This work was supported by a grant from the NIH R01 GM128983-01.

1. Assembly of Platform Incubator with Movable XY stage
NOTE: The new platform includes the incubation system, the positioning stage and controllers, the peristaltic pumps, the 248 nm KrF excimer laser, and the optical mirrors assembled on an Imperial optical breadboard.
<ol>
	<li>Assemble the incubation system: the temperature unit, carbon dioxide unit, humidifier, air pump, and touch monitoring system (Figure 2A-E). 
	NOTE: Detailed assembly instructions are provided by the manufacturer. The incubation system must stabilize to 5% CO2, 37 &#176;C, and 85% humidity before growing cells within the incubator. These parameters may depend on the cell line.</li>
	<li>Assemble the custom six-well plate incubator, nanopositioning drive stage, and XY drive stage. The former screws into the latter, respectively. 
	NOTE: Detailed assembly instructions provided by the manufacturer.</li>
	<li>Connect the four peristaltic pumps in a &#34;daisy chain&#34; sequence via RS-232 cables, with an RS-232 to USB cable connected to the controlling computer. Connect 3.18 mm ID polymer tubing (e.g., Tygon) to every channel on each pump channel roller. 
	NOTE: Each pump has four rollers. Direction and flow rate of rollers are manually manipulated.</li>
	<li>Insert 1/16&#34; x 1/8&#34; connectors at the end of each 3.18 mm ID polymer tube. Insert the 1/16&#39;&#39; end of the connector into 1.59 ID polymer tubing, then insert the polymer tubing into the incubator via custom ports. Place the other end of the tube in the solution that will be infused during IC-FPOP experimentation. 
	NOTE: For the perfusion lines, the incubator has 36 custom ports for tubing lines all around the periphery to accommodate all the reagents used.</li>
	<li>Screw one 50 mm, 248 nm, 45&#176; excimer laser line mirror within a kinematic mirror mount for &#216;2&#34; optics into the breadboard 10-11 grid points from the 248 nm laser aperture. Place the second mirror at a 90&#176; angle to the first on the other side of the incubator. Angle the second mirror downward at approximately 45&#176; for laser beam guidance to the incubator (Figure 2F-J).</li>
</ol>
2. Synchronization and initial automation of system via integration software
<ol>
	<li>Install the latest version of the integration software needed to control the drivers and pumps.</li>
	<li>Referring to the pump manual, rename the pumps starting with &#39;5&#39; and increasing in value. The commands can be sent to the pump system using the Manual Control sub-program in the integration software. 
	NOTE: Setting a pump to Channel Mode automatically changes the pump naming convention into the set, 1, 2, 3 and 4, corresponding to the four pump channels.</li>
	<li>Open the integration software program for the automation of the platform incubator.</li>
	<li>Choose the appropriate USB comport device name (e.g., COM4) corresponding to the pump system USB cable from the connection dropdown menu labelled Comport for pumps.</li>
	<li>Click the Script Builder button to edit/create a script for the automated platform incubator platform. Click Save Script to save the sequence as a text file (Figure 3A). 
	NOTE: The script builder has a user interface for defining the script with definitions of pump number, direction, rate, volume, tubing diameter, channel mode, and timed delay.</li>
	<li>If channel mode is desired in the making of the script, a step in the script must be dedicated to changing the pump in and out of channel mode, and the following steps corresponding to the pump channels must be labelled as pumps 1-4. 
	NOTE: This ensures that no two pumps can simultaneously be in channel mode during a platform incubator script and that each pump is switched back to legacy mode after the commands have been sent to the needed channels.</li>
	<li>Click the Read Script button and choose the appropriate script file desired for the platform incubator operation.</li>
	<li>Switch the Run Sequence button to the ON position (green) to run the script and then click the START button (Figure 3B) .</li>
</ol>
3. Grow cells in the platform incubator
NOTE: Cells must be placed in the platform incubator under sterile conditions in a cell culture hood the day before experimentation.
<ol>
	<li>Unscrew the platform incubator from the nanopositioning stage and disconnect the temperature, gas, and humidifier lines. After spraying the incubator with 70% ethanol, place it in a cell culture hood.</li>
	<li>Grow cells in a T-175 to about 80-90% confluency prior to transfer. 
	NOTE: The term confluency is used as a measure of the number/coverage of the cells in a cell culture dish or a flask.</li>
	<li>Remove media and rinse with buffer.</li>
	<li>Detach cells using trypsin-EDTA using manufacturer&#39;s protocol.</li>
	<li>Resuspend in 8 mL of media and count the cells.</li>
	<li>Seed fibronectin/collagen14 coated six-well plates with approximately 90-95 &#956;L of resuspended cells in each well. This volume will be appropriate to achieve 80-90% confluency (~1.2 million cells) in each well on the next day. 
	NOTE: Six-well plates must be coated with collagen prior to seeding. The reagents used during IC-FPOP are infused with fast flow rates. Coated plates ensure cells are not prematurely detached due to infusion of reagents.</li>
	<li>Place the seeded plate into the platform incubator and cover with the quartz lid. 
	NOTE: During design and development, a glass incubator lid was changed to quartz, so it is compatible with the ultraviolet laser light.</li>
	<li>Replace and secure the platform incubator back on the nanopositioning drive stage. Reconnect the temperature, gas, and humidifier lines.</li>
	<li>Let cells grow to confluency overnight. 
	NOTE: The following cell culture steps are optional and are intended for experiments in which human cells are transiently transfected. These steps assess transfection efficiency under cell culture conditions.</li>
	<li>Transfect the plasmid containing the gene for the chimeric protein GCaMP2 into HEK 293 cells using a commercial cationic-lipid transfection kit.</li>
	<li>Perform transient transfections of GCaMP2 in HEK293T cells in two six-well plates.</li>
	<li>Incubate one six-well plate in the platform incubator, and the second six-well plate in a standard CO2 incubator.</li>
	<li>Compare transfection efficiency within each plate by fluorescence imaging using a fluorescence microscope.</li>
</ol>
4. Make quench buffer and H2O2
<ol>
	<li>Make 100 mL of quench buffer containing 125 mM N-tert-Butyl-&#945;-phenylnitrone (PBN) and 125 mM N, N&#8242;-Dimethylthiourea (DMTU). 
	NOTE: DMTU and PBN are free radical scavengers and are cell permeable.</li>
	<li>Dilute H2O2 to 200 mM. Each sample requires 6 mL of H2O2 to fully immerse the layer of cells at the bottom of each well. 
	&#8203;NOTE: The quench buffer is made the day before and stored at 4 &#176;C overnight, protected from light. Dilute the H2O2 on the day of the experiment.</li>
</ol>
5. Set up the platform incubator for IC-FPOP
NOTE: The platform incubator must be assembled under sterile conditions. Assemble the incubator in a sterile cell culture hood.
<ol>
	<li>Unscrew the platform incubator from the positioning stage and disconnect the temperature, gas, and humidifier lines.</li>
	<li>After spraying the incubator with 70% ethanol, place it in the cell culture hood.</li>
	<li>Remove the six-well plate from the platform incubator, secure the plate&#39;s original lid, and confirm cell confluency using a microscope.</li>
	<li>After cell confluency has been confirmed, replace the six-well plate with confluent cells back in the platform incubator inside the cell culture hood.</li>
	<li>Insert three precut (15 cm) 1.59 ID polymer tubes in each well via the embedded ports. Flush the tubes to the well walls and hold with custom 3D printed rings. 
	NOTE: Six 33 mm PLA filament 3D printed rings were custom designed to secure the tubing to the walls of the plate without disturbing the cells or getting in the way of the laser pulse.</li>
	<li>Cover the platform incubator with its quartz lid. Replace and secure the stage top incubator on the positioning system. Reconnect the temperature, gas, and humidifier lines.</li>
	<li>Connect 1.59 ID polymer tubing to 1/16&#34; end of the 1/16x1/8&#34; connectors.</li>
</ol>
6. Performing IC-FPOP in the platform incubator
<ol>
	<li>Prepare an integration software script for pump withdrawal. Use one peristaltic pump (Pump 8) to completely remove cell media from all six wells.</li>
	<li>Prime solvents in each channel of the other three peristaltic pumps (Pumps 5-7). Infuse H2O2 and quench buffer in their respective alternating tubes until the reagents reach the incubator ports.</li>
	<li>Confirm that the laser beam has been angled correctly by the mirrors and reaches the incubator uninhibited. 
	NOTE: Laser safety goggles must be worn whenever the laser is in use. Do not prematurely irradiate the cells during the angling/alignment process. Use cardboard to completely cover the quartz lid when aligning the beam. Also, use a printed outline on white paper of a six-well plate to further confirm the laser beam is hitting the center of each well. Use the Continuous pulse setting at the lowest frequency and energy for alignment.</li>
	<li>Check laser energy using an external sensor. Use one single laser pulse of 160 mJ at 50 Hz and 27 kV. 
	NOTE: A timer is needed for the following steps.</li>
	<li>Prepare the integration software script for pump infusion after confirming beam alignment.</li>
	<li>Begin the timer and press the Start button on the integration software pump script at the same time.</li>
	<li>Infuse 200 mM H2O2 at 35 mL/min into the first well (6-10 second mark on timer). 
	NOTE: There is a five second delay before a pump begins to infuse. It also takes the laser seven seconds before the pulse is triggered. The laser pulse must come immediately after H2O2 infusion.</li>
	<li>Press the Start button on the laser software at the 5 second mark to trigger the pulse at the 11 second mark on the timer.</li>
	<li>Infuse 125 mM quench solution at 35 mL/min into the first well immediately after the laser pulse. Manually move the positioning stage to align the next well with the laser beam.</li>
	<li>Repeat the above steps 6.5-6.9 until each well has been processed. 
	NOTE: IC-POP is performed in technical triplicate of three laser and three non-laser samples. One processed six-well plate serves as one biological replicate.</li>
	<li>In a cell culture hood, use a cell scraper to transfer the cells from each well into individual 15 mL conical tubes. Centrifuge cells at 1,200 x g for 5 minutes.</li>
	<li>Discard the supernatant and resuspend cells in 100 &#956;L of RIPA lysis buffer.</li>
	<li>Transfer cells to individual 1.2 mL polypropylene tubes.</li>
	<li>Flash freeze all samples in liquid nitrogen and place in a -80 &#176;C freezer until use. 
	&#8203;NOTE: The protocol can be paused here.</li>
</ol>
7. Protein extraction, purification, and proteolysis
<ol>
	<li>Thaw the samples and heat at 95 &#176;C in a heat block for 5 minutes.</li>
	<li>After heating, cool on ice for 5 minutes.</li>
	<li>Add 25 units of nuclease to the cell lysate to degrade single-stranded, double-stranded, linear and circular DNA and RNA and incubate at room temperate for 15 minutes.</li>
	<li>Centrifuge samples at 16,000 x g for 10 minutes at 4 &#176;C.</li>
	<li>Collect the supernatant and transfer to a clean polypropylene tube.</li>
	<li>Check the protein concentration using a colorimetric protein assay.</li>
	<li>Transfer 100 &#181;g of sample to a clean polypropylene tube and bring to 100 &#181;L with cell lysis buffer.</li>
	<li>Reduce samples with 10 mM dithiothreitol (DTT) at 50 &#176;C for 45 minutes.</li>
	<li>Cool samples at room temperature for 10 minutes.</li>
	<li>Alkylate with 50 mM iodoacetamide (IAA) at room temperature for 20 minutes. 
	NOTE: Protect IAA from light</li>
	<li>Add 460 &#181;L of pre-chilled (-20 &#176;C) acetone. Vortex samples and place at -20 &#176;C overnight. 
	NOTE: The protocol can be paused here.</li>
	<li>Next day, centrifuge samples at 16,000 x g for 10 minutes at 4 &#176;C.</li>
	<li>Remove acetone without disrupting the protein pellet.</li>
	<li>Add 50 &#181;L of 90% pre-chilled (-20 &#176;C) acetone. Vortex samples to mix and centrifuge at 16,000 x g for an additional 5 minutes at 4 &#176;C.</li>
	<li>Remove acetone and let samples dry for 2-3 minutes.</li>
	<li>Resuspend protein pellet with 10 mM Tris buffer pH 8.</li>
	<li>Resuspend MS grade trypsin (20 &#181;g stock) in 40 &#181;L of 10 mM Tris buffer pH 8 and add 2.5 &#181;g of trypsin to each sample.</li>
	<li>Incubate samples at 37 &#176;C overnight. 
	&#8203;NOTE: The protocol can be paused here.</li>
	<li>Assess peptide concentration using a colorimetric peptide assay.</li>
	<li>Quench the samples with 5% formic acid.</li>
	<li>Transfer 10 &#181;g of sample to a clean polypropylene tube.</li>
	<li>Dry the sample using a vacuum centrifuge and resuspend with 20 &#181;L of MS grade 0.1% formic acid (FA) in water.</li>
	<li>Transfer each sample to clean autosampler vials with pre-slit caps.</li>
</ol>
8. High performance Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)
<ol>
	<li>To localize FPOP modifications, analyze the digested cell lysate using LC-MS/MS analysis.</li>
	<li>Use mobile phases of 0.1% FA in water (A) and 0.1% FA in acetonitrile (ACN) (B).</li>
	<li>Load 0.5 &#181;g of sample onto a 180 &#181;m x 20 mm C18 (5 &#181;m and 100 &#197;) trapping column and wash the column with 99% (A) and 1% (B) for 15 minutes.</li>
	<li>Using a 75 &#181;m x 30 cm C18 (5 &#181;m and 125 &#197;) analytical column, elute and separate digested peptides with a flow rate of 0.300 &#181;L/min for 120 minutes.</li>
	<li>Run LC gradient as follows: 0&#8722;1 min, 3% solvent B; 2&#8722;100 min, 10&#8722;45% B;100&#8722;110 min, 45-100% B; 110&#8722;115 min, 100% B.</li>
	<li>Recondition the column at 3% (B) from 115-116 minutes and hold at 3% (B) from 116-120 minutes.</li>
	<li>Analyze eluted peptides in positive ion mode with nano electrospray ionization.</li>
	<li>Acquire MS1 spectra over a m/z scan range of 375-1500 at a resolution of 60,000.</li>
	<li>Set the automatic gain control (AGC) target to 5.0e5 with a maximum injection time of 50 ms and 5.0e4 intensity threshold.</li>
	<li>Isolate precursor ions with charge states 2-6 via data dependent acquisition (DDA) with an isolation window of 1.2 m/z and a cycle time of 4 seconds.</li>
	<li>Subject MS2 ions to high-energy collisional dissociation (HCD) (32% normalized energy).</li>
	<li>Exclude peptides after 1 MS/MS acquisition for 60 seconds.</li>
	<li>Set MS/MS resolution to 15,000 with an AGC target of 5.0e4 and a maximum injection time of 35 ms.</li>
</ol>
9. Proteome discoverer/data processing
<ol>
	<li>Search tandem raw data files on available bottom-up proteomics analysis software against a relevant Homo sapiens protein database and digest enzyme.</li>
	<li>Set the protein analysis search parameters.</li>
	<li>Set fragment tolerance to 0.02 Da and parent ion tolerance to 10 ppm.</li>
	<li>Set enzyme specificity to trypsin and allow for one missed cleavage.</li>
	<li>Set mass range to 375-1500 m/z.</li>
	<li>Establish peptide confidence at 95% (medium) and residue confidence at 99% (high).</li>
	<li>Accept proteins if at least two distinct peptides are identified with the 5% discovery rate (FDR) filter.</li>
	<li>Set carbamidomethylation as a static modification and all known hydroxyl radical side-chain modifications15,16&#160;as dynamic modifications.</li>
	<li>Once files are finished searching, export sequence, modification locations, protein accession, spectrum file, precursor abundance, and retention time information to an electronic database.</li>
	<li>Calculate the extent of modification per peptide or residue from this equation: 
	<img alt="Equation 1" src="/files/ftp_upload/62153/62153eq01.jpg" /> 
	NOTE: 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. Over time, protein in the presence of hydrogen peroxide will oxidize, resulting in background oxidations. To calculate the extent of modification, the area of the modified peptide is divided by the total area. A non-irradiated control sample accounts for background oxidation. The background oxidation from the control sample is subtracted out from the laser treated sample to identify an FPOP modification.</li>
</ol>

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The authors declare no competing financial interest. 
The research presented herein is associated with the below referenced patent application: 
U.S. Non-Provisional Patent Application Number: 17/042,565 
Title: &#34;Device and Method for Determining Protein Folding&#34; 
UMB Docket Number: LJ-2018-104 UMass Ref: UMA 18-059.

Proteins perform much of the work in living cells. Given this importance, detailed data on protein function and higher order structure (HOS) in the cellular environment is needed to deepen understanding of the intricacies in larger complexes and enzymatic reactions in cells as opposed to purified systems. To do this, a hydroxyl radical protein foot printing (HRFP) method was adopted entitled In-Cell Fast Photochemical Oxidation of Proteins (IC-FPOP). Most FPOP studies have been done in vitro in relatively pure protein systems, which markedly contrasts with the crowded molecular environment which affects binding interactions and protein conformational dynamics. As a result, there is a chasm between the findings from in vitro experiments18 and those that would be obtained in an actual cellular environment. To bridge the gap between the idealized conditions of an in vitro FPOP experiment&#160;and the complex nature of the cell, a new automated six-well plate-based in cell-FPOP platform has been developed. This novel FPOP technology is capable of identifying and characterizing these molecular species and tracing their dynamic molecular interactions in both healthy and diseased states. This new platform is called Platform Incubator with Movable XY stage (PIXY).
FPOP has been successfully used to characterize the structural information within the proteome. However, every biological technique has certain limitations that require further improvement. Specific reagents are required during laser photolysis and to efficiently quench unreacted hydroxyl radicals. Separation of digested peptides can require large amounts of time to maximize structural information.This wealth of information can also require extensive quantitation during post-MS data analysis1. The platform incubator, including the peripheral machinery needed for cell culture and IC-FPOP at the laser platform, comes with a large cost that may not be feasible for some labs. As progress continues to be made, robust software and analysis tools should advance the technique further; some of which is showcased in this study. Current studies in this platform incubator have been performed on HEK293T cells and in C. elegans. The IC-FPOP method has been shown to be compatible with a wide variety of cell lines including Chinese hamster ovary (CHO), Vero, MCF-7, and MCF10-A cells19. Since the general IC-FPOP method is translatable to this static platform, these cell lines should be amenable for study using PIXY as well.
IC-FPOP utilizes H2O2 to oxidatively modify solvent accessible side chains of amino acids, to then further discern protein interactions, structure, and metabolic effects within viable cells which is significant in providing biological context. It is essential before an IC-FPOP experiment to confirm that the cells are viable after H2O2 addition. Cell viability studies demonstrated that the cells were viable in the presence of H2O2 concentrations up to 200 mM 13. It is also important to make sure H2O2 is infused at a final concentration of 200 mM directly on cells after media is removed. Failure to completely remove cell culture media will cause varying concentrations of H2O2. Compared to standard conditions, increasing the incubation time to 10 seconds along with increasing the H2O2 concentration led to a higher number of proteins modified by IC-FPOP in the platform incubator. It is imperative to prime peristaltic pumps before use to ensure pumps are working properly and liquid is being dispersed. Failure to do so may cause air bubbles in the tubing, insufficient volume of H2O2 to immerse cells, and/or insufficient volume of quench solution.
Another issue that may arise is unwanted delays in the system. An example of this is the process of verifying received commands for the pump systems which adds significant delays on the order of 1000 or more milliseconds using the integration software. This problem can be fixed by minimizing the communication with the pumps during the experiment and using pre-set commands ahead of time as much as possible.
In the future, the goal for PIXY is producing a fully automated and integrated system. In addition to the peristaltic pumps, the triggering of the laser pulse will be automated. A new positioning system will also be utilized for the rapid movement of the platform incubator to enhance speed and accuracy. All components of the system will continue to be programmed using the integration software to further increase throughput.

Protein footprinting techniques can reveal profound information on the organization of proteins. These essential structural biology MS-based techniques are a component of the mass spectrometry toolbox. These methods probe protein higher order structure (HOS) and synergy via covalent labeling1,2,3,4. Fast photochemical oxidation of proteins (FPOP) employs hydroxyl radicals to oxidatively modify solvent accessible side chains of amino acids5,6 (Table 1). The method utilizes an excimer laser at 248 nm for photolysis of hydrogen peroxide (H2O2) to generate hydroxyl radicals. Theoretically, 19 of the 20 amino acids can be oxidatively modified with Gly being the lone exception. However, owing to the varying&#160;reactivity rates of amino acids with hydroxyl radicals, modification of only a subset of these has been observed experimentally. Still, the method does have the potential for analysis over the length of a protein sequence5. FPOP modifies proteins on the microsecond timescale, making it useful in studying weak interactions with fast off rates. Solvent accessibility changes upon ligand-binding or a change in protein conformation, thus, the power of the method lies in the comparison of the labeling pattern of a protein in multiple states (i.e., ligand-free compared to ligand-bound). As a result, FPOP has been successful in identifying protein-protein and protein-ligand interaction sites and regions of conformational change7,8,9,10. The FPOP method has been extended from the study of purified protein systems to in-cell analysis. In-cell FPOP (IC-FPOP) can oxidatively modify over a thousand proteins in cells to provide structural information across the proteome11,12. The conventional IC-FPOP platform utilizes a flow system to flow cells single file past the laser beam. The development of this system allowed individual cells to have equal exposure to laser irradiation. This led to a 13-fold rise in the number of oxidatively labeled proteins12. However, a limitation of the flow system is the length of a single sample experiment consisting of a 10-minute irradiation interval during which modification takes place and an additional 10-minute wash cycle. The time constraints of IC-FPOP makes it unsuitable for studying short lived protein folding intermediates or changes that exist among interaction networks in biochemical signaling cascades. This temporal limitation inspired the design of a new IC-FPOP platform equipped with higher throughput.
To accurately measure protein higher order structure in the native cell environment, the new design allows cell culture to be accomplished directly at the laser platform, which enables IC-FPOP to be high throughput. This setup also allows minimized perturbations to the cellular environment, in contrast to IC-FPOP using flow where adherent cells must be removed from the substrate. The new platform permits IC-FPOP to occur in a sterile incubation system using a CO2 and temperature-controlled stage top chamber while utilizing configured mirror optics for laser beam guidance, a positioning system for XY motion, and peristaltic pumps for chemical exchange. The new platform for conducting IC-FPOP is entitled Platform Incubator with Movable XY Stage (PIXY) (Figure 1). In PIXY, IC-FPOP is carried out on human cells grown in six-well plates within the platform incubator chamber. For this configuration, the laser beam is reflected downward onto the plate using beam compatible mirrors as a positioning stage that holds the incubator is moved, in the XY-plane, so the laser beam is strategically aligned to only irradiate one well at a time. Validation studies show that IC-FPOP can be performed faster in PIXY than in the flow system and leads to increased amino acid modifications per protein. The development of this new IC-FPOP platform will expound upon the knowledge that can be gained from cellular experiments13.

<table><tbody><tr><td>Ismatec Reglo ICC Peristaltic Pumps</td><td>Cole-Palmer</td><td>122270050</td><td></td></tr><tr><td>&amp;nbsp;Kinematic Mirror Mount for &amp;Oslash;2&quot; Optics</td><td>Thor Labs</td><td></td><td></td></tr><tr><td>10X trypsin&amp;minus;EDTA</td><td>Corning</td><td>AB00490-00005</td><td></td></tr><tr><td>50.0mm 248nm 45&amp;deg;, Excimer Laser Line Mirror</td><td>Edmond Optics</td><td></td><td></td></tr><tr><td>Acetone, HPLC Grade</td><td>Fisher Scientific</td><td></td><td></td></tr><tr><td>Acetonitrile with 0.1% Formic Acid (v/v), LC/MS Grade</td><td>Fisher Scientific</td><td></td><td></td></tr><tr><td>ACQUITY UPLC M-Class Symmetry C18 Trap Column, 100&amp;Aring;, 5 &amp;micro;m, 180 &amp;micro;m x 20 mm, 2G, V/M, 1/pkg</td><td>Waters</td><td>23275</td><td>other high resolution instruments (e.g. Q exactive Orbitrap or Orbitrap Fusion) can be used</td></tr><tr><td>ACQUITY UPLC M-Class System</td><td>Waters</td><td>A53225</td><td></td></tr><tr><td>Afinia H480 3D Printer</td><td>(Innovation Space University of Maryland Baltimore Campus Library)</td><td></td><td></td></tr><tr><td>air pump</td><td>OKOlabs</td><td>D12345</td><td></td></tr><tr><td>Aluminum Foil</td><td>Fisher Scientific</td><td>Stock #63-120</td><td></td></tr><tr><td>Aqua 5 &amp;micro;m C18 125 &amp;Aring; packing material</td><td>Phenomenex</td><td></td><td></td></tr><tr><td>carbon dioxide unit</td><td>OKOlabs</td><td>MadMotor&amp;reg;-UHV</td><td></td></tr><tr><td>Centrifuge</td><td>Eppendorf</td><td></td><td></td></tr><tr><td>connectors (Y PP 1/16&amp;rdquo; and 1/16x1/8&amp;rdquo;)</td><td>Cole-Palmer</td><td>116891000</td><td></td></tr><tr><td>Delicate Task Wipers</td><td>Fisher Scientific</td><td>022625501</td><td></td></tr><tr><td>Dithiothreiotol (DTT)</td><td>AmericanBio</td><td></td><td></td></tr><tr><td>DMSO, Anhydrous</td><td>Invitrogen</td><td>LS118-500</td><td></td></tr><tr><td>Dulbecco&amp;rsquo;s phosphate-buffered saline (DPBS)</td><td>Corning</td><td>SK-78001-82</td><td></td></tr><tr><td>EX350 excimer laser</td><td>GAM Laser</td><td>PI89900</td><td></td></tr><tr><td>Fetal bovine serum (FBS)</td><td>Corning</td><td>SK-12023-78</td><td></td></tr><tr><td>Formic Acid, LC/MS Grade</td><td>Fisher Scientific</td><td>A929-4</td><td>4 L quantity is not necessary</td></tr><tr><td>HEK293T cells</td><td>Paul Shapiro Lab (University of Maryland Baltimore)</td><td></td><td></td></tr><tr><td>humidifier</td><td>OKOlabs</td><td>Nano-LPMW stage</td><td></td></tr><tr><td>HV3-2 VALVE</td><td>Hamilton</td><td>BP152-500</td><td></td></tr><tr><td>Hydrogen Peroxide</td><td>Fisher Scientific</td><td>LS120-500</td><td></td></tr><tr><td>Iodoacetamide (IAA)</td><td>ACROS Organics</td><td></td><td></td></tr><tr><td>LABVIEW Professional 2018</td><td>National Instruments</td><td>86728</td><td></td></tr><tr><td>MadMotor Positioning system and controllers</td><td>Mad City Labs</td><td>W6-4</td><td></td></tr><tr><td>Methanol, LC/MS Grade</td><td>Fisher Scientific</td><td>01-213-100</td><td>any brand is sufficient</td></tr><tr><td>Microcentrifuge</td><td>Thermo Scientific</td><td>H301-T Unit-BL-PLUS</td><td></td></tr><tr><td>N,N&amp;prime;-Dimethylthiourea (DMTU)</td><td>ACROS Organics</td><td></td><td></td></tr><tr><td>Nanopositioinging stage</td><td>Mad City Labs</td><td></td><td></td></tr><tr><td>N-tert-Butyl-&amp;alpha;-phenylnitrone (PBN)</td><td>ACROS Organics</td><td></td><td></td></tr><tr><td>OKO Touch Monitoring System</td><td>OKOlabs</td><td></td><td></td></tr><tr><td>Orbitrap Fusion Lumos Tribrid Mass Spectrometer</td><td>Thermo Scientific</td><td>7Z02936</td><td></td></tr><tr><td>PE50-C pyroelectric energy meter</td><td>Ophir Optronics</td><td></td><td></td></tr><tr><td>Penicillin-streptomycin</td><td>Corning</td><td></td><td></td></tr><tr><td>Pierce Quantitative Colorimetric Peptide Assay</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>Pierce Rapid Gold BCA Protein Assay Kit</td><td>Thermo Scientific</td><td></td><td></td></tr><tr><td>Pierce Trypsin Protease, MS Grade</td><td>Thermo Scientific</td><td>75002436</td><td></td></tr><tr><td>Pierce Universal Nuclease for Cell Lysis</td><td>Fisher Scientific</td><td>06-666A</td><td></td></tr><tr><td>pressure gauge</td><td>OKOlabs</td><td>OKO-AIR-PUMP-BL</td><td></td></tr><tr><td>PTFE filter</td><td>OKOlabs</td><td>CO2-UNIT-BL</td><td></td></tr><tr><td>Six 33 mm PLA filament rings</td><td>(Innovation Space University of Maryland Baltimore Campus Library)</td><td></td><td></td></tr><tr><td>sterile incubator</td><td>OKOlabs</td><td></td><td></td></tr><tr><td>temperature unit</td><td>OKOlabs</td><td>OKO-TOUCH</td><td></td></tr><tr><td>Thermo Scientific Pierce RIPA Buffer</td><td>Fisher Scientific</td><td>A117-50</td><td></td></tr><tr><td>TiNKERcad</td><td>(Innovation Space University of Maryland Baltimore Campus Library)</td><td></td><td></td></tr><tr><td>Tris Base</td><td>Fisher Scientific</td><td>H325-100</td><td>any 30% hydrogen peroxide is sufficient</td></tr><tr><td>tubing (Tygon 3.18 and 1.59 ID)</td><td>Cole-Palmer</td><td>177350250</td><td></td></tr><tr><td>Water with 0.1% Formic Acid (v/v), LC/MS Grade</td><td>Fisher Scientific</td><td>A454SK-4</td><td>4 L quantity is not necessary</td></tr><tr><td>Water, LC/MS Grade</td><td>Fisher Scientific</td><td>88702</td><td></td></tr><tr><td></td><td></td><td>90058</td><td></td></tr><tr><td></td><td></td><td>KM200</td><td></td></tr><tr><td></td><td></td><td>186007496</td><td></td></tr></tbody></table>

platform incubator with movable xy stage: a new platform for implementing in-cell fast photochemical oxidation of proteins

Fast Photochemical Oxidation of proteins (FPOP) coupled with mass spectrometry (MS) has become an invaluable tool in structural proteomics to interrogate protein interactions, structure, and protein conformational dynamics as a function of solvent accessibility. In recent years, the scope of FPOP, a hydroxyl radical protein foot printing (HRPF) technique, has been expanded to protein labeling in live cell cultures, providing the means to study protein interactions in the convoluted cellular environment. In-cell protein modifications can provide insight into ligand induced structural changes or conformational changes accompanying protein complex formation, all within the cellular context. Protein footprinting has been accomplished employing a customary flow-based system and a 248 nm KrF excimer laser to yield hydroxyl radicals via photolysis of hydrogen peroxide, requiring 20 minutes of analysis for one cell sample.To facilitate time-resolved FPOP experiments, the use of a new 6-well plate-based IC-FPOP platform was pioneered. In the current system, a single laser pulse irradiates one entire well, which truncates the FPOP experimental time frame resulting in 20 seconds of analysis time, a 60-fold decrease. This greatly reduced analysis time makes it possible to research cellular mechanisms such as biochemical signaling cascades, protein folding, and differential experiments (i.e., drug-free vs. drug bound) in a time-dependent manner. This new instrumentation, entitled Platform Incubator with Movable XY Stage (PIXY), allows the user to perform cell culture and IC-FPOP directly on the optical bench using a platform incubator with temperature, CO2 and humidity control. The platform also includes a positioning stage, peristaltic pumps, and mirror optics for laser beam guidance. IC-FPOP conditions such as optics configuration, flow rates, transient transfections, and H2O2 concentration in PIXY have been optimized and peer-reviewed. Automation of all components of the system will reduce human manipulation and increase throughput.

To confirm that the platform incubator conditions are sufficient for cell culture at the laser platform, GCaMP2 was transiently transfected into HEK293T and transfection efficiency for both plates was assessed via fluorescence imaging (Figure 4A). GCaMP2 is a calcium sensing fluorescent protein used as a genetically encoded intracellular calcium indicator. It is a fusion of green fluorescent protein (GFP) and the calcium-binding protein, calmodulin. A luciferase assay was performed on HEK 293 cells transfected with plasmid prl-TK in order to quantify transfection efficiency (Figure 4B). These results show that the platform incubator exceeded the performance of the standard incubator, with a 1.13-fold increase in transfection efficiency, providing a quantitative benchmark for optimal cell culture environment.
FPOP modifications in HEK293T cells labeled in the flow system were compared to those labeled in the platform incubator and showed that the platform incubator outperforms the flow system both in the number of proteins modified (Figure 5)&#160;and the total FPOP coverage in those proteins. The number of FPOP modified proteins acquired in the platform incubator was approximately 1051, 2.2- fold more than those acquired in a typical experiment. Modifications were combined between two biological replicates for each experiment. Furthermore, PIXY provides higher throughput.
To demonstrate the advantage of higher modification coverage across a protein, IC-FPOP modifications were localized on the peptide level and the extent of modification was quantified to distinguish differences in outcomes between the systems for actin, a 375 amino acid protein. In the flow system, two modified peptides were detected, providing limited structural information (Figure 6A). However, five modified peptides spanning the actin sequence were detected in the platform incubator. Tandem mass spectra indicate that residue Pro322 was both modified and detected in each experiment (Figure 6B). The five peptides modified in the platform incubator samples contained twelve modified residues, while only four residues were modified with the flow system (Figure 6C). The increase in oxidation coverage provides more structural information across the protein.
Espino et al. demonstrated the capacity of FPOP to be performed in vivo (IV-FPOP) within C. elegans, a worm model for human disease states17.While IV-FPOP is also performed via a flow system, the PIXY system was tested for compatibility with the worms. Approximately 10,000 worms were incubated in each well in the platform incubator at 20 &#176;C. LC&#8722;MS/MS analysis revealed that 792 proteins were modified by IV-FPOP in the platform incubator compared to the 545 proteins modified with the flow system (Figure 7). These results demonstrate that in addition to 2D cell culture, this new methodology is also compatible with the study of other biological systems such as C. elegans.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/62153/62153fig01.jpg" /> 
Figure 1. Schematic of PIXY System. System components: (A) stage-top incubator, (B) positioning system , (C) peristaltic pumps, and (D) perfusion lines. Cell culture media is removed from each well via pumps before H2O2 and quench solutions are infused at calculated timepoints. Laser path for irradiation showcased in white. Reprinted with permission from Johnson, D. T., Punshon-Smith, B., Espino, J. A., Gershenson, A., Jones, L. M., Implementing In-Cell Fast Photochemical Oxidation of Proteins in a Platform Incubator with a Movable XY Stage. Analytical Chemistry, 92(2), 1691-1696 2019. Copyright 2020 American Chemical Society. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/62153fig01large.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/62153/62153fig02.jpg" /> 
Figure 2. Fully Assembled PIXY system. (A) Touch monitoring system, (B) carbon dioxide unit, (C) temperature unit, (D) air pump, (E) humidifier, (F) optical mirrors, (G) platform incubator, (H) positioning stage, (I) 248nm KrF excimer laser, and (J) peristaltic pumps. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/62153fig02large.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/62153/62153fig03.jpg" /> 
Figure 3.&#160;Automation of Peristaltic Pumps. (A) Example command script in LABVIEW. Command options include volume, flow rate, pauses, flow direction. Speed, stage distance, and location are currently being automated. (B) Script reader in LABVIEW. Here, command scripts are uploaded then Run Sequence and START are pressed to initiate pumps. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/62153fig03large.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/62153/62153fig04.jpg" /> 
Figure 4. HEK cell transfection efficiency. (A) Mean fluorescent intensity of GCaMP2 transfection comparison between standard incubator (Control) and stage-top incubator (PIXY). Dots and squares represent each point in a well where a measure was taken. (B) Transfection efficiency quantitated and validated with a different vector plasmid, pRL-TK. P-value&#60; 0.005. Reprinted with permission from Johnson, D. T., Punshon-Smith, B., Espino, J. A., Gershenson, A., Jones, L. M., Implementing In-Cell Fast Photochemical Oxidation of Proteins in a Platform Incubator with a Movable XY Stage. Analytical Chemistry, 92(2), 1691-1696 2019. Copyright 2020 American Chemical Society. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/62153fig04large.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/62153/62153fig05.jpg" /> 
Figure 5. Comparison of proteins modified in the single cell flow system and PIXY. Venn diagram of proteins modified using in the flow system (purple) and in PIXY (green). Reprinted with permission from Johnson, D. T., Punshon-Smith, B., Espino, J. A., Gershenson, A., Jones, L. M., Implementing In-Cell Fast Photochemical Oxidation of Proteins in a Platform Incubator with a Movable XY Stage. Analytical Chemistry, 92(2), 1691-1696 2019. Copyright 2020 American Chemical Society. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/62153fig05large.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/62153/62153fig06.jpg" /> 
Figure 6. Localization of IC-FPOP modifications. Comparison of IC-FPOP modifications between systems. (A) Bar graph of oxidatively modified peptides within actin from the flow system (purple) vs platform incubator (green). (B) Tandem MS spectra of actin (peptide 316-326) with modified proline in both systems and unmodified actin peptide (C) FPOP modified residues of actin (PDB: 6ZXJ, chain A 11 modified residues in platform incubator (green), 3 modified residues in the flow system (purple), 1 overlapping modified residue (yellow). Reprinted with permission from Johnson, D. T., Punshon-Smith, B., Espino, J. A., Gershenson, A., Jones, L. M., Implementing In-Cell Fast Photochemical Oxidation of Proteins in a Platform Incubator with a Movable XY Stage. Analytical Chemistry, 92(2), 1691-1696 2019. Copyright 2020 American Chemical Society. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/62153fig06large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" class="xfigimg" src="/files/ftp_upload/62153/62153fig07.jpg" /> 
Figure 7.&#160;Comparison of FPOP modified proteins in C. elegans by flow vs PIXY. There is a 1.5-fold increase in oxidatively modified proteins using PIXY when compared to the flow system. Reprinted with permission from Johnson, D. T., Punshon-Smith, B., Espino, J. A., Gershenson, A., Jones, L. M., Implementing In-Cell Fast Photochemical Oxidation of Proteins in a Platform Incubator with a Movable XY Stage. Analytical Chemistry, 92(2), 1691-1696 2019. Copyright 2020 American Chemical Society. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/62153fig07large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Table 1. Workflow modification distribution and mass shifts (Da). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/62153/Table 1.docx" target="_blank">Please click here to download&#160;this table.</a>

Watch this Scientific Journal Video about Platform Incubator with Movable XY Stage: A New Platform for Implementing In-Cell Fast Photochemical Oxidation of Proteins at JoVE.com

Platform Incubator with Movable XY Stage: A New Platform for Implementing In-Cell Fast Photochemical Oxidation of Proteins

A new static platform is used to characterize protein structure and interaction sites in the native cell environment utilizing a protein footprinting technique called in-cell fast photochemical oxidation of proteins (IC-FPOP).

Fast Photochemical Oxidation of proteins (FPOP) coupled with mass spectrometry (MS) has become an invaluable tool in structural proteomics to interrogate ...

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Nanyang Technological University

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Biochemistry

3.3K Views.  University of Maryland Baltimore. Deze methode biedt oplossingen voor de veeleisende biologische vragen van vandaag. Vanuit een in-cell FPOP-experiment kunnen we eiwit-ligandinteracties, eiwit-eiwitinteractieplaatsen en regio's van conformationele verandering bestuderen. Het voordeel van deze technologie is het gebruik van een geautomatiseerd zes-put plaat-gebaseerd IC-FPOP platform dat het mogelijk maakt om cellen te laten groeien en in-cell FPOP studies uit te voeren direct aan de laser.Deze methode kan worden gebrui...

Video: Platform Incubator with Movable XY Stage: A New Platform for Implementing In-Cell Fast Photochemical Oxidation of Proteins

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. ...

Spatiotemporally Controlled Nuclear Translocation of Guests in Living Cells Using Caged Molecular Glues as Photoactivatable Tags

The cell nucleus is one of the most important organelles as a subcellular drug-delivery target, since modulation of gene replication and expression is effective for treating various diseases. Here, we demonstrate light-triggered nuclear translocation of guests using caged molecular glue (CagedGlue-R) tags, whose multiple guanidinium ion (Gu+) pendants are protected by an anionic photocleavable group (butyrate-substituted nitroveratryloxycarbonyl; BANVOC). Guests tagged with CagedGlue-R are taken up into living cells via endocytosis and remain in endosomes. However, upon photoirradiation, CagedGlue-R is converted into uncaged molecular glue (UncagedGlue-R) carrying multiple Gu+ pendants, which facilitates the endosomal escape and subsequent nuclear translocation of the guests. This method is promising for site-selective nuclear-targeting drug delivery, since the tagged guests can migrate into the cytoplasm followed by the cell nucleus only when photoirradiated. CagedGlue-R tags can deliver macromolecular guests such as quantum dots (QDs) as well as small-molecule guests. CagedGlue-R tags can be uncaged with not only UV light but also two-photon near-infrared (NIR) light, which can deeply penetrate into tissue.

This protocol describes light-triggered nuclear translocation of guests in living cells using caged molecular glue tags. This method is promising for site-selective nuclear-targeting drug delivery.

The cell nucleus is one of the most important organelles as a subcellular drug-delivery target, since modulation of gene replication and expression is ...

Chemistry

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.

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. ...

Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes

Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area of proteins. This technique relies on the reaction of amino acid side chains with hydroxyl radicals freely diffusing in solution. FPOP generates these radicals in situ by laser photolysis of hydrogen peroxide, creating a burst of hydroxyl radicals that is depleted on the order of a microsecond. When these hydroxyl radicals react with a solvent-accessible amino acid side chain, the reaction products exhibit a mass shift that can be measured and quantified by mass spectrometry. Since the rate of reaction of an amino acid depends in part on the average solvent accessible surface of that amino acid, measured changes in the amount of oxidation of a given region of a protein can be directly correlated to changes in the solvent accessibility of that region between different conformations (e.g., ligand-bound versus ligand-free, monomer vs. aggregate, etc.) FPOP has been applied in a number of problems in biology, including protein-protein interactions, protein conformational changes, and protein-ligand binding. As the available concentration of hydroxyl radicals varies based on many experimental conditions in the FPOP experiment, it is important to monitor the effective radical dose to which the protein analyte is exposed. This monitoring is efficiently achieved by incorporating an inline dosimeter to measure the signal from the FPOP reaction, with laser fluence adjusted in real-time to achieve the desired amount of oxidation. With this compensation, changes in protein topography reflecting conformational changes, ligand-binding surfaces, and/or protein-protein interaction interfaces can be determined in heterogeneous samples using relatively low sample amounts.

Fast photochemical oxidation of proteins is an emerging technique for the structural characterization of proteins. Different solvent additives and ligands have varied hydroxyl radical scavenging properties. To compare the protein structure in different conditions, real-time compensation of hydroxyl radicals generated in the reaction is required to normalize reaction conditions.

Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area ...

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM)

Protein-protein interactions (PPIs) are key molecular events to biology. However, it remains a challenge to visualize PPIs with sufficient resolution and sensitivity in cells because the resolution of conventional light microscopy is diffraction-limited to ~250 nm. By combining bimolecular fluorescence complementation (BiFC) with photoactivated localization microscopy (PALM), PPIs can be visualized in cells with single molecule sensitivity and nanometer spatial resolution. BiFC is a commonly used technique for visualizing PPIs with fluorescence contrast, which involves splitting of a fluorescent protein into two non-fluorescent fragments. PALM is a recent superresolution microscopy technique for imaging biological samples at the nanometer and single molecule scales, which uses phototransformable fluorescent probes such as photoactivatable fluorescent proteins (PA-FPs). BiFC-PALM was demonstrated by splitting PAmCherry1, a PA-FP compatible with PALM, for its monomeric nature, good single molecule brightness, high contrast ratio, and utility for stoichiometry measurements. When split between amino acids 159 and 160, PAmCherry1 can be made into a BiFC probe that reconstitutes efficiently at 37 &#176;C with high specificity to PPIs and low non-specific reconstitution. Ras-Raf interaction is used as an example to show how BiFC-PALM helps to probe interactions at the nanometer scale and with single molecule resolution. Their diffusion can also be tracked in live cells using single molecule tracking (smt-) PALM. In this protocol, factors to consider when designing the fusion proteins for BiFC-PALM are discussed, sample preparation, image acquisition, and data analysis steps are explained, and a few exemplary results are showcased. Providing high spatial resolution, specificity, and sensitivity, BiFC-PALM is a useful tool for studying PPIs in intact biological samples.

Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation BiFC-PALM

Protein-protein interactions are visualized in cells with nanometer spatial resolution by combining bimolecular fluorescence complementation (BiFC) with photoactivated localization microscopy (PALM). Described here is the use of BiFC-PALM for imaging Ras-Raf interactions in U2OS cells for visualizing the nanoscale clustering and diffusion of individual Ras-Raf complexes.

Protein-protein interactions (PPIs) are key molecular events to biology. However, it remains a challenge to visualize PPIs with sufficient resolution and ...

Bioengineering

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

Unraveling the interaction network of molecules in-vivo is key to understanding the mechanisms that regulate cell function and metabolism. A multitude of methodological options for addressing molecular interactions in cells have been developed, but most of these methods suffer from being rather indirect and therefore hardly quantitative. On the contrary, a few high-end quantitative approaches were introduced, which however are difficult to extend to high throughput. To combine high throughput capabilities with the possibility to extract quantitative information, we recently developed a new concept for identifying protein-protein interactions (Schwarzenbacher et al., 2008). Here, we describe a detailed protocol for the design and the construction of this system which allows for analyzing interactions between a fluorophore-labeled protein ("prey") and a membrane protein ("bait") in-vivo. Cells are plated on micropatterned surfaces functionalized with antibodies against the bait exoplasmic domain. Bait-prey interactions are assayed via the redistribution of the fluorescent prey. The method is characterized by high sensitivity down to the level of single molecules, the capability to detect weak interactions, and high throughput capability, making it applicable as screening tool.

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

This video shows experiments with subsequent analysis of protein-protein interactions by the use of micro-patterned surfaces. The approach offers the possibility to detect protein interactions in living cells and combines high throughput capabilities with the possibility to extract quantitative information.

Unraveling the interaction network of molecules in-vivo is key to understanding the mechanisms that regulate cell function and metabolism. A multitude of ...

Biology

Photoconversion of Purified Fluorescent Proteins and Dual-probe Optical Highlighting in Live Cells

Photoconvertible fluorescent proteins (pc-FPs) are a class of fluorescent proteins with "optical highlighter" capability, meaning that the color of fluorescence can be changed by exposure to light of a specific wavelength. Optical highlighting allows noninvasive marking of a subpopulation of fluorescent molecules, and is therefore ideal for tracking single cells or organelles.
Critical parameters for efficient photoconversion are the intensity and the exposure time of the photoconversion light. If the intensity is too low, photoconversion will be slow or not occur at all. On the other hand, too much intensity or too long exposure can photobleach the protein and thereby reduce the efficiency of photoconversion.
This protocol describes a general approach how to set up a confocal laser scanning microscope for pc-FP photoconversion applications. First, we describe a procedure for preparing purified protein droplet samples. This sample format is very convenient for studying the photophysical behavior of fluorescent proteins under the microscope. Second, we will use the protein droplet sample to show how to configure the microscope for photoconversion. And finally, we will show how to perform optical highlighting in live cells, including dual-probe optical highlighting with mOrange2 and Dronpa.

This protocol describes a general approach to perform photoconversion of fluorescent proteins on a confocal laser scanning microscope. We describe procedures for the photoconversion of puried protein samples, as well as for dual-probe optical highlighting in live cells with mOrange2 and Dronpa.

Photoconvertible fluorescent proteins (pc-FPs) are a class of fluorescent proteins with "optical highlighter" capability, meaning that the color of ...

Spatial and Temporal Control of T Cell Activation Using a Photoactivatable Agonist

T lymphocytes engage in rapid, polarized signaling, occurring within minutes following TCR activation. This induces formation of the immunological synapse, a stereotyped cell-cell junction that regulates T cell activation and directionally targets effector responses. To study these processes effectively, an imaging approach that is tailored to capturing fast, polarized responses is necessary. This protocol describes such a system, which is based on a photoactivatable peptide-major histocompatibility complex (pMHC) that is non-stimulatory until it is exposed to ultraviolet light. Targeted decaging of this reagent during videomicroscopy experiments enables precise spatiotemporal control of TCR activation and high-resolution monitoring of subsequent cellular responses by total internal reflection (TIRF) imaging. This approach is also compatible with genetic and pharmacological perturbation strategies. This allows for the assembly of well-defined molecular pathways that link TCR signaling to the formation of the polarized cytoskeletal structures that underlie the immunological synapse.

This protocol describes an imaging-based method to activate T lymphocytes using photoactivatable peptide-MHC, enabling precise spatiotemporal control of T cell activation.

T lymphocytes engage in rapid, polarized signaling, occurring within minutes following TCR activation. This induces formation of the immunological ...

Immunology and Infection

4D Imaging of Protein Aggregation in Live Cells

One of the key tasks of any living cell is maintaining the proper folding of newly synthesized proteins in the face of ever-changing environmental conditions and an intracellular environment that is tightly packed, sticky, and hazardous to protein stability1. The ability to dynamically balance protein production, folding and degradation demands highly-specialized quality control machinery, whose absolute necessity is observed best when it malfunctions. Diseases such as ALS, Alzheimer's, Parkinson's, and certain forms of Cystic Fibrosis have a direct link to protein folding quality control components2, and therefore future therapeutic development requires a basic understanding of underlying processes. Our experimental challenge is to understand how cells integrate damage signals and mount responses that are tailored to diverse circumstances.
The primary reason why protein misfolding represents an existential threat to the cell is the propensity of incorrectly folded proteins to aggregate, thus causing a global perturbation of the crowded and delicate intracellular folding environment1. The folding health, or "proteostasis," of the cellular proteome is maintained, even under the duress of aging, stress and oxidative damage, by the coordinated action of different mechanistic units in an elaborate quality control system3,4. A specialized machinery of molecular chaperones can bind non-native polypeptides and promote their folding into the native state1, target them for degradation by the ubiquitin-proteasome system5, or direct them to protective aggregation inclusions6-9.
In eukaryotes, the cytosolic aggregation quality control load is partitioned between two compartments8-10: the juxtanuclear quality control compartment (JUNQ) and the insoluble protein deposit (IPOD) (Figure 1 - model). Proteins that are ubiquitinated by the protein folding quality control machinery are delivered to the JUNQ, where they are processed for degradation by the proteasome. Misfolded proteins that are not ubiquitinated are diverted to the IPOD, where they are actively aggregated in a protective compartment.
Up until this point, the methodological paradigm of live-cell fluorescence microscopy has largely been to label proteins and track their locations in the cell at specific time-points and usually in two dimensions. As new technologies have begun to grant experimenters unprecedented access to the submicron scale in living cells, the dynamic architecture of the cytosol has come into view as a challenging new frontier for experimental characterization. We present a method for rapidly monitoring the 3D spatial distributions of multiple fluorescently labeled proteins in the yeast cytosol over time. 3D timelapse (4D imaging) is not merely a technical challenge; rather, it also facilitates a dramatic shift in the conceptual framework used to analyze cellular structure.
We utilize a cytosolic folding sensor protein in live yeast to visualize distinct fates for misfolded proteins in cellular aggregation quality control, using rapid 4D fluorescent imaging. The temperature sensitive mutant of the Ubc9 protein10-12 (Ubc9ts) is extremely effective both as a sensor of cellular proteostasis, and a physiological model for tracking aggregation quality control. As with most ts proteins, Ubc9ts is fully folded and functional at permissive temperatures due to active cellular chaperones. Above 30 &deg;C, or when the cell faces misfolding stress, Ubc9ts misfolds and follows the fate of a native globular protein that has been misfolded due to mutation, heat denaturation, or oxidative damage. By fusing it to GFP or other fluorophores, it can be tracked in 3D as it forms Stress Foci, or is directed to JUNQ or IPOD.

Cellular viability depends on timely and efficient management of protein misfolding. Here we describe a method for visualizing the different potential fates of a misfolded protein: refolding, degradation, or sequestration in inclusions. We demonstrate the use of a folding sensor, Ubc9ts, for monitoring proteostasis and aggregation quality control in live cells using 4D microscopy.

One of the key tasks of any living cell is maintaining the proper folding of newly synthesized proteins in the face of ever-changing environmental ...

Live Cell Imaging of Early Autophagy Events: Omegasomes and Beyond

Autophagy is a cellular response triggered by the lack of nutrients, especially the absence of amino acids. Autophagy is defined by the formation of double membrane structures, called autophagosomes, that sequester cytoplasm, long-lived proteins and protein aggregates, defective organelles, and even viruses or bacteria. Autophagosomes eventually fuse with lysosomes leading to bulk degradation of their content, with the produced nutrients being recycled back to the cytoplasm. Therefore, autophagy is crucial for cell homeostasis, and dysregulation of autophagy can lead to disease, most notably neurodegeneration, ageing and cancer.	
	Autophagosome formation is a very elaborate process, for which cells have allocated a specific group of proteins, called the core autophagy machinery. The core autophagy machinery is functionally complemented by additional proteins involved in diverse cellular processes, e.g. in membrane trafficking, in mitochondrial and lysosomal biology. Coordination of these proteins for the formation and degradation of autophagosomes constitutes the highly dynamic and sophisticated response of autophagy. Live cell imaging allows one to follow the molecular contribution of each autophagy-related protein down to the level of a single autophagosome formation event and in real time, therefore this technique offers a high temporal and spatial resolution.	
	Here we use a cell line stably expressing GFP-DFCP1, to establish a spatial and temporal context for our analysis. DFCP1 marks omegasomes, which are precursor structures leading to autophagosomes formation. A protein of interest (POI) can be marked with either a red or cyan fluorescent tag. Different organelles, like the ER, mitochondria and lysosomes, are all involved in different steps of autophagosome formation, and can be marked using a specific tracker dye. Time-lapse microscopy of autophagy in this experimental set up, allows information to be extracted about the fourth dimension, i.e. time. Hence we can follow the contribution of the POI to autophagy in space and time.

Time-lapse microscopy of fluorescently labeled autophagy markers allows monitoring of the dynamic autophagy response with high temporal resolution. Using specific autophagy and organelle markers in a combination of 3 different colors, we can follow the contribution of a protein to autophagosome formation in a robust spatial and temporal context.

Autophagy is a  cellular response triggered by the lack of nutrients, especially the absence of  amino acids. Autophagy is defined by the formation of ...

Platform Incubator with Movable XY Stage: A New Platform for Implementing In-Cell Fast Photochemical Oxidation of Proteins

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