;">Molex</td>
			<td style="width:161px;">1068680064</td>
			<td>any capillary tubing cutter is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Polymicro Flexible Fused Silica Capillary Tubing, Inner Diameter 250&#181;m, Outer Diameter 350&#181;m, TSP250350</td>
			<td style="width:179px;">Polymicro Technologies</td>
			<td style="width:161px;">1068150026</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:708px;">Polymicro Flexible Fused Silica Capillary Tubing, Inner Diameter 450&#181;m, Outer Diameter 670&#181;m, TSP450670</td>
			<td style="width:179px;">Polymicro Technologies</td>
			<td style="width:161px;">1068150625</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:708px;">Polymicro Flexible Fused Silica Capillary Tubing, Inner Diameter 75&#181;m, Outer Diameter 375&#181;m, TSP075375</td>
			<td style="width:179px;">Polymicro Technologies</td>
			<td style="width:161px;">1068150019</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Potassium Phosphate Monobasic</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">P382-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Proteome Discover (bottom-up proteomics software)</td>
			<td style="width:179px;">Thermo Scientific</td>
			<td style="width:161px;">OPTON-30799</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Rotary Magnetic Tumble Stirrer</td>
			<td style="width:179px;">V&#38;P Scientific, Inc.</td>
			<td style="width:161px;">VP 710D3</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Rotary Magnetic Tumble Stirrer, accessory kit for use with Syringe Pumps</td>
			<td style="width:179px;">V&#38;P Scientific, Inc.</td>
			<td style="width:161px;">VP 710D3-4</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Scissors</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">50-111-1315</td>
			<td>any scissors are sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Self-Adhesive Label Tape</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">15937</td>
			<td>one roll is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Snap-Cap Microcentrifuge Flex-Tube Tubes</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">05-402</td>
			<td>any brand is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Sodium Chloride</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">S271-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Sodium Dodecyl Sulfate (SDS)</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">15-525-017</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Sodium Phosphate Dibasic Heptahydrate</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">S373-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Stereo Zoom Microscope</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">03-000-014</td>
			<td>a magnifying glass is sufficient</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Super Flangeless Ferrule w/SST Ring, Tefzel (ETFE), 1/4-28 Flat-Bottom, for 1/16&#34; OD</td>
			<td style="width:179px;">IDEX Health &#38; Sciene</td>
			<td style="width:161px;">P-259X</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Super Flangeless Nut PEEK 1/4-28 Flat-Bottom, for 1/16&#34; &#38; 1/32&#34; OD</td>
			<td style="width:179px;">IDEX Health &#38; Sciene</td>
			<td style="width:161px;">P-255X</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Super Tumble Stir Discs, 3.35 mm diameter, 0.61 mm thick</td>
			<td style="width:179px;">V&#38;P Scientific, Inc.</td>
			<td style="width:161px;">VP 722F</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Tris Base</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">BP152-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Universal Base Plate, 2.5&#34; x 2.5&#34; x 3/8&#34;</td>
			<td style="width:179px;">Thorlabs Inc.</td>
			<td style="width:161px;">UBP2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Urea</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">U5378</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">VHP MicroTight Union for 360&#181;m OD</td>
			<td style="width:179px;">IDEX Health &#38; Sciene</td>
			<td style="width:161px;">UH-436</td>
			<td>2 minimum</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Water with 0.1% Formic Acid (v/v), LC/MS Grade</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">LS118-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:708px;">Water, LC/MS Grade</td>
			<td style="width:179px;">Fisher Scientific</td>
			<td style="width:161px;">W6-4</td>
			<td></td>
		</tr>
	</tbody>
</table>

in vivo hydroxyl radical protein footprinting for the study of protein interactions in caenorhabditis elegans

Fast oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting (HRPF) method used to study protein structure, protein-ligand interactions, and protein-protein interactions. FPOP utilizes a KrF excimer laser at 248 nm for photolysis of hydrogen peroxide to generate hydroxyl radicals which in turn oxidatively modify solvent-accessible amino acid side chains. Recently, we expanded the use of FPOP of in vivo oxidative labeling in Caenorhabditis elegans (C. elegans), entitled IV-FPOP. The transparent nematodes have been used as model systems for many human diseases. Structural studies in C. elegans by IV-FPOP is feasible because of the animal&#8217;s ability to uptake hydrogen peroxide, their transparency to laser irradiation at 248 nm, and the irreversible nature of the modification. The assembly of a microfluidic flow system for IV-FPOP labeling, IV-FPOP parameters, protein extraction, and LC-MS/MS optimized parameters are described herein.

In the microfluidic flow system used for IV-FPOP, H2O2 and the worms are kept separated until just prior to laser irradiation. This separation eliminates breakdown of H2O2 by endogenous catalase and other cellular mechanisms12. The use of a 250 &#181;m i.d. capillary shows a total sample recovery between 63&#8211;89% across two biological replicates, while the 150 &#181;m i.d. capillary only shows 21&#8211;31% recovery (Figure 3A). The use of a larger i.d. capillary (250 &#181;m) leads to better worm flow during IV-FPOP and single worm flow (Figure 3B) when compared to a smaller i.d. capillary (150 &#181;m) (Figure 3C). The 150 &#181;m i.d. capillary does not allow for single worm flow (Figure 3C) and multiple worms are seen flowing together at the laser irradiating window which decreases the amount of laser exposure per single worm.
IV-FPOP is a covalent labeling technique that probes solvent accessibility in C. elegans. Figure 4A shows a representative extracted ion chromatograms (EIC) of a FPOP modified and unmodified peptide. The hydroxyl radical label changes the chemistry of oxidatively modified peptides, thus making FPOP modified peptides more polar. In reverse phase chromatography, IV-FPOP modified peptides have earlier retention times than unmodified peptides. MS/MS fragmentation of isolated peptides allows for the identification of oxidatively modified residues (Figure 4B).
IV-FPOP has shown to oxidatively modified a total of 545 proteins across two biological replicates within C. elegans (Figure 5A,B). An advantage of IV-FPOP as a protein footprinting method relies on the technique&#8217;s ability to modify proteins in a variety of body systems within the worms (Figure 5C). This method would allow to probe protein structure and protein interactions regardless of body tissue or organ within the worm. Further, tandem MS analysis confirms IV-FPOP probes solvent accessibility in vivo. The oxidation pattern of the heat shock protein 90 (Hsp90) in complex with the myosin chaperon protein UNC-45 was analyzed (Figure 6). MS/MS analysis for Hsp90 shows four oxidatively modified residues (Figure 6C,D), the normalized extent of FPOP modification (ln(PF))5 indicates Hsp90&#8217;s residue M698 to be less solvent accessible than residues R697, E699, and E700 when bound to UNC-45 (Figure 6C). These differences in oxidation are validated by literature solvent accessible surface area (SASA) calculations (PDB 4I2Z13). Residue M698 has a SASA value of 0.03 which is consider to be a buried residue when compared to residues R697, E699, and E700 with higher SASA values (Figure 6C).14
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/60910/60910fig1.jpg" /> 
Figure 1. In vivo FPOP microfluidic flow system schematic. (A) The two infusing lines (orange) of the IV-FPOP flow system are shown inside the FEP tubing (yellow), the correct binding position of the epoxy resin is represented by the light blue circle. (B) Complete assembled mixing-T formed by the three 250 &#181;m i.d. capillaries. The correct resin binding position of the outlet capillary to the FEP tubing is represented by the light blue circle. (C) The complete assembled flow system for in vivo covalent labeling of C. elegans. Prior to FPOP, worms are kept separated from H2O2 until just prior to labeling; the laser irradiation window is shown in light blue and the laser beam is represented by the purple lightning bolt. Figures are not to scale. This figure has been modified from Espino et al.4. <a href="https://www.jove.com/files/ftp_upload/60910/60910fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/60910/60910fig2.jpg" /> 
Figure 2. Microfluidic system during IV-FPOP. (A) Representative picture of C. elegans inside the 5 mL syringe. Without stirring, the worms settle at the bottom of the syringe (left). The magnetic stirrers and stirrer block keep the worms in suspension during the IV-FPOP experiments (right). (B) Representative picture of a 5 mL syringe, infusing capillary, and withdrawing capillary connected to the 3-2 valve. The 3-2 valve handle is shown in the withdrawing position. (C) Microfluidic flow system during IV-FPOP, the magnetic stirrer block is position above the worms&#8217; 5 mL syringe. (D) Outlet capillary secured to the radiating stage. <a href="https://www.jove.com/files/ftp_upload/60910/60910fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/60910/60910fig3.jpg" /> 
Figure 3. Comparison of C. elegans flow and recovery using two i.d. capillaries. (A) Percent recovery of worms after IV-FPOP for two biological replicates (BR) with 250 (gray) and 150 (black) &#956;m i.d. capillaries. Error bars are calculated from the standard deviation across technical triplicates. C. elgans flowing through the laser irradiating window through a 250 &#181;m (B) and 150 &#181;m (C) i.d. capillaries. The worms are more tightly compacted in the smaller capillary. The 150 &#181;m i.d. capillary shows clumping of worms. This figure has been modified from Espino et al.4. <a href="https://www.jove.com/files/ftp_upload/60910/60910fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/60910/60910fig4.jpg" /> 
Figure 4. Representative LC-MS/MS results following IV-FPOP. (A) EIC of a FPOP modified peptide (red) and unmodified (blue). The selected peptide belongs to the actin-1 protein. (B) MS/MS spectrum of doubly charged unmodified actin-1 peptide 317-327. (C) MS/MS spectrum of doubly charged FPOP modified actin-1 peptide 317-327, in this example P323 was oxidatively modified (y5+ ion, red). <a href="https://www.jove.com/files/ftp_upload/60910/60910fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/60910/60910fig5.jpg" /> 
Figure 5. IV-FPOP oxidatively modifies proteins within C. elegans. (A) Venn diagram of oxidatively modified proteins in the presence of 200 mM hydrogen peroxide at 50 Hz across two biological replicates (BR), BR1 is in blue and BR2 is in yellow. (B) Venn diagram of oxidatively modified proteins identified in irradiated samples, hydrogen peroxide control, and worm-only control in BR2 across technical triplicates. (C) Pie chart of oxidatively modified proteins within different C. elegans body systems. This figure has been modified from Espino et al.4. <a href="https://www.jove.com/files/ftp_upload/60910/60910fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/60910/60910fig6.jpg" /> 
Figure 6. Correlating IV-FPOP modifications to solvent accessibility. (A) Myosin chaperon protein UNC-45 (gray) (PDB ID 4I2Z13) highlighting two modified peptides identified by LC/MS/MS analysis, 669&#8722;680 and 698&#8722;706 (green, left inset). UNC-45 is bound to the Hsp90 peptide fragment (blue). Oxidatively modified residues within this fragment are shown in sticks (red), and UNC-45 is rendered as a surface (right inset). (B) Tandem MS spectra of UNC-45 peptide 669&#8722;680 (top) and 698&#8722;706 (bottom) showing b- and y-ions for the loss of CO2, an FPOP modification. (C) The calculated ln(PF) for the Hsp90 oxidatively modified residues, R697, M698, E699, and E700. Calculated SASA values for Hsp90 are denoted above each residue. (D) Tandem MS spectra for R697, M698, E699, and E700 showing a +16 FPOP modification. This figure has been modified from Espino et al.4. <a href="https://www.jove.com/files/ftp_upload/60910/60910fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans at JoVE.com

In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans

In vivo fast photochemical oxidation of proteins (IV-FPOP) is a hydroxyl radical protein footprinting technique that allows for mapping of protein structure in their native environment. This protocol describes the assembly and set-up of the IV-FPOP microfluidic flow system.

In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans

Fast oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting (HRPF) method used to study protein structure, protein-ligand interactions, ...

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Biochemistry

6.8K Views.  University of Maryland. In vivo fast photochemical oxidation of proteins (IV-FPOP) is a hydroxyl radical protein footprinting technique that allows for mapping of protein structure in their native environment. This protocol describes the assembly and set-up of the IV-FPOP microfluidic flow system.

Video: In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Protein-protein interactions play an essential role in the function of a living organism. Once an interaction has been identified and validated it is necessary to characterize it at the structural and mechanistic level. Several biochemical and biophysical methods exist for such purpose. Among them, fluorescence anisotropy is a powerful technique particularly used when the fluorescence intensity of a fluorophore-labeled protein remains constant upon protein-protein interaction. In this technique, a fluorophore-labeled protein is excited with vertically polarized light of an appropriate wavelength that selectively excites a subset of the fluorophores according to their relative orientation with the incoming beam. The resulting emission also has a directionality whose relationship in the vertical and horizontal planes defines anisotropy (r) as follows: r=(IVV-IVH)/(IVV+2IVH), where IVV and IVH are the fluorescence intensities of the vertical and horizontal components, respectively. Fluorescence anisotropy is sensitive to the rotational diffusion of a fluorophore, namely the apparent molecular size of a fluorophore attached to a protein, which is altered upon protein-protein interaction. In the present text, the use of fluorescence anisotropy as a tool to study protein-protein interactions was exemplified to address the binding between the protein mutated in the Shwachman-Diamond Syndrome (SBDS) and the Elongation factor like-1 GTPase (EFL1). Conventionally, labeling of a protein with a fluorophore is carried out on the thiol groups (cysteine) or in the amino groups (the N-terminal amine or lysine) of the protein. However, SBDS possesses several cysteines and lysines that did not allow site directed labeling of it. As an alternative technique, the dye 4&#39;,5&#39;-bis(1,3,2 dithioarsolan-2-yl) fluorescein was used to specifically label a tetracysteine motif, Cys-Cys-Pro-Gly-Cys-Cys, genetically engineered in the C-terminus of the recombinant SBDS protein. Fitting of the experimental data provided quantitative and mechanistic information on the binding mode between these proteins.

Protein interactions are at the heart of a cell&#39;s function. Calorimetric and spectroscopic techniques are commonly used to characterize them. Here we describe fluorescence anisotropy as a tool to study the interaction between the protein mutated in the Shwachman-Diamond Syndrome (SBDS) and the Elongation factor-like 1 GTPase (EFL1).

Protein-protein interactions play an essential role in the function of a living organism. Once an interaction has been identified and validated it is ...

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 ...

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. Hydrogen-Deuterium Exchange (HDX) measured at rapid time scales is uniquely suited to detect structures and hydrogen bonding networks that are briefly populated, allowing for the characterization of transient conformers in native ensembles. Coupling of HDX to mass spectrometry offers several key advantages, including high sensitivity, low sample consumption and no restriction on protein size. This technique has advanced greatly in the last several decades, including the ability to monitor HDX labeling times on the millisecond time scale. In addition, by incorporating the HDX workflow onto a microfluidic platform housing an acidic protease microreactor, we are able to localize dynamic properties at the peptide level. In this study, Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS) coupled to HDX was used to provide a detailed picture of residual structure in the tau protein, as well as the conformational shifts induced upon hyperphosphorylation.

Conformational flexibility plays a critical role in protein function. Herein, we describe the use of time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange for probing the rapid structural changes that drive function in ordered and disordered proteins.

Intrinsically disordered proteins (IDPs) have long been a challenge to structural biologists due to their lack of stable secondary structure elements. ...

Biotinylated Cell-penetrating Peptides to Study Intracellular Protein-protein Interactions

Here we present a protocol to study intracellular protein-protein interactions that is based on the widely used biotin-avidin pull-down system. The modification presented includes the combination of this technique with cell-penetrating sequences. We propose to design cell-penetrating baits that can be incubated with living cells instead of cell lysates and therefore the interactions found will reflect those that occur within the intracellular context. Connexin43 (Cx43), a protein that forms gap junction channels and hemichannels is down-regulated in high-grade gliomas. The Cx43 region comprising amino acids 266-283 is responsible for the inhibition of the oncogenic activity of c-Src in glioma cells. Here we use TAT as the cell-penetrating sequence, biotin as the pull-down tag and the region of Cx43 comprised between amino acids 266-283 as the target to find intracellular interactions in the hard-to-transfect human glioma stem cells. One of the limitations of the proposed method is that the molecule used as bait could fail to fold properly and, consequently, the interactions found could not be associated with the effect. However, this method can be especially interesting for the interactions involved in signal transduction pathways because they are usually carried out by intrinsically disordered regions and, therefore, they do not require an ordered folding. In addition, one of the advantages of the proposed method is that the relevance of each residue on the interaction can be easily studied. This is a modular system; therefore, other cell-penetrating sequences, other tags, and other intracellular targets can be employed. Finally, the scope of this protocol is far beyond protein-protein interaction because this system can be applied to other bioactive cargoes such as RNA sequences, nanoparticles, viruses or any molecule that can be transduced with cell-penetrating sequences and fused to pull-down tags to study their intracellular mechanism of action.

This is a protocol to study intracellular protein-protein interactions based on the biotin-avidin pull-down system with the novelty of combining cell-penetrating sequences. The main advantage is that the target sequence is incubated with living cells instead of cell lysates and therefore the interactions will occur within the cellular context.

Here we present a protocol to study intracellular protein-protein interactions that is based on the widely used biotin-avidin pull-down system. The ...

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Here we describe a simple protocol for rapidly producing hundreds of nematode growth media agar, 96-well culture plates with consistent numbers of Caenorhhabditis elegans per well. These cultures are useful for the phenotypic screening of whole organisms. We focus here on using these cultures to screen chemicals for pro-longevity effects.

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages ...

Small-Scale Colorimetric Assays of Intracellular Lactate and Pyruvate in the Nematode Caenorhabditis elegans

Lactate and pyruvate are key intermediates of intracellular energy metabolic pathways. Monitoring the lactate/pyruvate ratio in cells helps to determine whether there is an imbalance in age-related energy metabolism between mitochondrial oxidative phosphorylation and aerobic glycolysis. Here, we show the utilization of commercial colorimetric assay kits for lactate and pyruvate in the model organism C. elegans. Recently, the sensitivity and accuracy of the colorimetric/fluorimetric assay kits have been improved greatly by the research and development conducted by reagent manufacturers. The improved reagents have enabled the use of small-scale assays with a 96-well plate in C. elegans. In general, a fluorimetric assay is superior in sensitivity to a colorimetric assay; however, the colorimetric approach is more suitable for the use in common laboratories. Another important issue in these assays for quantitative determination is protein precipitation of homogenized C. elegans samples. In our protein precipitation method, common precipitants (e.g., trichloroacetic acid, perchloric acid and metaphosphoric acid) are used for sample preparation. A protein-free assay sample is prepared by directly adding cold precipitant (final concentration of 5%) during homogenization.

Small-Scale Colorimetric Assays of Intracellular Lactate and Pyruvate in the Nematode Caenorhabditis elegans

We describe a modified small-scale extraction and colorimetric assays of lactate and pyruvate in the nematode C. elegans. When utilizing commercial assay kits, the technical development of their sensitivity and accuracy is important. Protein precipitation in extraction is the most critical step for the quantitative determination of intracellular metabolites.

Lactate and pyruvate are key intermediates of intracellular energy metabolic pathways. Monitoring the lactate/pyruvate ratio in cells helps to determine ...

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 ...

Application of Biolayer Interferometry (BLI) for Studying Protein-Protein Interactions in Transcription

A transcription factor&#160;(TF) is a protein that regulates gene expression by interacting with the RNA polymerase, another TF, and/or template DNA. GrgA is a novel transcription activator found specifically in the obligate intracellular bacterial pathogen Chlamydia. Protein pulldown assays using affinity beads have revealed that GrgA binds two &#963; factors, namely &#963;66 and &#963;28, which recognize different sets of promoters for genes whose products are differentially required at developmental stages. We have used BLI to confirm and further characterize the interactions. BLI demonstrates several advantages over pulldown: 1) It reveals real-time association and dissociation between binding partners, 2) It generates quantitative kinetic parameters, and 3) It can detect bindings that pulldown assays often fail to detect. These characteristics have enabled us to deduce the physiological roles of GrgA in gene expression regulation in Chlamydia, and possible detailed interaction mechanisms. We envision that this relatively affordable technology can be extremely useful for studying transcription and other biological processes.

Application of Biolayer Interferometry BLI for Studying Protein-Protein Interactions in Transcription

Interactions of transcription factors (TFs) with the RNA polymerase are usually studied using pulldown assays. We apply a Biolayer Interferometry (BLI) technology to characterize the interaction of GrgA with the chlamydial RNA polymerase. Compared to pulldown assays, BLI detects real-time association and dissociation, offers higher sensitivity, and is highly quantitative.

A transcription factor&#160;(TF) is a protein that regulates gene expression by interacting with the RNA polymerase, another TF, and/or template DNA. GrgA ...

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

Hydroxyl Radical Protein Footprinting (HRPF) is an emerging and promising higher order structural analysis technique that provides information on changes in protein structure, protein-protein interactions, or protein-ligand interactions. HRPF utilizes hydroxyl radicals (&#9642;OH) to irreversibly label a protein&#8217;s solvent accessible surface. The inherent complexity, cost, and hazardous nature of performing HRPF have substantially limited broad-based adoption in biopharma. These factors include: 1) the use of complicated, dangerous, and expensive lasers that demand substantial safety precautions; and 2) the irreproducibility of HRPF caused by background scavenging of &#9642;OH that limit comparative studies. This publication provides a protocol for operation of a laser-free HRPF system. This laser-free HRPF system utilizes a high energy, high-pressure plasma light source flash oxidation technology with in-line radical dosimetry. The plasma light source is safer, easier to use, and more efficient in generating hydroxyl radicals than laser-based HRPF systems, and the in-line radical dosimeter increases the reproducibility of studies. Combined, the laser-free HRPF system addresses and surmounts the mentioned shortcomings and limitations of laser-based techniques.

This protocol presents a method to use inline radical dosimetry and a plasma light source to perform flash oxidation protein footprinting. This method replaces the hazardous UV laser to simplify and improve the reproducibility of fast photochemical oxidation of protein studies.

Hydroxyl Radical Protein Footprinting (HRPF) is an emerging and promising higher order structural analysis technique that provides information on changes ...

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

RNA adopts diverse structural folds, which are essential for its functions and thereby can impact diverse processes in the cell. In addition, the structure and function of an RNA can be modulated by various trans-acting factors, such as proteins, metabolites or other RNAs. Frameshifting RNA molecules, for instance, are regulatory RNAs located in coding regions, which direct translating ribosomes into an alternative open reading frame, and thereby act as gene switches. They may also adopt different folds after binding to proteins or other trans-factors. To dissect the role of RNA-binding proteins in translation and how they modulate RNA structure and stability, it is crucial to study the interplay and mechanical features of these RNA-protein complexes simultaneously.&#160;This work illustrates how to employ single-molecule-fluorescence-coupled optical tweezers to explore the conformational and thermodynamic landscape of RNA-protein complexes at a high resolution. As an example, the interaction of the SARS-CoV-2 programmed ribosomal frameshifting element with the trans-acting factor short isoform of zinc-finger antiviral protein is elaborated. In addition, fluorescence-labeled ribosomes were monitored using the confocal unit, which would ultimately enable the study of translation elongation. The fluorescence coupled OT assay can be widely applied to explore diverse RNA-protein complexes or trans-acting factors regulating translation and could facilitate studies of RNA-based gene regulation.

This protocol presents a complete experimental workflow for studying RNA-protein interactions using optical tweezers. Several possible experimental setups are outlined including the combination of optical tweezers with confocal microscopy.