Name: evaluation of protein&#8211;protein interactions using an on-membrane digestion technique
Uploaded: 2019-07-19T13:30:00
Description: Watch this Scientific Journal Video about Evaluation of Proteinâ€“Protein Interactions using an On-Membrane Digestion Technique at JoVE.com

This study was supported in part by Japan Society for the Promotion of Science KAKENHI Grant Number 17K09869 (to AM), Japan Society for the Promotion of Science KAKENHI Grant Number 15K09418 (to TM), a research grant from Kanehara Ichiro Medical Science Foundation and a research grant from Suzuken Memorial Foundation (all to TM).

1. Immunoprecipitation
NOTE: We used non-sodium dodecyl sulfate (SDS) lysis buffer and citrate elution, as described in the following sections. However, the use of an alternative in-house immunoprecipitation technique may be also applicable for preparing LC-MS/MS samples.
<ol>
	<li>Transfect cultured cells with vectors encoding an epitope tag alone or a fusion protein. For acquiring representative data, transfer J774 cells (1 x 106) with vectors encoding green fluorescent protein ...

<ol>
	<li>Thommen, M., Holtkamp, W., Rodnina, M. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Co-translational+protein+folding:+progress+and+methods.">Co-translational protein folding: progress and methods.</a> Current Opinion in Structural Biology. 42, 83-89 (2017).</li><li>Miyazaki, T., Miyazaki, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Defective+protein+catabolism+in+atherosclerotic+vascular+inflammation.">Defective protein catabolism in atherosclerotic vascular inflammation.</a> Frontiers in Cardiovascular Medicine. 4, 79 (2017).</li><li>Miyazaki, T., Miyazaki, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dysregulation+of+calpain+proteolytic+systems+underlies+degenerative+vascular+disorders.">Dysregulation of calpain proteolytic systems underlies degenerative vascular disorders.</a> Journal of Atherosclerosis and Thrombosis. 25 (1), 1-15 (2018).</li><li>Steckelberg, A. L., Boehm, V., Gromadzka, A. M., Gehring, N. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CWC22+connects+pre-mRNA+splicing+and+exon+junction+complex+assembly.">CWC22 connects pre-mRNA splicing and exon junction complex assembly.</a> Cell Reports. 2 (3), 454-461 (2012).</li><li>Turriziani, B., von Kriegsheim, A., Pennington, 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=Protein-protein+interaction+detection+via+mass+spectrometry-based+proteomics.">Protein-protein interaction detection via mass spectrometry-based proteomics.</a> Advances in Experimental Medicine and Biology. 919, 383-396 (2016).</li><li>Obama, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+modified+apolipoprotein+B-100+structures+formed+in+oxidized+low-density+lipoprotein+using+LC-MS/MS.">Analysis of modified apolipoprotein B-100 structures formed in oxidized low-density lipoprotein using LC-MS/MS.</a> Proteomics. 7 (13), 2132-2141 (2007).</li><li>Matsudaira, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sequence+from+picomole+quantities+of+proteins+electroblotted+onto+polyvinylidene+difluoride+membranes.">Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes.</a> The Journal of Biological Chemistry. 262 (21), 10035-10038 (1987).</li><li>Yamaguchi, 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=High-throughput+method+for+N-terminal+sequencing+of+proteins+by+MALDI+mass+spectrometry.">High-throughput method for N-terminal sequencing of proteins by MALDI mass spectrometry.</a> Analytical Chemistry. 77 (2), 645-651 (2005).</li><li>Iwamatsu, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=S-carboxymethylation+of+proteins+transferred+onto+polyvinylidene+difluoride+membranes+followed+by+in+situ+protease+digestion+and+amino+acid+microsequencing.">S-carboxymethylation of proteins transferred onto polyvinylidene difluoride membranes followed by in situ protease digestion and amino acid microsequencing.</a> Electrophoresis. 13 (3), 142-147 (1992).</li><li>Strader, M. B., Tabb, D. L., Hervey, W. J., Pan, C., Hurst, G. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+and+specific+trypsin+digestion+of+microgram+to+nanogram+quantities+of+proteins+in+organic-aqueous+solvent+systems.">Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems.</a> Analytical Chemistry. 78 (1), 125-134 (2006).</li><li>Miyazaki, T., Miyazaki, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emerging+roles+of+calpain+proteolytic+systems+in+macrophage+cholesterol+handling.">Emerging roles of calpain proteolytic systems in macrophage cholesterol handling.</a> Cellular and Molecular Life Sciences. 74 (16), 3011-3021 (2017).</li><li>Miyazaki, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Calpain-6+confers+atherogenicity+to+macrophages+by+dysregulating+pre-mRNA+splicing.">Calpain-6 confers atherogenicity to macrophages by dysregulating pre-mRNA splicing.</a> Journal of Clinical Investigation. 126 (9), 3417-3432 (2016).</li><li>Tonami, K., 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=Calpain-6,+a+microtubule-stabilizing+protein,+regulates+Rac1+activity+and+cell+motility+through+interaction+with+GEF-H1.">Calpain-6, a microtubule-stabilizing protein, regulates Rac1 activity and cell motility through interaction with GEF-H1.</a> Journal of Cell Science. 124 (Pt 8), 1214-1223 (2011).</li><li>Rodnina, M. V., Wintermeyer, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+elongation,+co-translational+folding+and+targeting.">Protein elongation, co-translational folding and targeting.</a> Journal of Molecular Biology. 428 (10 Pt B), 2165-2185 (2016).</li><li>Bunai, K., 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=Proteomic+analysis+of+acrylamide+gel+separated+proteins+immobilized+on+polyvinylidene+difluoride+membranes+following+proteolytic+digestion+in+the+presence+of+80%+acetonitrile.">Proteomic analysis of acrylamide gel separated proteins immobilized on polyvinylidene difluoride membranes following proteolytic digestion in the presence of 80% acetonitrile.</a> Proteomics. 3 (9), 1738-1749 (2003).</li></ol>

We have previously described an analysis of the oxidative modifications of apolipoprotein B-100 in oxidized low-density lipoprotein using LC-MS/MS preceded by an on-membrane digestion technique6. In the present study, we combined this technique with immunoprecipitation and have identified several calpain-6-associated proteins. This novel technique represents a convenient method of screening for candidate associated proteins. Calpain-6 is a non-proteolytic member of the calpain proteolytic family<s...

Although proteins play constitutive roles in living organisms, they are continually synthesized, processed, and degraded in the intracellular environment. Furthermore, intracellular proteins frequently physically and biochemically interact, which affects the function of one or both1,2,3. For example, the direct binding of spliceosome-associated protein homolog CWC22 with eukaryotic translation initiation factor 4A3 (eIF4A3) is necessary for the assembly of the exon junction complex4. Consistent with this, an eIF4A3 mutant that lacks affinity for CWC22 fails to facilitate exon junction complex-driven mRNA splicing4. Thus, the study of protein interactions is crucial for the precise understanding of physiologic regulation as well as of cellular functions.
Recent advances in mass spectrometry (MS) have been applied to the comprehensive analysis of protein-protein interactions. For instance, the co-precipitation of endogenous proteins or exogenously introduced tagged proteins with their associated proteins, followed by MS analysis, enables the identification of novel protein interactions5. However, one major bottleneck of MS/MS analysis is poor recovery from tryptic digests of protein samples. For conducting proteomic analyses on cell lysates, in-gel and on-membrane digestion techniques are generally employed to prepare MS/MS samples. We have previously compared an in-gel digestion procedure with an on-membrane digestion technique6, and showed that the latter was associated with better sequence coverage. Polyvinylidene difluoride (PVDF) membrane may be suitable for this purpose because it is mechanically robust and resistant to high concentrations of organic solvents7,8, permitting the enzymatic digestion of immobilized proteins in the presence of 80% acetonitrile9. Furthermore, immobilization on a membrane can induce conformational changes in target proteins, leading to improvements in tryptic digestion efficiency10. Accordingly, in this article, we have described the use of immunoprecipitation-LC/MS/MS analysis of protein interactions using an on-membrane digestion technique. This simple method facilitates the convenient analysis of protein-protein interactions even in non-specialist laboratories.

<table>
	<tbody>
		<tr>
			<td>Acetonitrile</td>
			<td>Wako</td>
			<td>014-00386</td>
			<td></td>
		</tr>
		<tr>
			<td>Citric acid</td>
			<td>Wako</td>
			<td>030-05525</td>
			<td></td>
		</tr>
		<tr>
			<td>DiNA</td>
			<td>KYA Tech Co.</td>
			<td></td>
			<td>nanoflow high-performance liquid chromatography</td>
		</tr>
		<tr>
			<td>DiNa AI</td>
			<td>KYA Tech Co.</td>
			<td></td>
			<td>nanoflow high-performance liquid chromatography equipped with autosampler</td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Nacalai tesque</td>
			<td>14112-94</td>
			<td></td>
		</tr>
		<tr>
			<td>Dynabeads protein G</td>
			<td>Thermo Fisher Scientific</td>
			<td>10003D</td>
			<td></td>
		</tr>
		<tr>
			<td>Formic acid</td>
			<td>Wako</td>
			<td>066-00461</td>
			<td></td>
		</tr>
		<tr>
			<td>HiQ Sil C18W-3</td>
			<td>KYA Tech Co.</td>
			<td>E03-100-100</td>
			<td>0.10mmID * 100mmL</td>
		</tr>
		<tr>
			<td>Iodoacetamide</td>
			<td>Wako</td>
			<td>095-02151</td>
			<td></td>
		</tr>
		<tr>
			<td>Lipofectamine 3000</td>
			<td>Thermo Fisher Scientific</td>
			<td>L3000008</td>
			<td></td>
		</tr>
		<tr>
			<td>Living Colors A.v. Monoclonal Antibody (JL-8)</td>
			<td>Clontech</td>
			<td>632380</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Wako</td>
			<td>191-01665</td>
			<td></td>
		</tr>
		<tr>
			<td>NH4HCO3</td>
			<td>Wako</td>
			<td>018-21742</td>
			<td></td>
		</tr>
		<tr>
			<td>Nonidet P-40</td>
			<td>Sigma</td>
			<td>N6507</td>
			<td>poly(oxyethelene) octylphenyl ether (n=9)</td>
		</tr>
		<tr>
			<td>peptide standard</td>
			<td>KYA Tech Co.</td>
			<td>tBSA-04</td>
			<td>tryptic digests of bovine serum albumin</td>
		</tr>
		<tr>
			<td>PP vial</td>
			<td>KYA Tech Co.</td>
			<td>03100S</td>
			<td>plastic sample tube</td>
		</tr>
		<tr>
			<td>Protease inhibitor cooctail</td>
			<td>Sigma</td>
			<td>P8465</td>
			<td></td>
		</tr>
		<tr>
			<td>ProteinPilot software</td>
			<td>Sciex</td>
			<td>5034057</td>
			<td>software for protein identification</td>
		</tr>
		<tr>
			<td>Sequencing Grade Modified Trypsin</td>
			<td>Promega</td>
			<td>V5111</td>
			<td>trypsin</td>
		</tr>
		<tr>
			<td>Sodium orthovanadate</td>
			<td>Sigma</td>
			<td>S6508</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate dibasic dihydrate</td>
			<td>Sigma</td>
			<td>71643</td>
			<td></td>
		</tr>
		<tr>
			<td>TFA</td>
			<td>Wako</td>
			<td>206-10731</td>
			<td></td>
		</tr>
		<tr>
			<td>trap column</td>
			<td>KYA Tech Co.</td>
			<td>A03-05-001</td>
			<td>0.5mmID * 1mmL</td>
		</tr>
		<tr>
			<td>TripleTOF 5600 system</td>
			<td>Sciex</td>
			<td>4466015</td>
			<td>Hybrid quadrupole time-of-flight tandem mass spectrometer</td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Wako</td>
			<td>207-06275</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Wako</td>
			<td>160-21211</td>
			<td></td>
		</tr>
	</tbody>
</table>

evaluation of protein&#8211;protein interactions using an on-membrane digestion technique

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions largely depend on intracellular protein&#8211;protein interactions. Therefore, research regarding these interactions is indispensable to facilitating the understanding of physiologic processes. Co-precipitation of associated proteins, followed by mass spectrometry (MS) analysis, enables the identification of novel protein interactions. In this study, we have provided details of the novel technique of immunoprecipitation-liquid chromatography (LC)-MS/MS analysis combined with on-membrane digestion for the analysis of protein&#8211;protein interactions. This technique is suitable for crude immunoprecipitants and can improve the throughput of proteomic analyses. Tagged recombinant proteins were precipitated using specific antibodies; next, immunoprecipitants blotted onto polyvinylidene difluoride membrane pieces were subjected to reductive alkylation. Following trypsinization, the digested protein residues were analyzed using LC-MS/MS. Using this technique, we were able to identify several candidate associated proteins. Thus, this method is convenient and useful for the characterization of novel protein&#8211;protein interactions.

By means of the above-described procedure, immunoprecipitants were analyzed using LC-MS/MS (Figure 1). After the exclusion of exogenously derived proteins (proteins from other species and IgGs), 17 proteins were identified in calpain-6-associated immunoprecipitants (Table 1) and 15 proteins were identified in GFP-associated immunoprecipitants (Table 2). Of the calpain-6 and GFP-associated proteins, 11 were identified in both ...

Watch this Scientific Journal Video about Evaluation of Proteinâ€“Protein Interactions using an On-Membrane Digestion Technique at JoVE.com

Evaluation of Protein&amp;#8211;Protein Interactions using an On-Membrane Digestion Technique

Here, we present a protocol for an on-membrane digestion technique for the preparation of samples for mass spectrometry. This technique facilitates the convenient analysis of protein&#8211;protein interactions.

Evaluation of Protein&#8211;Protein Interactions using an On-Membrane Digestion Technique

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions ...

Researching protein-protein interaction is indispensable for understanding physiological processes in several field. In this video we introduce on-membrane digestion technique which allows the researchers to perform a comprehensive analysis of binding proteins by MS in a convenient manner. The main advantage of this technique is that we can improve the throughput of proteomic analysis for crude immunoprecipitants because separation of proteins by polyacrylamide gel electrophoresis is not necessary.Begin conjugating the antibody to the magnetic beads, by mixing the anti-GFP antibody with the beads in 500 microliters of citrate phosphate buffer. Rotate the mixture at 50 RPM for one hour at room temperature. And then wash the conjugated beads three times with citrate phosphate buffer containing 1%polysorbate 20.Lyse transfected cells according to manuscript directions. Scrape the dish and transfer the lysate into the 1.5 milliliter test tube. Then clear the lysate by centrifuging at 15, 000 x g for five minutes and collect the supernatant.Prepare unlabeled magnetic beads by washing them three times with 500 microliters of citrate phosphate buffer. After the final wash, remove the buffer and add cell lysate to the beads. Rotate the mixture at 50 RPM for 30 minutes at room temperature.Perform magnetic separation on the magnetic stand and collect the cell lysate. To bind the target proteins to the immunoglobulin conjugated beads, place the beads on the magnetic stand for five minutes. Discard the citrate buffer and add the cell lysate to the beads.Rotate the mixture for one hour at 50 RPM. To separate target proteins from the free non-target proteins, wash the beads three times with 500 microliters of citrate phosphate buffer containing 1%polysorbate 20. After the final wash, add 30 microliters of citrate buffer, and let the beads sit for five minutes at room temperature to elute the target proteins.To prepare the membrane, cut PVDF membranes into 3 millimeter by 3 millimeter pieces using surgical scissors that were cleaned immediately prior to use. Place the pieces of membrane on aluminum foil and add two to five microliters of ethanol to each piece. Before membranes are completely dry, add two to five microliters of the protein eluent to each piece and air dry them until the membrane surface becomes matte.Then transfer membranes into 1.5 milliliter tubes and store them at four degrees Celsius. If using immediately, add two to 30 microliters of ethanol which will make them hydrophilic. Remove the ethanol with a pipette, but before the membranes dry, completely add 200 microliters of DTT-based reaction solution to each tube, and incubate them at 56 degrees Celsius for one hour.After incubation, replace the reaction solution with 300 microliters of iodoacetamide solution, and incubate in the dark for 45 minutes. Then wash the membranes twice with distilled water and once with 2%acetonitrile by vortexing for at least ten seconds. Working with diaphanous-related acetonitrile can be extremely hazardous.A mask, glasses and gloves should always be worn when performing the on-membrane digestion procedure. Prepare trypsin according to manuscript directions, and add 100 microliters of trypsin reaction solution to each membrane. Incubate overnight at 37 degrees Celsius for digestion.The next day, transfer the reaction solution into a clean 1.5 milliliter tube, and add 100 microliters of wash solutions to the membrane. Incubate the membrane at 60 degrees Celsius for two hours, then collect the wash solution and mix it with the reaction solution. Add another 100 microliters of wash solution to the membrane and sonicate it for 10 minutes.Then collect the wash solution and mix it with the reaction solution. Cover the test tube with a piece of laboratory film and make small holes in the film with a needle. Dry the solution using a vacuum concentrator, and dissolve the residue in 10 microliters of 2%formic acid.Centrifuge the tube at 12, 000 x g for three minutes, and transfer the supernatant into a sample tube. Analyze the sample using a mass spectrometer linked to a nano LC/HPLC system. Using this protocol, 17 proteins were identified in the Calpain-6 associated immunoprecipitant, 15 in the GFP-associated immunoprecipitant, and 11 were identified in both.It's important to note that detection of at least one high fidelity peptide fragment is required for positive identification of a candidate protein. Proteins that precipitated in the GFP-expressing lysate as well as histones, exogenous and ribosomal proteins were omitted from the list. Washing the membranes before tryptic digestion with distilled water and 2%acetonitrile is the most important step in the procedure of on-membrane digestion over proteins.Following this method, it is possible to confirm co-precipitation of target protein by conducting other experiments, such as immunoprecipitation and Western blot analysis. This simple method allows the researchers to explore the novel protein-protein interactions with convenient and high-sensitive analysis.

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An Efficient Method for the Synthesis of Peptoids with Mixed Lysine-type/Arginine-type Monomers and Evaluation of Their Anti-leishmanial Activity

This protocol describes the manual solid-phase synthesis of linear peptoids that contain two differently functionalized cationic monomers. In this procedure amino functionalized 'lysine' and guanido functionalized 'arginine' peptoid monomers can be included within the same peptoid sequence. This procedure uses on-resin (N-(1-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl) or Dde protection, orthogonal conditions to the Boc protection of lysine monomers. Subsequent deprotection allows an efficient on-resin guanidinylation reaction to form the arginine residues. The procedure is compatible with the commonly used submonomer method of peptoid synthesis, allowing simple peptoids to be made using common laboratory equipment and commercially available reagents. The representative synthesis, purification and characterization of two mixed peptoids is described. The evaluation of these compounds as potential anti-infectives in screening assays against Leishmania mexicana is also described. The protozoan parasite L. mexicana is a causative agent of cutaneous leishmaniasis, a neglected tropical disease that affects up to 12 million people worldwide.

A protocol to synthesize peptoids with mixed cationic functionality in the same sequence is presented (lysine- and arginine-type monomers). Subsequent testing of these compounds against Leishmania mexicana, the protozoan parasites that cause cutaneous leishmaniasis, is also described.

This protocol describes the manual solid-phase synthesis of linear peptoids that contain two differently functionalized cationic monomers. In this ...

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

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

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

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

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

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

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

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

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

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. Atomic force microscopy (AFM) can address this problem by enabling stretching and relaxation of single protein molecules, which gives direct evidence of specific unfolding and refolding characteristics. AFM-based single-molecule force-spectroscopy (AFM-SMFS) provides a means to consistently measure high-energy conformations in proteins that are not possible in traditional bulk (biochemical) measurements. Although numerous papers were published to show principles of AFM-SMFS, it is not easy to conduct SMFS experiments due to a lack of an exhaustively complete protocol. In this study, we briefly illustrate the principles of AFM and extensively detail the protocols, procedures, and data analysis as a guideline to achieve good results from SMFS experiments. We demonstrate representative SMFS results of single protein mechanical unfolding measurements and we provide troubleshooting strategies for some commonly encountered problems.

We describe the detailed procedures and strategies to measure the mechanical properties and mechanical unfolding pathways of single protein molecules using an atomic force microscope. We also show representative results as a reference for selection and justification of good single protein molecule recordings.

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. ...

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions

Single-molecule F&#246;rster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together&#160;with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM). Therefore, multi-color smFRET is a versatile tool for studying biomolecular complexes in a quantitative manner and in a previously unachievable detail.
Here, we demonstrate how to overcome the special challenges of multi-color smFRET experiments on proteins. We present detailed protocols for obtaining the data and for extracting kinetic information. This includes trace selection criteria, state separation, and the recovery of state trajectories from the noisy data using a 3D ensemble Hidden Markov Model (HMM). Compared to other methods, the kinetic information is not recovered from dwell time histograms but directly from the HMM. The maximum likelihood framework allows us to critically evaluate the kinetic model and to provide meaningful uncertainties for the rates.
By applying our method to the heat shock protein 90 (Hsp90), we are able to disentangle the nucleotide binding and the global conformational changes of the protein. This allows us to directly observe the cooperativity between the two nucleotide binding pockets of the Hsp90 dimer.

Here, we present a protocol to obtain three-color smFRET data and its analysis with a 3D ensemble Hidden Markov Model. With this approach, scientists can extract kinetic information from complex protein systems, including cooperativity or correlated interactions.

Single-molecule F&#246;rster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For ...

Detection of Detergent-sensitive Interactions Between Membrane Proteins

Our ability to explore protein-protein interactions is the key to understanding regulatory connections in the cell. However, detection of protein-protein interactions in many cases is associated with significant experimental challenges. In particular, sorting receptors interact with their protein cargo in the lumen of the membrane compartments often in a detergent-sensitive fashion, making co-immunoprecipitation of these proteins unusable. Binding of the sorting receptor sortilin to glucose transporter GLUT4 may serve as an example of weak luminal interactions between membrane proteins. Here, we describe a fast, simple, and inexpensive assay to validate the interaction between sortilin and GLUT4. For that, we have designed and chemically synthesized the myc-tagged peptide corresponding to the potential sortilin-binding epitope in the luminal part of GLUT4. Sortilin tagged with six histidines was expressed in mammalian cells, and isolated from cell lysates using Cobalt beads. Sortilin immobilized on the beads was incubated with the peptide solution at different pH values, and the eluted material was analyzed by Western blotting. This assay can be easily adapted to study other detergent-sensitive protein-protein interactions.

We describe a protocol for detection of detergent-sensitive interactions between membrane proteins using binding of the sorting receptor, sortilin, to the first luminal loop of the glucose transporter protein, GLUT4, as an example.

Our ability to explore protein-protein interactions is the key to understanding regulatory connections in the cell. However, detection of protein-protein ...

Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay

Regulated protein-protein interactions are a guiding principle for many signaling events, and the detection of such events is an important element in understanding how such pathways are organized and how they function. There are many methods to detect protein-protein interactions in cells, but relatively few can be used to detect interactions between endogenous proteins. One such method, the proximity ligation assay (PLA), has several advantages to recommend its use. Compared to other common methods of protein-protein interaction analysis, PLA has relatively high sensitivity and specificity, can be performed with minimal cell manipulation, and, in the protocol described herein, requires only two target-specific antibodies derived from different species (e.g., from mouse and rabbit) and one specialized reagent: a set of secondary antibodies that are covalently linked to specific oligonucleotides that, when brought in close proximity of one another, create an amplifiable platform for in situ PCR or rolling circle amplification. In this presentation, we show how to apply the PLA technique to visualize changes in MST1 and MST2 proximity in fixed cells. The technique described in this manuscript is particularly applicable for the analysis of cell signaling studies.

Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay

Here, we show how to use a Proximity Ligation Assay (PLA) to visualize MST1/MST2 heterodimerization in fixed cells with high sensitivity.

Regulated protein-protein interactions are a guiding principle for many signaling events, and the detection of such events is an important element in ...

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Filter-aided sample protocol (FASP) is widely used for proteomics sample preparation because it allows to concentrate diluted samples and it is compatible with a wide variety of detergents. Bottom-up proteomics workflows like FASP increasingly rely on LC-MS/MS methods performed in data-independent analysis (DIA) mode, a scanning method that allows deep proteome coverage and low incidence of missing values. 
In this report, we will provide the details of a workflow that combines a FASP protocol, a double StageTip purification step and LC-MS/MS in DIA mode for urinary proteome mapping. As a model sample, we analyzed expressed prostatic secretions (EPS)-urine, a sample collected after a digital rectal exam (DRE), which is of interest in prostate cancer biomarker discovery studies.

Here, we present an optimized on-filter digestion protocol with detailed information about the following: protein digestion, peptide purification and data independent acquisition analysis. This strategy is applied to the analysis of expressed prostatic secretions-urine samples and allows high proteome coverage and low missing value label-free profiling of the urinary proteome.

Filter-aided sample protocol (FASP) is widely used for proteomics sample preparation because it allows to concentrate diluted samples and it is compatible ...

Studies of Chaperone-Cochaperone Interactions using Homogenous Bead-Based Assay

Targeting the heat shock protein 90 (Hsp90)-cochaperone interactions provides the possibility to specifically regulate Hsp90-dependent intracellular processes. The conserved MEEVD pentapeptide at the C-terminus of Hsp90 is responsible for the interaction with the tetratricopeptide repeat (TPR) motif of co-chaperones. FK506-binding protein (FKBP) 51 and FKBP52 are two similar TPR-motif co-chaperones involved in steroid hormone-dependent diseases with different functions. Therefore, identifying molecules specifically blocking interactions between Hsp90 and FKBP51 or FKBP52 provides a promising therapeutic potential for several human diseases. Here, we describe the protocol for an amplified luminescent proximity homogenous assay to probe interactions between Hsp90 and its partner co-chaperones FKBP51 and FKBP52. First, we have purified the TPR motif-containing proteins FKBP51 and FKBP52 in glutathione S-transferase (GST)-tagged form. Using the glutathione-linked donor beads with GST-fused TPR-motif proteins and the acceptor beads coupled with a 10-mer C-terminal peptide of Hsp90, we have probed protein-protein interactions in a homogeneous environment. We have used this assay to screen small molecules to disrupt Hsp90-FKBP51 or Hsp90-FKBP52 interactions and identified potent and selective Hsp90-FKBP51 interaction inhibitors.

This protocol presents a technique for probing protein-protein interactions using glutathione-linked donor beads with GST-fused TPR-motif co-chaperones and acceptor beads coupled with an Hsp90-derived peptide. We have used this technique to screen small molecules to disrupt Hsp90-FKBP51 or Hsp90-FKBP52 interactions and identified potent and selective Hsp90-FKBP51 interaction inhibitors.

Targeting the heat shock protein 90 (Hsp90)-cochaperone interactions provides the possibility to specifically regulate Hsp90-dependent intracellular ...

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Biomolecular visualization skills are paramount to understanding key concepts in the biological sciences, such as structure-function relationships and molecular interactions. Various programs allow a learner to manipulate 3D structures, and biomolecular modeling promotes active learning, builds computational skills, and bridges the gap between two dimensional textbook images and the three dimensions of life. A critical skill in this area is to model a protein active site, displaying parts of the macromolecule that can interact with a small molecule, or ligand, in a way that shows binding interactions. In this protocol, we describe this process using four freely available macromolecular modeling programs: iCn3D, Jmol/JSmol, PyMOL, and UCSF ChimeraX. This guide is intended for students seeking to learn the basics of a specific program, as well as instructors incorporating biomolecular modeling into their curriculum. The protocol enables the user to model an active site using a specific visualization program, or to sample several of the free programs available. The model chosen for this protocol is human glucokinase, an isoform of the enzyme hexokinase, which catalyzes the first step of glycolysis. The enzyme is bound to one of its substrates, as well as a non-reactive substrate analog, which allows the user to analyze interactions in the catalytic complex.

A key skill in biomolecular modeling is displaying and annotating active sites in proteins. This technique is demonstrated using four popular free programs for macromolecular visualization: iCn3D, Jmol, PyMOL, and UCSF ChimeraX.

Biomolecular visualization skills are paramount to understanding key concepts in the biological sciences, such as structure-function relationships and ...