Name: laser-free hydroxyl radical protein footprinting to perform higher order structural analysis of proteins
Uploaded: 2021-06-04T13:00:00
Description: Watch this Scientific Journal Video about Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins at JoVE.com

This work was funded by the National Institute of General Medical Sciences (R43GM125420 and R44GM125420).

1. Installing the capillary tube
<ol>
	<li>Using a silica cleaving stone, cleave 250 &#181;m inner diameter (ID) silica capillary to 27 inches. Check the capillary ends for a clean, straight cut.</li>
	<li>Create two windows roughly 15 mm in length by burning away the polyimide coating. Starting from the &#8220;lower end&#8221; make the first photolysis window 90 mm away from the &#8220;lower end&#8221; and the second dosimeter window 225 mm away from the &#8220;lower end&#8221;. 
	NOTE: Once the coating is burned...

<ol>
	<li>Nagarkar, R. P., Murphy, B. M., Yu, X., Manning, M. C., Al-Azzam, W. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+protein+higher+order+structure+using+vibrational+circular+dichroism+spectroscopy.">Characterization of protein higher order structure using vibrational circular dichroism spectroscopy.</a> Current Pharmaceutical Biotechnology. 14 (2), 199-208 (2013).</li><li>Giezen, T. J., Schneider, C. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Safety+assessment+of+biosimilars+in+Europe:+a+regulatory+perspective.">Safety assessment of biosimilars in Europe: a regulatory perspective.</a> Generics and Biosimilars Initiative Journal. , 1-8 (2014).</li><li>Giezen, T. J., Mantel-Teeuwisse, A. 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M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complementary+MS+methods+assist+conformational+characterization+of+antibodies+with+altered+S-S+bonding+networks.">Complementary MS methods assist conformational characterization of antibodies with altered S-S bonding networks.</a> Journal of American Society of Mass Spectrometry. 24 (6), 835-845 (2013).</li><li>Storek, K. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monoclonal+antibody+targeting+the+&#946;-barrel+assembly+machine+of+Escherichia+coli+is+bactericidal.">Monoclonal antibody targeting the &#946;-barrel assembly machine of Escherichia coli is bactericidal.</a> Proceedings of the National Academy of Sciences. , (2018).</li><li>Vij, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+targeted+boost-and-sort+immunization+strategy+using+Escherichia+coli+BamA+identifies+rare+growth+inhibitory+antibodies.">A targeted boost-and-sort immunization strategy using Escherichia coli BamA identifies rare growth inhibitory antibodies.</a> Scientific Reports. 8 (1), 7136 (2018).</li><li>Liu, X. R., Zhang, M. M., Rempel, D. L., Gross, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Single+Approach+Reveals+the+Composite+Conformational+Changes,+Order+of+Binding,+and+Affinities+for+Calcium+Binding+to+Calmodulin.">A Single Approach Reveals the Composite Conformational Changes, Order of Binding, and Affinities for Calcium Binding to Calmodulin.</a> Analytical Chemistry. 91 (9), 5508-5512 (2019).</li><li>Lu, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fast+Photochemical+Oxidation+of+Proteins+Maps+the+Topology+of+Intrinsic+Membrane+Proteins:+Light-Harvesting+Complex+2+in+a+Nanodisc.">Fast Photochemical Oxidation of Proteins Maps the Topology of Intrinsic Membrane Proteins: Light-Harvesting Complex 2 in a Nanodisc.</a> Analytical Chemistry. 88 (17), 8827-8834 (2016).</li><li>Marty, M., Zhang, H., Cui, W., Gross, M., Sligar, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interpretation+and+Deconvolution+of+Nanodisc+Native+Mass+Spectra.">Interpretation and Deconvolution of Nanodisc Native Mass Spectra.</a> Journal of American Society of Mass Spectrometry. 25, (2013).</li><li>Johnson, D. T., Di Stefano, L. H., Jones, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fast+photochemical+oxidation+of+proteins(FPOP):+A+powerful+mass+spectrometry+based+structural+proteomics+tool.">Fast photochemical oxidation of proteins(FPOP): A powerful mass spectrometry based structural proteomics tool.</a> Journal of Biological Chemistry. , (2019).</li><li>Chea, E. E., Jones, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+the+structure+of+macromolecules+in+their+native+cellular+environment+using+hydroxyl+radical+footprinting.">Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting.</a> Analyst. 143 (4), 798-807 (2018).</li><li>Aprahamian, M. L., Chea, E. E., Jones, L. M., Lindert, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rosetta+Protein+Structure+Prediction+from+Hydroxyl+Radical+Protein+Footprinting+Mass+Spectrometry+Data.">Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data.</a> Analytical chemistry. 90 (12), 7721-7729 (2018).</li><li>Linde. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Linde Specialty Gases of North America. , (2009).</li><li>Aye, T. T., Low, T. Y., Sze, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanosecond+laser-induced+photochemical+oxidation+method+for+protein+surface+mapping+with+mass+spectrometry.">Nanosecond laser-induced photochemical oxidation method for protein surface mapping with mass spectrometry.</a> Analytical Chemistry. 77 (18), 5814-5822 (2005).</li><li>Niu, B., Zhang, H., Giblin, D., Rempel, D. L., Gross, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dosimetry+determines+the+initial+OH+radical+concentration+in+fast+photochemical+oxidation+of+proteins+(FPOP).">Dosimetry determines the initial OH radical concentration in fast photochemical oxidation of proteins (FPOP).</a> Journal of American Society of Mass Spectrometry. 26 (5), 843-846 (2015).</li><li>Misra, S. K., Orlando, R., Weinberger, S. R., Sharp, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compensated+Hydroxyl+Radical+Protein+Footprinting+Measures+Buffer+and+Excipient+Effects+on+Conformation+and+Aggregation+in+an+Adalimumab+Biosimilar.">Compensated Hydroxyl Radical Protein Footprinting Measures Buffer and Excipient Effects on Conformation and Aggregation in an Adalimumab Biosimilar.</a> American Association of Pharmaceutical Scientists Journal. 21 (5), 87 (2019).</li><li>Olson, L. J., Misra, S. K., Ishihara, M., Battaile, K. P., Grant, O. C., Sood, A., Woods, R. J., Kim, J. P., Tiemeyer, M., Ren, G., Sharp, J. S., Dahms, N. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Allosteric+regulation+of+lysosomal+enzyme+recognition+by+the+cation-independent+mannose+6-phosphate+receptor.">Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor.</a> Communications Biology. 3 (1), 498 (2020).</li><li>Sharp, J. S., Misra, S. K., Persoff, J. J., Egan, R. W., Weinberger, S. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real+Time+Normalization+of+Fast+Photochemical+Oxidation+of+Proteins+Experiments+by+Inline+Adenine+Radical+Dosimetry.">Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry.</a> Analytical Chemistry. 90 (21), 12625-12630 (2018).</li><li>Misra, S. K., Sharp, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enabling+Real-Time+Compensation+in+Fast+Photochemical+Oxidations+of+Proteins+for+the+Determination+of+Protein+Topography+Changes.">Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes.</a> Journal of Visualized Experiments. 163, (2020).</li><li>Hambly, D. M., Gross, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser+flash+photolysis+of+hydrogen+peroxide+to+oxidize+protein+solvent-accessible+residues+on+the+microsecond+timescale.">Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale.</a> Journal of American Society of Mass Spectrometry. 16 (12), 2057-2063 (2005).</li><li>Liu, X. R., Zhang, M. M., Gross, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+Spectrometry-Based+Protein+Footprinting+for+Higher-Order+Structure+Analysis:+Fundamentals+and+Applications.">Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications.</a> Chemical Reviews. 120 (10), 4355 (2020).</li><li>Jones, L. M., Sperry, B. J., Carroll, A. J., Gross, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fast+photochemical+oxidation+of+proteins+for+epitope+mapping.">Fast photochemical oxidation of proteins for epitope mapping.</a> Analytical chemistry. 83 (20), 7657-7661 (2011).</li><li>Li, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+the+Energetic+Epitope+of+an+Antibody/Interleukin-23+Interaction+with+Hydrogen/Deuterium+Exchange,+Fast+Photochemical+Oxidation+of+Proteins+Mass+Spectrometry,+and+Alanine+Shave+Mutagenesis.">Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave Mutagenesis.</a> Analytical chemistry. 89 (4), 2250-2258 (2017).</li><li>Liu, X. R., Zhang, M. M., Rempel, D. L., Gross, M. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Single+Approach+Reveals+the+Composite+Conformational+Changes,+Order+of+Binding,+and+Affinities+for+Calcium+Binding+to+Calmodulin.">A Single Approach Reveals the Composite Conformational Changes, Order of Binding, and Affinities for Calcium Binding to Calmodulin.</a> Analytical Chemistry. 91 (9), 5508-5512 (2019).</li><li>Kiselar, J. G., Janmey, P. A., Almo, S. C., Chance, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+analysis+of+gelsolin+using+synchrotron+protein+footprinting.">Structural analysis of gelsolin using synchrotron protein footprinting.</a> Molecular and Cellular Proteomics. 2 (10), 1120-1132 (2003).</li><li>Chea, E. E., Deredge, D. J., Jones, L. 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There are several critical steps to ensure proper labeling of proteins during any HRPF experiment. First, an appropriate flow rate and source flash rate are selected to make certain each bolus of the sample is irradiated once. This ensures that the protein is exposed to a single bolus of newly formed &#9642;OH. Once a protein is oxidized, the higher order protein structure can be altered. To be confident the native protein structure is probed, each protein molecule must be modified in a single instant. Dosimet...

Protein conformation and associated higher order structure (HOS) are the principal determinants of proper biological function and aberrant behavior1. The same applies to biopharmaceuticals, whose structure and functional activity is dependent on various aspects of their production and environment. Biopharmaceutical change in HOS have been linked to adverse drug reactions (ADR) attributed to undesirable pharmacology and patient immunological response2,3. The appearance of ADRs has alerted the biopharmaceutical industry to the critical role that protein HOS plays in the safety and efficacy of biotherapeutics, and they have established the need for new and improved HOS analytics4.
Hydroxyl Radical Protein Footprinting (HRPF) is a promising technique to track the change in protein HOS. HRPF involves the irreversible labeling of a protein&#8217;s exterior with &#9642;OH followed with mass spectrometry (MS) analysis to identify the solvent accessible surface of the protein5,6,7. HRPF has successfully been used to detect defects in protein HOS and its function8,9, characterize the HOS of monoclonal antibodies (mAb)10,11,12,13, determine the binding Kd of a ligand14, and much more15,16,17,18,19. A common method to generate the &#9642;OH for HRPF is Fast Photochemical Oxidation of Proteins (FPOP), which employs high-energy, fast UV lasers to produce &#9642;OH from photolysis of H2O2. For the most part, FPOP uses expensive excimer lasers employing hazardous gas (KrF) that demands substantial safeguards to avoid respiratory and eye injury20. To avoid inhalation hazards, others have used frequency quadrupled neodymium yttrium aluminum garnet (Nd:YAG) lasers21, which eliminates the use of toxic gas but are still costly, require significant operational expertise, and demand extensive stray light controls to protect users from eye injury.
Although ample information can be obtained using HRPF, broad adoption in biopharma has not been met. Two barriers for the limited HRPF adoption include: 1) the use of dangerous and expensive lasers that demand substantial safety precautions20; and 2) the irreproducibility of HRPF caused by background scavenging of &#9642;OH that limit comparative studies22. To supplant laser use, a high-speed, high energy plasma flash photolysis unit was developed to safely perform FPOP in a facile manner. To improve on the irreproducibility of HRPF experiments, real-time radical dosimetry is implemented.
The practice of HRPF has been limited by irreproducibility attributed to background scavenging of &#9642;OH22. While &#9642;OH are excellent probes of protein topography, they also react with many constituents found in preparations, making it necessary to measure the effective concentration of radical available to oxidize a target protein. Variations in buffer preparation, hydrogen peroxide concentration, ligand properties, or photolysis can result in oxidation differences between control and experimental groups that create ambiguity in HOS differential studies. The addition of real-time radical dosimetry enables the adjustment of the effect &#9642;OH load and therefore increases the confidence and reproducibility during an HRPF experiment. The use of radical dosimetry in FPOP has been described elsewhere23,24,25, and is further discussed in detail in a recent publication26. Here, we describe the use of a novel flash photolysis system and real-time dosimetry to label equine apo-myoglobin (aMb), comparing levels of peptide oxidation in an FPOP experiment to that of obtained when using an excimer laser.

<table>
	<tbody>
		<tr>
			<td>15 mL Conical Centrifuge Tubes</td>
			<td>Fisher Scientific</td>
			<td>14-959-53A</td>
			<td>any brand is sufficient</td>
		</tr>
		<tr>
			<td>50 &#181;L SGE Gastight Syringes</td>
			<td>Fisher Scientific</td>
			<td>SG-00723</td>
			<td></td>
		</tr>
		<tr>
			<td>Acclaim PepMap 100 C18 nanocolumn (0.75 mm X 150 mm, 2 &#181;m)</td>
			<td>Thermo 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>LS120-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Apomyoglobin</td>
			<td>Sigma-Aldrich</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Catalase</td>
			<td>Sigma-Aldrich</td>
			<td>C9322</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Eppendorf</td>
			<td>022625501</td>
			<td></td>
		</tr>
		<tr>
			<td>Delicate Task Wipers</td>
			<td>Fisher Scientific</td>
			<td>06-666A</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrogen Peroxide</td>
			<td>Fisher Scientific</td>
			<td>H325-100</td>
			<td>any 30% hydrogen peroxide is sufficient</td>
		</tr>
		<tr>
			<td>Methionine amide</td>
			<td>Chem-Impex</td>
			<td>03109</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge</td>
			<td>Thermo Scientific</td>
			<td>75002436</td>
			<td></td>
		</tr>
		<tr>
			<td>Orbitrap Fusion Lumos Tribrid Mass Spectrometer</td>
			<td>Thermo Scientific</td>
			<td>Orbitrap Fusion Lumos Tribrid Mass Spectrometer</td>
			<td>other high resolution instruments (e.g. Q exactive Orbitrap or Orbitrap Fusion) can be used</td>
		</tr>
		<tr>
			<td>Pierce Trypsin Protease, MS Grade</td>
			<td>Thermo Scientific</td>
			<td>90058</td>
			<td></td>
		</tr>
		<tr>
			<td>Polymicro Cleaving Stone, 1&#34; x 1&#34; x 1/32&#8221;</td>
			<td>Molex</td>
			<td>1068680064</td>
			<td>any capillary tubing cutter is sufficient</td>
		</tr>
		<tr>
			<td>UPLC</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Water with 0.1% Formic Acid (v/v), LC/MS Grade</td>
			<td>Fisher Scientific</td>
			<td>LS118-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Water, LC/MS Grade</td>
			<td>Fisher Scientific</td>
			<td>W6-4</td>
			<td></td>
		</tr>
	</tbody>
</table>

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.

The high-pressure plasma source coupled with real-time dosimetry allows better control of &#9642;OH yield to observe changes in higher-order protein structure more accurately. The addition of adenine allows for an effective real-time radical dosimeter. Upon oxidation, adenine loses UV absorbance at 265 nm (Figure 2A). The change in adenine absorbance is directly related to the concentration of radicals available for HRPF thus providing a means to effectively monitor changes in rad...

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

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 ...

Laser-free hydroxyl radical protein footprinting makes identifying protein interaction sites and regions of confirmational change much easier, accelerating research in protein aggregation, structure, and stability studies. With inline radical dosimetry, users can adjust the effective hydroxyl radical load in real time, and with real time radical dosimetry, you can save experimental time and precious sample while improving labeling reproducibility. To begin, cleave a 250 micrometer inner diameter silica capillary to 27 inches with a silica cleaving stone, checking the ends of the capillary for a clean and straight cut.Create two windows of roughly 15 millimeter length. From the lower end of the capillary, burn away the polyimide coating 90 millimeters up to create the photolysis window and 225 millimeters for the dosimeter window. Insert the lower end of the capillary just beyond the conical end of a nut and ferrule.Add the capillary to port five, tightening just beyond finger tight with a wrench. Remove the photolysis cell cap of the photolysis module by pulling it straight out, then remove the magnetically mounted metal mask, which will hold the capillary in place. Open the dosimeter cell by pushing on the tab on the left and swing the dosimeter cell open to the right.Remove the magnetically mounted clips that will hold the capillary in place. Then place the capillary into the grooved channel at the base of the photolysis cell, and center the capillary window with the photolysis cell window. Hold the capillary in position and add the magnetic mask.Place the photolysis cap back in position. Place the capillary into the grooved channel at the base of the dosimeter cell, and center the second capillary window on the small aperture at the center of the dosimeter cell. While holding the capillary in position with one hand, place the two magnetic clips in position to hold the capillary in place.Close the dosimeter cell until it clicks closed. Finally, insert the capillary through the knurled knob atop the capillary lift of the product collector, extending the capillary to just above the bottom of the vial. Cut the desired length of Teflon tubing using a cutter and check the ends for a clean straight cut.Insert one end of the new injection loop through one of the nuts, and place a new ferrule onto the end of the tube. Hold the nut and ferrule in place while inserting the tube in port six of the injection valve until it bottoms out. Tighten the nut with a wrench, then confirm that the nut and ferrule are securely in place.Once both ends have a nut and fixed ferrule, loosely screw one end to port three and the other end to port six. Once in position, tighten both sides to finger tight, then a quarter turn past finger tight with a wrench. Turn on the laser-free HRPF system by starting the fluidics module, followed by the photolysis module, dosimeter module, product collector, and the system computer.Launch the system software. Fully submerge the tubing into 10 milliliters of buffer from the valve position on the syringe pump. Direct the tubing from the waste position and the tubing from port two on the syringe port to an empty container to collect waste.Place 1.5 milliliter microcentrifuge tubes at the position marked HN6 on the product collector carousel. Rinse out the injection loop five times by injecting 25 microliters of HPLC grade water with the valve set to the load position. Manually turn the injection valve to flush the rest of the system.Select Process on the control software to begin flowing water until a droplet forms. Make a solution containing two millimolar adenine and 10 micromolar protein. Then make a quench solution using 0.3 milligrams per milliliter catalase and 35 millimolar methianine amide.Aliquot 25 microliters of quench solution into a 200 microliter micro tube. Dilute hydrogen peroxide to 200 millimolar, keeping it on ice. Start the flash voltage at zero volts on the control software.This zero volt control will determine any background oxidation on the protein of interest. Select Start Data AutoZero, followed by Process then Ready. Finally, turn the injection valve down to the load position.Place the quench solution in position one on the product collector carousel, then change the product vial to one on the system control software. Immediately before injection, mix 12.5 microliters of the adenine and protein mixture with 12.5 microliters of hydrogen peroxide. Pipette the mixture up and down to mix, then quickly spin it down.Inject 25 microliters of this solution using the injection port within 10 seconds of mixing. Switch the injection valve to the inject position and wait while the sample is being processed. Turn up the flash voltage to 750 volts on the control software, and repeat the labeling steps.Then record the absorbance of each sample. First, click Select, then manually select the beginning and end of the peak absorbance. In the available space, write in a description of the sample.Repeat this for all acquired data. Copy and paste the data into a spreadsheet to calculate the average change in adenine absorbance for each voltage. After all samples have been collected, flush out the syringe port and sample loop by setting the injection valve down to the load position and inject 25 microliters of HPLC water five times.Turn the injection valve up to the inject position to flush the rest of the system with HPLC water. Once flushed, stop the flow, exit the system control software, and turn off the modules, starting with the product collector, dosimeter module, photolysis module, and finally the fluidics module. Upon oxidation, adenine used for dosimetry decreases in UV absorbance at 265 nanometers.Buffer 2 contains a radical scavenger, which decreases the change in adenine absorbance compared to Buffer 1. Apomyoglobin was modified in the presence of hydrogen peroxide and adenine at four increasing plasma lamp voltages. Six peptides were detected, with a linear increase in oxidation with respect to the change of adenine absorbance at 265 nanometers.These six oxidized peptides are labeled on a crystal structure of myoglobin. The extent of oxidation detected from the high pressure plasma lamp is much higher than the laser-based method. This increase arises from the high pressure plasma lamp's broad spectrum UV emission spectrum.By producing a broad UV spectrum, the high pressure plasma lamp better overlaps the absorbance domain of hydrogen peroxide, resulting in a more efficient production of hydroxyl radicals through the photolysis of hydrogen peroxide, as compared to the Kr F Excimer Laser and Nd YAG Laser. The high pressure plasma lamp significantly increases the production of hydroxyl radicals beyond what is typically observed using a Kr F Excimer Laser. Using 100 millimolar peroxide can cause high levels of background oxidation.If the protein system is susceptible to peroxide-induced oxidation, decrease the concentration to as low as 10 millimolar. HRPF's irreversible label allows for downstream sample handling, including long protease digestions, you can add in tandem mass tag for multiplexing, and perform 2D chromatography, all improving peptide detection and concoordinate structural information.

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Unit 1

Protein Structure

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Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins

Obtaining crystals for structure determination can be a difficult and time consuming proposition for any protein. Coiled-coil proteins and domains are found throughout nature, however, because of their physical properties and tendency to aggregate, they are traditionally viewed as being especially difficult to crystallize. Here, we utilize a variety of quick and simple techniques designed to identify a series of possible domain boundaries for a given coiled-coil protein, and then quickly characterize the behavior of these proteins in solution. With the addition of a strongly fluorescent tag (mRuby2), protein characterization is simple and straightforward. The target protein can be readily visualized under normal lighting and can be quantified with the use of an appropriate imager. The goal is to quickly identify candidates that can be removed from the crystallization pipeline because they are unlikely to succeed, affording more time for the best candidates and fewer funds expended on proteins that do not produce crystals. This process can be iterated to incorporate information gained from initial screening efforts, can be adapted for high-throughput expression and purification procedures, and is augmented by robotic screening for crystallization.

We describe a framework incorporating straightforward biochemical and computational analysis to guide the characterization and crystallization of large coiled-coil domains. This framework can be adapted for globular proteins or extended to incorporate a variety of high-throughput techniques.

Obtaining crystals for structure determination can be a difficult and time consuming proposition for any protein. Coiled-coil proteins and domains are ...

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 ...

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

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

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

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

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

Modifying Baculovirus Expression Vectors to Produce Secreted Plant Proteins in Insect Cells

It has been a challenge for scientists to express recombinant secretory eukaryotic proteins for structural and biochemical studies. The baculovirus-mediated insect cell expression system is one of the systems used to express recombinant eukaryotic secretory proteins with some post-translational modifications. The secretory proteins need to be routed through the secretory pathways for protein glycosylation, disulfide bonds formation, and other post-translational modifications. To improve the existing insect cell expression of secretory plant proteins, a baculovirus expression vector is modified by the addition of either a GP67 or a hemolin signal peptide sequence between the promoter and multiple-cloning sites. This newly designed modified vector system successfully produced a high yield of soluble recombinant secreted plant receptor proteins of Arabidopsis thaliana. Two of the expressed plant proteins, the extracellular domains of Arabidopsis TDR and PRK3 plasma membrane receptors, were crystallized for X-ray crystallographic studies. The modified vector system is an improved tool that can potentially be used for the expression of recombinant secretory proteins in the animal kingdom as well.

Here, we present the protocols for utilizing the insect cell and baculovirus protein expression system to produce large quantities of plant secreted proteins for protein crystallization. A baculovirus expression vector has been modified with either GP67 or insect hemolin signal peptide for plant protein secretion expression in insect cells.

It has been a challenge for scientists to express recombinant secretory eukaryotic proteins for structural and biochemical studies. The ...

Ion Exchange Chromatography (IEX) Coupled to Multi-angle Light Scattering (MALS) for Protein Separation and Characterization

Ion-exchange chromatography with multi-angle light scattering (IEX-MALS) is a powerful method for protein separation and characterization. The combination of the high-specificity separation technique IEX with the accurate molar mass analysis achieved by MALS allows the characterization of heterogeneous protein samples, including mixtures of oligomeric forms or protein populations, even with very similar molar masses. Therefore, IEX-MALS provides an additional level of protein characterization and is complementary to the standard size-exclusion chromatography with multi-angle light scattering (SEC-MALS) technique.
Here we describe a protocol for a basic IEX-MALS experiment and demonstrate this method on bovine serum albumin (BSA). IEX separates BSA to its oligomeric forms allowing a molar mass analysis by MALS of each individual form. Optimization of an IEX-MALS experiment is also presented and demonstrated on BSA, achieving excellent separation between BSA monomers and larger oligomers. IEX-MALS is a valuable technique for protein quality assessment since it provides both fine separation and molar mass determination of multiple protein species that exist in a sample.

Ion Exchange Chromatography IEX Coupled to Multi-angle Light Scattering MALS for Protein Separation and Characterization

This protocol describes the use of high-specificity ion-exchange chromatography with multi-angle light scattering for an accurate molar mass determination of proteins, protein complexes, and peptides in a heterogeneous sample. This method is valuable for quality assessment, as well as for the characterization of native oligomers, charge variants, and mixed-protein samples.

Ion-exchange chromatography with multi-angle light scattering (IEX-MALS) is a powerful method for protein separation and characterization. The combination ...

Characterization of Proteins by Size-Exclusion Chromatography Coupled to Multi-Angle Light Scattering (SEC-MALS)

Analytical size-exclusion chromatography (SEC), commonly used for the determination of the molecular weight of proteins and protein-protein complexes in solution, is a relative technique that relies on the elution volume of the analyte to estimate molecular weight. When the protein is not globular or undergoes non-ideal column interactions, the calibration curve based on protein standards is invalid, and the molecular weight determined from elution volume is incorrect. Multi-angle light scattering (MALS) is an absolute technique that determines the molecular weight of an analyte in solution from basic physical equations. The combination of SEC for separation with MALS for analysis constitutes a versatile, reliable means for characterizing solutions of one or more protein species including monomers, native oligomers or aggregates, and heterocomplexes. Since the measurement is performed at each elution volume, SEC-MALS can determine if an eluting peak is homogeneous or heterogeneous and distinguish between a fixed molecular weight distribution versus dynamic equilibrium. Analysis of modified proteins such as glycoproteins or lipoproteins, or conjugates such as detergent-solubilized membrane proteins, is also possible. Hence, SEC-MALS is a critical tool for the protein chemist who must confirm the biophysical properties and solution behavior of molecules produced for biological or biotechnological research. This protocol for SEC-MALS analyzes the molecular weight and size of pure protein monomers and aggregates. The data acquired serve as a foundation for further SEC-MALS analyses including those of complexes, glycoproteins and surfactant-bound membrane proteins.

Characterization of Proteins by Size-Exclusion Chromatography Coupled to Multi-Angle Light Scattering SEC-MALS

This protocol describes the combination of size exclusion chromatography with multi-angle light scattering (SEC-MALS) for absolute characterization of proteins and complexes in solution. SEC-MALS determines the molecular weight and size of pure proteins, native oligomers, heterocomplexes and modified proteins such as glycoproteins.

Analytical size-exclusion chromatography (SEC), commonly used for the determination of the molecular weight of proteins and protein-protein complexes in ...

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 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.

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

Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis

Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal transduction; from sensing environmental signals to biological response; from metabolic regulation to developmental control. Accurate structural information of protein-protein interactions is crucial for understanding the molecular mechanisms of membrane protein complexes and for the design of highly specific molecules to modulate these proteins. Many in vivo and in vitro approaches have been developed for the detection and analysis of protein-protein interactions. Among them the structural biology approach is unique in that it can provide direct structural information of protein-protein interactions at the atomic level. However, current membrane protein structural biology is still largely limited to detergent-based methods. The major drawback of detergent-based methods is that they often dissociate or denature membrane protein complexes once their native lipid bilayer environment is removed by detergent molecules. We have been developing a&#160;native cell membrane nanoparticle system for membrane protein structural biology. Here, we demonstrate the use of this system in the analysis of protein-protein interactions on the cell membrane with a case study of the oligomeric state of AcrB.

Presented here is a protocol for the determination of oligomeric state of membrane proteins that utilizes a native cell membrane nanoparticle system in conjunction with electron microscopy.

Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal ...

Production of Recombinant PRMT Proteins using the Baculovirus Expression Vector System

Protein arginine methyltransferases (PRMTs) methylate arginine residues on a wide variety of proteins that play roles in numerous cellular processes. PRMTs can either mono- or dimethylate arginine guanidino groups symmetrically or asymmetrically. The enzymology of these proteins is a complex and intensely investigated area that requires milligram quantities of high-quality recombinant protein. The baculovirus expression vector system (BEVS) employing Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Spodoptera frugiperda 9 (Sf9) insect cells has been used for expression screening and production of many PRMTs, including PRMT 1, 2, and 4 through 9. To simultaneously screen for the expression of multiple constructs of these proteins, including domains and truncated fragments as well as the full-length proteins, we have applied scalable methods utilizing adjustable and programmable multichannel pipettes, combined with 24- and 96-well plates and blocks. Overall, these method adjustments enabled a large-scale generation of bacmid DNA, recombinant viruses, and protein expression screening. Using culture vessels with a high-fill volume of Sf9 cell suspension helped to overcome space limitations in the production pipeline for single batch large-scale protein production. Here, we describe detailed protocols for the efficient and cost-effective expression of functional PRMTs for biochemical, biophysical, and structural studies.

The baculovirus expression vector system (BEVS) is a robust platform for expression screening and production of protein arginine methyltransferases (PRMTs) to be used for biochemical, biophysical, and structural studies. Milligram quantities of material can be produced for the majority of PRMTs and other proteins of interest requiring a eukaryotic expression platform.

Protein arginine methyltransferases (PRMTs) methylate arginine residues on a wide variety of proteins that play roles in numerous cellular processes. ...

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

With recent advances in mass spectrometry-based proteomics technologies, deep profiling of hundreds of proteomes has become increasingly feasible. However, deriving biological insights from such valuable datasets is challenging. Here we introduce a systems biology-based software JUMPn, and its associated protocol to organize the proteome into protein co-expression clusters across samples and protein-protein interaction (PPI) networks connected by modules (e.g., protein complexes). Using the R/Shiny platform, the JUMPn software streamlines the analysis of co-expression clustering, pathway enrichment, and PPI module detection, with integrated data visualization and a user-friendly interface. The main steps of the protocol include installation of the JUMPn software, the definition of differentially expressed proteins or the (dys)regulated proteome, determination of meaningful co-expression clusters and PPI modules, and result visualization. While the protocol is demonstrated using an isobaric labeling-based proteome profile, JUMPn is generally applicable to a wide range of quantitative datasets (e.g., label-free proteomics). The JUMPn software and protocol thus provide a powerful tool to facilitate biological interpretation in quantitative proteomics.

We present a systems biology tool JUMPn to perform and visualize network analysis for quantitative proteomics data, with a detailed protocol including data pre-processing, co-expression clustering, pathway enrichment, and protein-protein interaction network analysis.