Name: measuring biomolecular dsc profiles with thermolabile ligands to rapidly characterize folding and binding interactions
Uploaded: 2017-11-21T12:30:00
Description: Watch this Scientific Journal Video about Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions at JoVE.com

R. W. H. V was supported by the McGill Natural Sciences and Engineering Research Council of Canada (NSERC) Training Program in Bionanomachines. A. K. M. and P. E. J. were supported by NSERC grants 327028-09 (A. K. M) and 238562 (P. E. J.).

1. Sample Preparation
<ol>
	<li>Purify the desired biomolecule13. 
	NOTE: This protocol uses purchased cocaine-binding DNA aptamer MN4 after exchanging against 2 M NaCl three times followed by three rounds of deionized water using a centrifugal filter with a 3 kDa molecular weight cut-off membrane.</li>
	<li>Synthesize and purify, or purchase the desired thermolabile ligand13. 
	NOTE: MN4 binds the thermolabile ligand cocaine. MN4 also binds quinine, which is us...

<ol>
	<li>Bruylants, G., Wouters, J., Michaux, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+scanning+calorimetry+in+life+science:+thermodynamics,+stability,+molecular+recognition+and+application+in+drug+design.">Differential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design.</a> Curr Med Chem. 12 (17), 2011-2020 (2005).</li><li>Privalov, P. L., Dragan, A. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microcalorimetry+of+biological+macromolecules.">Microcalorimetry of biological macromolecules.</a> Biophys Chem. 126 (1-3), 16-24 (2007).</li><li>Brandts, J. F., Lin, L. 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B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermodynamic+studies+for+drug+design+and+screening.">Thermodynamic studies for drug design and screening.</a> Expert Opin Drug Dis. 7 (4), 299-314 (2012).</li><li>Holdgate, G. A., Ward, W. H. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurements+of+binding+thermodynamics+in+drug+discovery.">Measurements of binding thermodynamics in drug discovery.</a> Drug Discov Today. 10 (22), 1543-1550 (2005).</li><li>Plotnikov, V., 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=An+autosampling+differential+scanning+calorimeter+instrument+for+studying+molecular+interactions.">An autosampling differential scanning calorimeter instrument for studying molecular interactions.</a> Assay Drug Dev Technol. 1 (1), 83-90 (2002).</li><li>Schon, A., Lam, S. Y., Freire, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermodynamics-based+drug+design:+strategies+for+inhibiting+protein-protein+interactions.">Thermodynamics-based drug design: strategies for inhibiting protein-protein interactions.</a> Future Med Chem. 3 (9), 1129-1137 (2011).</li><li>Peri&#225;nez Parraga, L., G-L, A., Gam&#243;n Runnenberg, I., Seco Melantuche, R., Delgado S&#225;nchez, O., Puigvent&#243;s Latorre, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermolabile+Drugs.+Operating+Procedure+In+the+Event+of+Cold+Chain+Failure.">Thermolabile Drugs. Operating Procedure In the Event of Cold Chain Failure.</a> Farmacia Hospitalaria. 35 (4), 1-28 (2011).</li><li>Murray, J. B., Alshora, H. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stability+of+Cocaine+in+Aqueous-Solution.">Stability of Cocaine in Aqueous-Solution.</a> J Clin Pharmacy. 3 (1), 1-6 (1978).</li><li>Waterman, K. C., 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=Hydrolysis+in+pharmaceutical+formulations.">Hydrolysis in pharmaceutical formulations.</a> Pharm. Dev. Technol. 7 (2), 113-146 (2002).</li><li>Mergny, J. L., Lacroix, L. <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+thermal+melting+curves.">Analysis of thermal melting curves.</a> Oligonucleotides. 13 (6), 515-537 (2003).</li><li>Neves, M. A., Reinstein, O., Johnson, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Defining+a+stem+length-dependent+binding+mechanism+for+the+cocaine-binding+aptamer.+A+combined+NMR+and+calorimetry+study.">Defining a stem length-dependent binding mechanism for the cocaine-binding aptamer. A combined NMR and calorimetry study.</a> Biochemistry. 49 (39), 8478-8487 (2010).</li><li>Bonifacio, G. F., Brown, T., Conn, G. L., Lane, A. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+the+electrophoretic+and+hydrodynamic+properties+of+DNA+and+RNA+oligonucleotide+duplexes.">Comparison of the electrophoretic and hydrodynamic properties of DNA and RNA oligonucleotide duplexes.</a> Biophys J. 73 (3), 1532-1538 (1997).</li><li>Durchschlag, H., Hinz, H. -. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+3.">Chapter 3.</a> Thermodynamic Data for Biochemistry and Biotechnology. , 45-128 (1986).</li><li>Hellman, L. M., Rodgers, D. W., Fried, M. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phenomenological+partial-specific+volumes+for+G-quadruplex+DNAs.">Phenomenological partial-specific volumes for G-quadruplex DNAs.</a> Eur Biophys J Biophy. 39 (3), 389-396 (2010).</li><li>Farber, P., Darmawan, H., Sprules, T., Mittermaier, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+Protein+Folding+Cooperativity+by+Differential+Scanning+Calorimetry+and+NMR+Spectroscopy.">Analyzing Protein Folding Cooperativity by Differential Scanning Calorimetry and NMR Spectroscopy.</a> J Am Chem Soc. 132 (17), 6214-6222 (2010).</li><li>Reinstein, O., 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=Quinine+binding+by+the+cocaine-binding+aptamer.+Thermodynamic+and+hydrodynamic+analysis+of+high-affinity+binding+of+an+off-target+ligand.">Quinine binding by the cocaine-binding aptamer. Thermodynamic and hydrodynamic analysis of high-affinity binding of an off-target ligand.</a> Biochemistry. 52 (48), 8652-8662 (2013).</li><li>Tellinghuisen, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical+error+propagation.">Statistical error propagation.</a> J Phys Chem. A. 105 (15), 3917-3921 (2001).</li><li>Drobnak, I., Vesnaver, G., Lah, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Model-based+thermodynamic+analysis+of+reversible+unfolding+processes.">Model-based thermodynamic analysis of reversible unfolding processes.</a> J Phys Chem B. 114 (26), 8713-8722 (2010).</li></ol>

Modifications and troubleshooting
The details of the global fitting analysis used in Figure 1 and Figure 2 have been described previously4. Here, we outline practical aspects of performing and analyzing DSC binding experiments with thermolabile ligands. Note that a DSC baseline obtained for the thermolabile ligand alone is subtracted from the ligand + biomolecule dataset, effectively cancelling ou...

Differential scanning calorimetry (DSC) is a powerful method for quantitating biomolecular binding and folding interactions1,2,3. The strengths of DSC include its ability to elucidate binding and folding mechanisms, and to yield the corresponding thermodynamic parameters2,3. Furthermore, DSC can be performed in solution under near-physiological conditions and does not require labeling of the biomolecule or ligand, e.g., with fluorophores, spin-labels or nuclear isotopes4. The instrument scans in temperature, measuring the amount of heat required to denature the biomolecule in the presence and absence of ligand. The resulting thermograms are used to extract the thermodynamic parameters governing the ligand binding and folding processes. The information provided by DSC or other thermodynamic techniques is critical to guiding the design of drugs targeting biomolecules1,5,6,7,8. However, the repeated scanning to high temperatures (~ 60 - 100 &#176;C) can be problematic. For example, many pharmaceutically important compounds undergo rearrangement or decomposition upon sustained exposure to high temperatures9,10,11, i.e., they are thermolabile. Examination of binding interactions by DSC typically requires multiple forward and reverse scans in order to verify the reproducibility of the thermogram for thermodynamic analyses12. Thermal conversion of an initial ligand to a secondary form with altered binding characteristics leads to pronounced differences in the shape and position of successive thermograms, since the concentration of the initial ligand decreases with each scan while the thermal conversion products accumulate. These datasets are not amenable to traditional analyses.
We have recently developed a global fitting method for thermolabile ligand DSC datasets that yields the complete set of thermodynamic parameters governing the biomolecular folding and binding interactions from a single ligand-bound experiment referenced to the requisite thermogram for the free biomolecule4. The analysis reduces the experimental time and sample required by ~ 10-fold compared to standard DSC approaches. We have accounted for ligand thermal conversion by assuming this happens during the high temperature portion of each scan where the thermogram does not depend on ligand concentration. Therefore, the ligand concentration is a constant within the portion of the thermogram that is used to extract thermodynamic parameters. We additionally demonstrated how the rate constant for ligand thermal conversion can be obtained by performing one supplementary experiment with a longer high temperature equilibration period. For systems where ligand thermal conversion is less temperature-dependent (i.e., occurring appreciably at all temperatures), the analysis can be modified to include variable ligand concentrations. Here we demonstrate this procedure for the DNA aptamer MN4 in the presence of the thermolabile ligand cocaine, which rapidly converts to benzoylecgonine at high temperatures (&#62;60 &#176;C). Quinine is used as a negative control for ligand thermolability since it does not undergo conversion at these experimental temperatures and also binds to MN4. We describe the acquisition of thermolabile ligand DSC datasets and their analysis yielding thermodynamic and kinetic parameters of the folding, binding, and ligand conversion processes.

<table>
	<tbody>
		<tr>
			<td>Sodium chloride</td>
			<td>Chem Impex</td>
			<td>#00829</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate monobasic dihydrate</td>
			<td>Sigma Aldrich</td>
			<td>71502</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate dibasic</td>
			<td>Sigma Aldrich</td>
			<td>S9763</td>
			<td></td>
		</tr>
		<tr>
			<td>Deioinized water for molecular biology</td>
			<td>Millipore</td>
			<td>H20MB1001</td>
			<td></td>
		</tr>
		<tr>
			<td>0.2 micron sterile syringe filters</td>
			<td>VWR</td>
			<td>CA28145-477</td>
			<td></td>
		</tr>
		<tr>
			<td>3 kDa centrifugal filters</td>
			<td>Millipore</td>
			<td>UFC900324</td>
			<td></td>
		</tr>
		<tr>
			<td>Dialysis tubing 0.5-1.0 kDa cutoff</td>
			<td>Spectrum Laboratories</td>
			<td>131048</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicon tubing</td>
			<td>VWR</td>
			<td>89068-474</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic DSC flange caps</td>
			<td>TA Instruments</td>
			<td>6111</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA aptamer MN4</td>
			<td>Integrated DNA Technologies</td>
			<td>https://www.idtdna.com/site/order/menu</td>
			<td></td>
		</tr>
		<tr>
			<td>Cocaine</td>
			<td>Sigma Aldrich</td>
			<td>C008</td>
			<td></td>
		</tr>
		<tr>
			<td>Quinine</td>
			<td>Sigma Aldrich</td>
			<td>22620</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoDSC-III microcalorimeter</td>
			<td>TA Instruments</td>
			<td>http://www.tainstruments.com/nanodsc/</td>
			<td></td>
		</tr>
		<tr>
			<td>DSCRun software</td>
			<td>TA Instruments</td>
			<td>http://www.tainstruments.com/support/software-downloads-support/instruments-by-software/</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoAnalyze software</td>
			<td>TA Instruments</td>
			<td>http://www.tainstruments.com/support/software-downloads-support/instruments-by-software/</td>
			<td></td>
		</tr>
		<tr>
			<td>Contrad-70</td>
			<td>VWR</td>
			<td>89233-152</td>
			<td></td>
		</tr>
	</tbody>
</table>

measuring biomolecular dsc profiles with thermolabile ligands to rapidly characterize folding and binding interactions

Differential scanning calorimetry (DSC) is a powerful technique for quantifying thermodynamic parameters governing biomolecular folding and binding interactions. This information is critical in the design of new pharmaceutical compounds. However, many pharmaceutically relevant ligands are chemically unstable at the high temperatures used in DSC analyses. Thus, measuring binding interactions is challenging because the concentrations of ligands and thermally-converted products are constantly changing within the calorimeter cell. Here, we present a protocol using thermolabile ligands and DSC for rapidly obtaining thermodynamic and kinetic information on the folding, binding, and ligand conversion processes. We have applied our method to the DNA aptamer MN4 that binds to the thermolabile ligand cocaine. Using a new global fitting analysis that accounts for thermolabile ligand conversion, the complete set of folding and binding parameters are obtained from a pair of DSC experiments. In addition, we show that the rate constant for thermolabile ligand conversion may be obtained with only one supplementary DSC dataset. The guidelines for identifying and analyzing data from several more complicated scenarios are presented, including irreversible aggregation of the biomolecule, slow folding, slow binding, and rapid depletion of the thermolabile ligand.

Representative data for the thermolabile ligand DSC are shown in Figure 1. The position and height of the thermolabile ligand-bound peak successively shifts down towards that of the unbound biomolecule as the thermolabile ligand is depleted with each scan (Figure 1a). The free denaturation profile is used as a reference for the endpoint of thermolabile ligand conversion (Figure 1b). Data for MN4 boun...

Watch this Scientific Journal Video about Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions at JoVE.com

Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

We present a protocol for rapid characterization of biomolecular folding and binding interactions with thermolabile ligands using differential scanning calorimetry.

Differential scanning calorimetry (DSC) is a powerful technique for quantifying thermodynamic parameters governing biomolecular folding and binding ...

The overall goal of this methodology is to extract the thermodynamic parameters governing biomolecular folding and binding interactions by differential scanning calorimetry, or DSC, using a thermolabile ligand in as little as two experiments. This method can help answer key questions in the biocalorimetry and drug design fields such as what are the relative magnitudes of the thermodynamic parameters governing interactions between biomolecules and tight binding inhibitors? The main advantage of this technique is that a full ligand titration is performed in a single experiment permitting rapid extraction of thermodynamic parameters from the global fitting analysis.To begin, prepare buffers for dialysis of the purified biomolecule into solution of ligands. Dialyze the biomolecule against at least one liter of buffer using dialysis tubing with 0.5 to 1.7 kilodalton cutoff. The most important step in obtaining high-quality DSC data is the dialysis of the biomolecule ligand against the desired buffer.This ensures that there are no buffer mismatched artifacts present in the DSC data. Filter the final buffer which is referred to as the working buffer through a 0.2-micron filter that has been thoroughly equilibrated with buffer. Weigh out the desired masses of the ligands and dissolve them in filtered working buffer.If the desired ligand concentrations require masses that are too small to accurately weigh, make a concentrated ligand stock solution. Filter the biomolecule stock solution through a 0.2-micron filter that has been thoroughly equilibrated with working buffer. Then, determine the biomolecule concentration by absorbance measurements.Store the prepared biomolecule and ligand in a four degrees Celsius refrigerator or at minus 20 or minus 80 degrees Celsius if the biomolecule and ligands tolerate freezing and long-term storage is required. Degas the buffer by a molecule and ligand solutions in a tabletop degasser prior to loading into the differential scanning calorimeter, or DSC. Unscrew the pressure handle from the DSC.Then, run silicon tubing from the working buffer and attach it to the front flange of the reference capillary. Create a bridge between the reference and sample capillaries by connecting the rear reference flange to the front simple flange. Next, attach a piece of silicon tubing to the rear sample flange that runs to a waste flask with a vacuum line attached.Turn on the vacuum line to flush the DSC with 200 milliliters of working buffer. Begin by attaching roughly three to five-centimeter sections of silicon tubing to the reference capillary flanges. Next, insert a one-milliliter pipette tip into the silicon tubing of the rear flange.Draw 0.8 milliliters of working buffer with a pipette and insert the pipette tip with buffer into the silicon tubing of the front reference flange. Gently press the pipette plunger down to pass the working buffer through the front silicon tubing into the reference capillary and up into the attached pipette tip of the rear flange. Press the pipette plunger down until the working buffer level reaches just above the front silicon tubing, then release the pipette plunger until the working buffer level reaches just above the rear silicon tubing.Continue passing the working buffer back and forth in the reference capillary to purge the volume of bubbles. Next, cap the rear pipette tip with a forefinger and gently pull up on the rear pipette tip and front pipette to remove them from the reference flanges with the silicon tubing attached. Load the sample capillary with working buffer as before.Place a black plastic cap on the rear reference sample flanges leaving the front flanges uncovered. Attach the pressure handle to the DSC and then open the DSC software and pressurize the instrument by clicking the red up arrow at the top of the interface once the power reading has stabilized. The DSC power is indicated in a box at the top right of the interface along with the instrument temperature and pressure reading.Equilibrate the DSC with working buffer by performing a forward and reverse scan in the experimental method tab on the left side of the screen. Ensure that the scanning option is selected to run the DSC and temperature scanning mode. In the temperature parameters inset under the experimental method tab, click the button for heating.Enter one and 100 degrees Celsius for the lower and upper experimental temperatures, one degree Celsius per minute for the scan rate and 60 seconds for the equilibration period. Click the AddSeries button under the input field for the equilibration period. Enter two into the steps to add field in the popup window and check the Alternate Heating/Cooling box.Click OK.The added scans appear in the lower portion of the interface. Check that the parameters for each scan are as desired. Start the experiment by clicking the green play button at the top of the interface.Navigate to the desired window and input a file name for saving the experiment in the popup window. View the experiment progress by clicking the data tab to the right of the experiment method tab. Run reference experiments for a baseline subtraction of the sample data by reloading the DSC with working buffer in both capillaries.Collect multiple forward and reverse scans over a suitable temperature range at one degree Celsius per minute with an up equilibration time of 120 seconds. Delete the previous buffer equilibration scans from the lower portion of the interface by highlighting each individually and clicking the red X to the middle right of the interface. Add the new scans by clicking the AddSeries button entering 20 in the field for steps to add and checking the Alternate Heating/Cooling box.Then, click OK and run the experiment by clicking the green play button as before. Repeat these steps with working buffer containing the desired concentration of ligand in both capillaries to obtain the reference experiments for the ligand. Collect two separate experiments to be used in acquiring the rate constant for thermolabile conversion.For the free biomolecule data set, ensure that the reference capillary contains the working buffer while the sample capillary contains the free biomolecule at the desired concentration in working buffer. Next, run the sample experiments using the same DSC loading procedure and experimental parameters used in the reference scans. For the ligand-bound experiments, ensure that the ligand is in the working buffer and the reference capillary and the biomolecule plus ligand are in the working buffer in the sample capillary.Flush the system between additions of different ligands as before. Perform one additional experiment with the biomolecule bound to the thermolabile ligand where the high-temperature equilibration period is increased to 600 seconds and all other experimental parameters are the same as before. Proceed to the data processing and analysis as described in the text protocol.The position and height of the thermolabile ligand bound peak successively shifts down towards that of the unbound molecule as the thermolabile ligand is depleted with each scan. The 3D maturation profile is used as a reference for the endpoint of thermolabile ligand conversion. Increasing the high-temperature equilibration period yields more pronounced reductions of the thermolabile ligand concentration with each scan relative to the short equilibration period dataset.Using the optimized global fit concentration parameters from the two datasets, the rate constant for ligand conversion at the high equilibration temperature can be calculated. Once mastered, this technique can be done in 72 hours if performed properly. When attempting this procedure, it is important to remember to degas the biomolecule ligand as well to purge the DSC capillaries of bubbles using the loading pipette to prevent data artifacts.After watching this video and reading the article, you should have a good understanding of how to perform DSC experiments on biomolecules as well as the implementation of global fitting analyses in order to rapidly extract thermodynamic parameters governing folding and binding interactions. Though this method can provide insight into equilibrium folding binding interactions, it can also be applied to other systems such as biomolecules that exhibit slow-folding and/or ligand-binding kinetics.

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Research

JoVE Journal

Biochemistry

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. ...

Measuring G-protein-coupled Receptor Signaling via Radio-labeled GTP Binding

G-Protein-Coupled Receptors (GPCRs) are a large family of transmembrane receptors that play critical roles in normal cellular physiology and constitute a major pharmacological target for multiple indications, including analgesia, blood pressure regulation, and the treatment of psychiatric disease. Upon ligand binding, GPCRs catalyze the activation of intracellular G-proteins by stimulating the incorporation of guanosine triphosphate (GTP). Activated G-proteins then stimulate signaling pathways that elicit cellular responses. GPCR signaling can be monitored by measuring the incorporation of a radiolabeled and non-hydrolyzable form of GTP, [35S]guanosine-5&#39;-O-(3-thio)triphosphate ([35S]GTP&#947;S), into G-proteins. Unlike other methods that assess more downstream signaling processes, [35S]GTP&#947;S binding measures a proximal event in GPCR signaling and, importantly, can distinguish agonists, antagonists, and inverse agonists. The present protocol outlines a sensitive and specific method for studying GPCR signaling using crude membrane preparations of an archetypal GPCR, the &#181;-opioid receptor (MOR1). Although alternative approaches to fractionate cells and tissues exist, many are cost-prohibitive, tedious, and/or require non-standard laboratory equipment. The present method provides a simple procedure that enriches functional crude membranes. After isolating MOR1, various pharmacological properties of its agonist, [D-Ala, N-MePhe, Gly-ol]-enkephalin (DAMGO), and antagonist, naloxone, were determined.

Guanosine triphosphate (GTP) binding is one of the earliest events in G-Protein-Coupled Receptor (GPCR) activation. This protocol describes how to pharmacologically characterize specific GPCR-ligand interactions by monitoring the binding of the radio-labeled GTP analog, [35S]guanosine-5&#39;-O-(3-thio)triphosphate ([35S]GTP&#947;S), in response to a ligand of interest.

G-Protein-Coupled Receptors (GPCRs) are a large family of transmembrane receptors that play critical roles in normal cellular physiology and constitute a ...

Measuring Protein Binding to F-actin by Co-sedimentation

Filamentous actin (F-actin) organization within cells is regulated by a large number of actin-binding proteins that control actin nucleation, growth, cross-linking and/or disassembly. This protocol describes a technique &#8211; the actin co-sedimentation, or pelleting, assay &#8211; to determine whether a protein or protein domain binds F-actin and to measure the affinity of the interaction (i.e., the dissociation equilibrium constant). In this technique, a protein of interest is first incubated with F-actin in solution. Then, differential centrifugation is used to sediment the actin filaments, and the pelleted material is analyzed by SDS-PAGE. If the protein of interest binds F-actin, it will co-sediment with the actin filaments. The products of the binding reaction (i.e., F-actin and the protein of interest) can be quantified to determine the affinity of the interaction. The actin pelleting assay is a straightforward technique for determining if a protein of interest binds F-actin and for assessing how changes to that protein, such as ligand binding, affect its interaction with F-actin.

This protocol describes a method to test the ability of a protein to co-sediment with filamentous actin (F-actin) and, if binding is observed, to measure the affinity of the interaction.

Filamentous actin (F-actin) organization within cells is regulated by a large number of actin-binding proteins that control actin nucleation, growth, ...

Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy (NMR) and Microscale Thermophoresis (MST)

Filamentous proteins such as vimentin provide organization within cells by providing a structural scaffold with sites that bind proteins containing plakin repeats. Here, a protocol for detecting and measuring such interactions is described using the globular plakin repeat domain of envoplakin and the helical coil of vimentin. This provides a basis for determining whether a protein binds vimentin (or similar filamentous proteins) and for measurement of the affinity of the interaction. The globular protein of interest is labeled with 15N and titrated with vimentin protein in solution. A two-dimensional NMR spectrum is acquired to detect interactions by observing changes in peak shape or chemical shifts, and to elucidate effects of solution conditions including salt levels, which influence vimentin quaternary structure. If the protein of interest binds the filamentous ligand, the binding interaction is quantified by MST using the purified proteins. The approach is a straightforward way for determining whether a protein of interest binds a filament, and for assessing how alterations, such as mutations or solution conditions, affect the interaction.

Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy NMR and Microscale Thermophoresis MST

Here, we present a protocol for the production and purification of proteins that are labeled with stable isotopes, and subsequent characterization of protein-protein interactions using Nuclear Magnetic Resonance (NMR) spectroscopy and MicroScale Thermophoresis (MST) experiments.

Filamentous proteins such as vimentin provide organization within cells by providing a structural scaffold with sites that bind proteins containing plakin ...

Measuring Nucleotide Binding to Intact, Functional Membrane Proteins in Real Time

We have developed a method to measure binding of adenine nucleotides to intact, functional transmembrane receptors in a cellular or membrane environment. This method combines expression of proteins tagged with the fluorescent non-canonical amino acid ANAP, and FRET between ANAP and fluorescent (trinitrophenyl) nucleotide derivatives. We present examples of nucleotide binding to ANAP-tagged KATP ion channels measured in unroofed plasma membranes and excised, inside-out membrane patches under voltage clamp. The latter allows for simultaneous measurements of ligand binding and channel current, a direct readout of protein function. Data treatment and analysis are discussed extensively, along with potential pitfalls and artefacts. This method provides rich mechanistic insights into the ligand-dependent gating of KATP channels and can readily be adapted to the study of other nucleotide-regulated proteins or any receptor for which a suitable fluorescent ligand can be identified.

This protocol presents a method for measuring adenine nucleotide binding to receptors in real time in a cellular environment. Binding is measured as F&#246;rster resonance energy transfer (FRET) between trinitrophenyl nucleotide derivatives and protein labeled with a non-canonical, fluorescent amino acid.

We have developed a method to measure binding of adenine nucleotides to intact, functional transmembrane receptors in a cellular or membrane environment. ...

Removal and Replacement of Endogenous Ligands from Lipid-Bound Proteins and Allergens

Many major allergens bind to hydrophobic lipid-like molecules, including Mus m 1, Bet v 1, Der p 2, and Fel d 1. These ligands are strongly retained and have the potential to influence the sensitization process either through directly stimulating the immune system or altering the biophysical properties of the allergenic protein. In order to control for these variables, techniques are required for the removal of endogenously bound ligands and, if necessary, replacement with lipids of known composition. The cockroach allergen Bla g 1 encloses a large hydrophobic cavity which binds a heterogeneous mixture of endogenous lipids when purified using traditional techniques. Here, we describe a method through which these lipids are removed using reverse-phase HPLC followed by thermal annealing to yield Bla g 1 in either its Apo-form or reloaded with a user-defined mixture of fatty acid or phospholipid cargoes. Coupling this protocol with biochemical assays reveal that fatty acid cargoes significantly alter the thermostability and proteolytic resistance of Bla g 1, with downstream implications for the rate of T-cell epitope generation and allergenicity. These results highlight the importance of lipid removal/reloading protocols such as the one described herein when studying allergens from both recombinant and natural sources. The protocol is generalizable to other allergen families including lipocalins (Mus m 1), PR-10 (Bet v 1), MD-2 (Der p 2) and Uteroglobin (Fel d 1), providing a valuable tool to study the role of lipids in the allergic response.

This protocol describes the removal of endogenous lipids from allergens, and their replacement with user-specified ligands through reverse-phase HPLC coupled with thermal annealing. 31P-NMR and circular dichroism allow for the rapid confirmation of ligand removal/loading, and the recovery of native allergen structure.

Many major allergens bind to hydrophobic lipid-like molecules, including Mus m 1, Bet v 1, Der p 2, and Fel d 1. These ligands are strongly retained and ...

Identifying the Binding Proteins of Small Ligands with the Differential Radial Capillary Action of Ligand Assay (DRaCALA)

The past decade has seen tremendous progress in the understanding of small signaling molecules in bacterial physiology. In particular, the target proteins of several nucleotide-derived secondary messengers (NSMs) have been systematically identified and studied in model organisms. These achievements are mainly due to the development of several new techniques including the capture compound technique and the differential radial capillary action of ligand assay (DRaCALA), which were used to systematically identify target proteins of these small molecules. This paper describes the use of the NSMs, guanosine penta- and tetraphosphates (p)ppGpp, as an example and video demonstration of the DRaCALA technique. Using DRaCALA, 9 out of 20 known and 12 new target proteins of (p)ppGpp were identified in the model organism, Escherichia coli K-12, demonstrating the power of this assay. In principle, DRaCALA could be used for studying small ligands that can be labeled by radioactive isotopes or fluorescent dyes. The critical steps, pros, and cons of DRaCALA are discussed here for further application of this technique.

Identifying the Binding Proteins of Small Ligands with the Differential Radial Capillary Action of Ligand Assay DRaCALA

The Differential Radial Capillary Action of Ligand Assay (DRaCALA) can be used to identify small ligand binding proteins of an organism by using an ORFeome library.

The past decade has seen tremendous progress in the understanding of small signaling molecules in bacterial physiology. In particular, the target proteins ...

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics

Short-lived or transient interactions of macromolecules at and with lipid membranes, an interface where a multitude of essential biological reactions take place, are inherently difficult to assess with standard biophysical methods. The introduction of mass-sensitive particle tracking (MSPT) constitutes an important step toward a thorough quantitative characterization of such processes. Technically, this was made possible through the advent of interferometric scattering microscopy (iSCAT)-based mass photometry (MP). When the background removal strategy is optimized to reveal the two-dimensional motion of membrane-associated particles, this technique allows the real-time analysis of both diffusion and molecular mass of unlabeled macromolecules on biological membranes. Here, a detailed protocol to perform and analyze mass-sensitive particle tracking of membrane-associated systems is described. Measurements performed on a commercial mass photometer achieve time resolution in the millisecond regime and, depending on the MP system, a mass detection limit down to 50 kDa. To showcase the potential of MSPT for the in-depth analysis of membrane-catalyzed macromolecule dynamics in general, results obtained for exemplary protein systems such as the native membrane interactor annexin V are presented.

This protocol describes an iSCAT-based image processing and single-particle tracking approach that enables the simultaneous investigation of the molecular mass and the diffusive behavior of macromolecules interacting with lipid membranes. Step-by-step instructions for sample preparation, mass-to-contrast conversion, movie acquisition, and post-processing are provided alongside directions to prevent potential pitfalls.

Short-lived or transient interactions of macromolecules at and with lipid membranes, an interface where a multitude of essential biological reactions take ...

Quantifying the Binding Interactions Between Cu(II) and Peptide Residues in the Presence and Absence of Chromophores

Copper(II) is an essential metal in biological systems, conferring unique chemical properties to the biomolecules with which it interacts. It has been reported to directly bind to a variety of peptides and play both necessary and pathological roles ranging from mediating structure to electron transfer properties to imparting catalytic function. Quantifying the binding affinity and thermodynamics of these Cu(II)-peptide complexes in vitro provides insight into the thermodynamic driving force of binding, potential competitions between different metal ions for the peptide or between different peptides for Cu(II), and the prevalence of the Cu(II)-peptide complex in vivo. However, quantifying the binding thermodynamics can be challenging due to a myriad of factors, including accounting for all competing equilibria within a titration experiment, especially in cases where there are a lack of discrete spectroscopic handles representing the peptide, the d-block metal ion, and their interactions.
Here, a robust set of experiments is provided for the accurate quantification of Cu(II)-peptide thermodynamics. This article focuses on the use of electronic absorption spectroscopy in the presence and absence of chromophoric ligands to provide the needed spectroscopic handle on Cu(II) and the use of label-free isothermal titration calorimetry. In both experimental techniques, a process is described to account for all competing equilibria. While the focus of this article is on Cu(II), the described set of experiments can apply beyond Cu(II)-peptide interactions, and provide a framework for accurate quantification of other metal-peptide systems under physiologically relevant conditions.

Quantifying the Binding Interactions Between CuII and Peptide Residues in the Presence and Absence of Chromophores

This article focuses on the use of electronic absorption spectroscopy and isothermal titration calorimetry to probe and quantify the thermodynamics of Cu(II) binding to peptides and proteins.

Copper(II) is an essential metal in biological systems, conferring unique chemical properties to the biomolecules with which it interacts. It has been ...

Folding and Probing of Nucleic Acid Constructs

Begin by pipetting G4-TBA, single-stranded TBA, and double-stranded TBA solutions into three different tubes for folding. Heat the samples to 95 degrees Celsius for five minutes. Let them cool slowly to room temperature.Once the tubes have cooled to room temperature, centrifuge the tubes. Next, organize three sets each of seven empty autoclaved 0.5-milliliter tubes. Add three microliters of ultrapure water into each tube.Pipette five microliters of the folded nucleic acid constructs into each tube of the set. Next, add two microliters of either 25 or 250-micromolar B-CEP1 to obtain the final probe concentration of five and 50 micromolar respectively. To the three control tubes, add ultrapure water instead of the compound and incubate all the samples at 37 degrees Celsius.Stop the reaction by placing the tubes at 20 degrees Celsius, then dry the samples in a vacuum centrifuge.