This work was financially supported by a research grant from the Dutch National Research School Combination, Catalysis Controlled by Chemical Design (NRSC-Catalysis). Dr. H.Y. Steensma and Dr. G.P.H. van Heusden from Leiden University are acknowledged for their support with the recombinant expression of S. cerevisiae Nar1.

1. Preparation of Setup and Solutions
<ol>
	<li>Prepare buffer solution containing 100 mM Tris, 250 mM NaCl and 10% glycerol at pH 8.5. Deaerate the buffer by flushing with argon. Introduce the buffer into an anaerobic chamber.</li>
	<li>Divide the buffer in two portions. To one portion (buffer A) add 1 mM DL-dithiothreitol (DTT, Mr 154.25 g/mol) and 1 mM L-cysteine. The other portion (buffer B) does not contain reducing agents.</li>
	<li>Prepare oxidant and reductant solutions. Make 1 ml solutions of 2, 20, and 200 mM potassium ferricyanide (FIC, Mr 329.26 g/mol) and of sodium dithionite (SD, Mr 174.11 g/mol) in anaerobic buffer B.</li>
	<li>Prepare mediator mix as follows:
	<ol>
		<li>Add 160 &#181;M of each of the following redox mediators and 50 mM NaCl to buffer B: N,N,N&#8217;,N&#8217;-tetramethyl-p-phenylendediamine (TMPD, Mr 237.17 g/mol, E&#8217;0 +0.276 V), 2,6-dichlorophenol indophenol (DCIP, Mr 290.08 g/mol, E&#8217;0 +0.217 V), phenazine ethosulphate (PES, Mr 334.4 g/mol, E&#8217;0 +0.055 V), Methylene blue (Mr 319.85 g/mol, E&#8217;0 +0.011 V), Resorufin (Mr 235.17 g/mol, E&#8217;0 -0.051 V), Indigodisulphonate (Mr 466.35 g/mol, E&#8217;0 -0.125 V), 2-hydroxy-1,4-naphtaquinone (Mr 174.15 g/mol, E&#8217;0 -0.145 V), Anthraquinone-2-sulfonate (Mr 328.28 g/mol, E&#8217;0 -0.225 V), Phenosafranin (Mr 322.8 g/mol, E&#8217;0 -0.252 V), Safranin O (Mr 350.84 g/mol, E&#8217;0 -0.280 V), neutral red (Mr 288.8 g/mol, E&#8217;0 -0.340 V), Benzyl viologen (Mr 409.4 g/mol, E&#8217;0 -0.350 V), and Methyl viologen (Mr 257.16 g/mol, E&#8217;0 -0.440 V).</li>
		<li>Wrap the bottle in aluminum foil to protect the mediators from light.</li>
	</ol>
	</li>
	<li>Prepare 10 mg/ml S. cerevisiae strep-tagged Nar1 protein (181 &#181;M, Mr 55.2 kDa) in buffer A. Express S. cerevisiae Nar1 in E. coli as a strep-tagged protein using a pET24A expression vector. Purify the protein in an anaerobic chamber using Strep-tactin chromatography media (IBA) and purify using a protein purification system such as Akta purifier (GE Healthcare).</li>
	<li>Prepare the redox titration setup in an anaerobic chamber as follows:
	<ol>
		<li>Connect a Ag/AgCl reference electrode and a platinum wire electrode to the titration vessel. Connect both electrodes to a voltmeter that can measure from mV up to V.</li>
		<li>Insert a small stirring bar.</li>
		<li>Place the titration vessel above a magnetic stirrer.</li>
		<li>Fill the titration vessel with Buffer B, mediator mix solution and protein solution to up to 2 ml, i.e. to final concentrations of 72 &#181;M protein and 38 &#181;M of each mediator. Note: depending on the protein concentration and the required mediator concentrations the amounts of the three solutions should be adjusted.</li>
		<li>Stir for 30 min and switch on the voltmeter.</li>
	</ol>
	</li>
	<li>Prepare 10 clean quartz glass EPR tubes. Introduce the tubes in the anaerobic chamber.</li>
	<li>Fill a small (circa 200 ml) liquid nitrogen dewar with liquid nitrogen.</li>
</ol>
2. Perform Redox Titration
<ol>
	<li>Wait until the potential of the solution is stable. Note: In practice this means that the potential drifts less than 1 mV per minute.</li>
	<li>Note down the potential given by the voltmeter.</li>
	<li>Draw the first sample of 200 &#181;l and inject into an EPR tube.</li>
	<li>Cap the tube with a rubber stopper and remove the tube from the anaerobic chamber.</li>
	<li>Freeze the tube in liquid nitrogen as follows: Caution! This has to be done slowly, otherwise the tube will break.
	<ol>
		<li>First insert the tip of the tube in the liquid nitrogen.</li>
		<li>Wait until a hissing sound can be heard. Note: This may take up to 10 sec.</li>
		<li>Slowly insert the rest of the tube so that the sample part is fully submerged.</li>
	</ol>
	</li>
	<li>Add a small aliquot 1-2 &#181;l of the 2 mM SD solution to the solution in the titration vessel to lower the potential of the solution to -0.6 V. 
	Note: If more than 10 &#181;l has to be added, switch to the 20 mM solution. As it is very difficult to poise to a specific potential value, the actual values recorded on the voltmeter are written down and used to construct the titration curve.</li>
	<li>Draw a sample as described in step 2.3-2.5.</li>
	<li>Note down the actual potential given by the voltmeter.</li>
	<li>Add oxidant until the potential has increased by circa 50 mV. Start by adding a small aliquot 1-2 &#181;l of the 2 mM FIC solution. If more than 10 &#181;l has to be added, switch to the 20 mM solution.</li>
	<li>Note down how much of the solutions has been added. Note: This is necessary to correct for sample dilution during the titration.</li>
	<li>Draw a sample as described in the steps 2.3-2.5.</li>
	<li>Note down the actual potential given by the voltmeter.</li>
	<li>Repeat steps 2.9 and 2.12 until the potential range from -0.6 V to +0.2 V has been covered and all 10 EPR tubes are filled each with 200 &#181;l. 
	Note: As the volume with every withdrawal is reduced the positioning of the electrodes may need to be adjusted have good contact with the solution without interference of the stirring. It may be difficult to measure the potential after withdrawal of the last sample and therefore the potential of that sample may be less accurate.</li>
	<li>Optionally, store the frozen EPR samples in liquid nitrogen until the EPR measurements can take place.</li>
</ol>
3. Measure Titration Samples Using EPR Spectroscopy and Data Analysis
<ol>
	<li>Record EPR spectra of the different titration samples as follows:
	<ol>
		<li>Use a high-vacuum pump to evacuate a quartz cryostat to &#60;10-5 bar.</li>
		<li>Switch on the water cooling of the EPR magnet. Open the flow of dry air through the EPR cavity.</li>
		<li>Switch on the power supply to the magnet and the computer of the EPR.</li>
		<li>Run a frequency calibration program. Set the EPR measurement parameters. Connect the cryostat to the liquid helium dewar. Cool the cavity to 9-16 K.</li>
		<li>Introduce the EPR sample in the cavity. Record the EPR spectrum.</li>
	</ol>
	</li>
	<li>Identify the different EPR species and use the best spectra to quantify the signals. Achieve EPR quantification by double integration of the spectra and comparison with the spectrum of an external copper standard solution 10 mM CuSO4/10 mM HCl/2 M NaClO4.8</li>
	<li>Make the titration curve as follows:
	<ol>
		<li>Plot the EPR signal amplitude at a g-value that is characteristic for the paramagnetic species of interest against the potential.</li>
		<li>Change the EPR signal amplitude scale to a spins/molecule scale by using the EPR quantification from step 3.2.</li>
		<li>Correct the signal amplitude of each sample for the dilution that has occurred due to the additions of oxidizing or reducing agent.</li>
		<li>Correct the potential for the midpoint potential of the Ag/AgCl reference electrode. 
		Note: The Ag/AgCl reference electrode (with saturated KCl) has a midpoint potential of +0.194 V versus the Standard Hydrogen Electrode (SHE) at 25 &#176;C. Therefore, if the potential on the voltmeter reads circa -0.6 V, the potential with reference to the SHE is -0.4 V.</li>
	</ol>
	</li>
	<li>Fit the signal to the Nernst equation as follows: 
	For a species that is paramagnetic in the reduced state: 
	<img alt="Equation 1" fo:content-width="2in" src="/files/ftp_upload/51611/51611eq1.jpg" width="200" /> 
	For a species that is paramagnetic in the oxidized state: 
	<img alt="Equation 2" fo:content-width="2in" src="/files/ftp_upload/51611/51611eq2.jpg" width="200" /> 
	For a species that is paramagnetic in an intermediate state: 
	<img alt="Equation 3" fo:content-width="2.2in" src="/files/ftp_upload/51611/51611eq3.jpg" width="220" /> 
	These equations are valid for redox reactions in which one electron is transferred, so n = 1. 
	E = potential in Volt 
	Em = midpoint potential in Volt 
	F = Faraday constant = 96,480 C&#183;mol-1 
	R = Gas constant = 8.314 J&#183;K-1&#183;mol-1 
	T = Temperature in Kelvin</li>
</ol>

<ol>
	<li>Lippard, S. J., Berg, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Principles of Bioinorganic Chemistry. , (1994).</li><li>Bertini, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Bioinorganic Chemistry. , 611 (1994).</li><li>Leger, 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=Enzyme+Electrokinetics:+Using+Protein+Film+Voltammetry+To+Investigate+Redox+Enzymes+and+Their+Mechanisms.">Enzyme Electrokinetics: Using Protein Film Voltammetry To Investigate Redox Enzymes and Their Mechanisms.</a> Biochemistry. 42, 8653-8662 (2003).</li><li>Hagen, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+Electron+Transfer+of+Redox+Proteins+at+the+Bare+Glassy+Carbon+Electrode.">Direct Electron Transfer of Redox Proteins at the Bare Glassy Carbon Electrode.</a> Eur. J. Biochem. 182, 523-530 (1989).</li><li>Pierik, A. 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=Redox+Properties+of+the+Iron-Sulfur+Clusters+in+Activated+Fe-Hydrogenase+from+Desulfovibrio+vulgaris+(Hildenborough).">Redox Properties of the Iron-Sulfur Clusters in Activated Fe-Hydrogenase from Desulfovibrio vulgaris (Hildenborough).</a> Eur. J. Biochem. 209, 63-72 (1992).</li><li>Balk, J., Pierik, A. J., Netz, D. J., Muhlenhoff, U., Lill, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Hydrogenase-like+Nar1p+is+Essential+for+Maturation+of+Cytosolic+and+Nuclear+Iron-Sulphur+Proteins.">The Hydrogenase-like Nar1p is Essential for Maturation of Cytosolic and Nuclear Iron-Sulphur Proteins.</a> EMBO J. 23, 2105-2115 (2004).</li><li>Sharma, A. K., Pallesen, L. J., Spang, R. J., Walden, W. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytosolic+Iron-Sulfur+Cluster+Assembly+(CIA)+System:+Factors,+Mechanism,+and+Relevance+to+Cellular+Iron+Regulation.">Cytosolic Iron-Sulfur Cluster Assembly (CIA) System: Factors, Mechanism, and Relevance to Cellular Iron Regulation.</a> J. Biol. Chem. 285, 26745-26751 (2010).</li><li>Aasa, R., V&#228;nng&#229;rd, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=EPR+Signal+Intensity+and+Powder+Shapes.">EPR Signal Intensity and Powder Shapes.</a> A Reexamination. J. Magn. Reson. 19, 308-315 (1975).</li><li>Balk, J., Pierik, A. J. A., Netz, ., J, D., M&#252;hlenhoff, U., Lill, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nar1p,+a+conserved+eukaryotic+protein+with+similarity+to+Fe-only+hydrogenases,+functions+in+cytosolic+iron-sulphur+protein+biogenesis.">Nar1p, a conserved eukaryotic protein with similarity to Fe-only hydrogenases, functions in cytosolic iron-sulphur protein biogenesis.</a> Biochem. Soc. Trans. 33, 86-89 (2005).</li><li>Hennessy, D. J., Reid, G. R., Smith, F. E., Thompson, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ferene+-+a+new+spectrophotometric+reagent+for+iron.">Ferene - a new spectrophotometric reagent for iron.</a> Can. J. Chem. 62, 721-724 (1984).</li><li>Flint, D. H., Emptage, M. H., Guest, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fumarase+A+from+Escherichia+coli:+purification+and+characterization+as+an+iron-sulfur+cluster+containing+enzyme.">Fumarase A from Escherichia coli: purification and characterization as an iron-sulfur cluster containing enzyme.</a> Biochemistry. 31, 10331-10337 (1992).</li><li>Hagedoorn, P. L., Driessen, M. C., Mvd Bosch, ., Landa, I., Hagen, W. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hyperthermophilic+Redox+Chemistry:+a+Re-evaluation.">Hyperthermophilic Redox Chemistry: a Re-evaluation.</a> FEBS Lett. 440, 311-314 (1998).</li><li>Tadesse, M. A., D'Annibale, A., Galli, C., Gentili, P., Sergi, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+assessment+of+the+relative+contributions+of+redox+and+steric+issues+to+laccase+specificity+towards+putative+substrates.">An assessment of the relative contributions of redox and steric issues to laccase specificity towards putative substrates.</a> Organic &amp; biomolecular chemistry. 6, 868-878 (2008).</li></ol>

The authors have nothing to disclose.

The series of 13 redox mediators allows a redox equilibrium in the solution in the range from -0.45 to +0.3 V versus SHE (Table 1 and Figure 3). Well above and below these potentials all mediators are either completely reduced or completely oxidized and hence no further equilibration with the redox active centers of the protein can occur. This is an important notion, as in literature sometimes redox titrations are performed with only two or three mediators, allowing only a narrow range t...

It is striking that the most fundamental chemical processes sustaining life on this planet, photosynthesis, nitrogen fixation and respiration, are catalyzed by large protein complexes containing a wide range of organic and inorganic redox cofactors. It has been estimated that approximately 30% of all proteins contain one or more metal cofactors.1,2 Identifying and characterizing the redox cofactors can be established using direct electrochemistry (e.g., protein film voltammetry) or redox titrations. The two techniques are complementary in their nature and applicability. Voltammetry offers fast determination of midpoint potentials and electron transfer kinetics of cofactors that can react with an electrode surface.3,4 Usually this works well for electron transfer proteins, such as cytochrome c or ferredoxin. And it sometimes works for more complex proteins that have been immobilized to an electrode surface. Detailed knowledge of the nature of cofactors in the protein has to be available, as the voltammogram will not give any direct information on the identity of the cofactor. Redox titrations are more laborious to execute and require mg quantities of protein. However, they offer information on the midpoint potential and the identity of the cofactor.5 Furthermore in a single titration multiple cofactors in a protein can be monitored.
The principle of a redox titration is that the redox active protein or enzyme is chemically reduced or oxidized. In order to make sure that the cofactors react with the reductant or oxidant redox mediators are used. These redox mediators also react with an electrode so that the potential of the solution can be measured. The mediators act as a redox buffer and equilibrate between the cofactors in the protein and the electrode. After chemically poising the potential to the desired value, a sample is drawn and quickly frozen in liquid nitrogen to await further analysis with spectroscopic techniques. EPR spectroscopy is particularly useful in this respect as it can be used to quantitatively measure paramagnetic metal centers or organic radicals.
The redox titration can be performed in two directions: from low to high or from high to low midpoint potential. The choice is dependent on the stability of the cofactors under study. Often it is wise to start at low potential and add oxidant to stepwise increase the potential. This is called an oxidative titration and is described here. Here we show the redox titration of the iron-sulfur cluster containing protein Nar1 from Saccharomyces cerevisiae. This protein is involved, likely as a scaffold protein, in the cytosolic iron-sulfur cluster biosynthetic machinery (CIA pathway).6,7

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Reference electrode (Ag/AgCl)</td>
			<td style="width:101px;">Radiometer</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Chemicals</td>
			<td style="width:101px;">Sigma-Aldrich</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">EPR spectrometer</td>
			<td style="width:101px;">Bruker</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:216px;">N,N,N&#8217;,N&#8217;-tetramethyl-p-phenylendediamine (TMPD) &#183;(HCl)2</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">637-01-4</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">2,6-dichlorophenol indophenol (DCIP), sodium salt</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">620-45-1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Phenazine ethosulfate (PES)</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">10510-77-7</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Methylene blue</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">122965-43-9</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Resorufin, sodium salt</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">34994-50-8</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">Indigodisulfonate (indigo carmine)</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">860-22-0</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">2-hydroxy-1,4-naphtaquinone</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">83-72-7</td>
		</tr>
		<tr height="47">
			<td height="47" style="height:47px;width:216px;">Anthraquinone-2-sulfonate Na+ H2O</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">153277-35-1</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Phenosafranin</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">81-93-6</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Safranin O</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">477-73-6</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Neutral red</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">553-24-2</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Benzyl viologen</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">1102-19-8</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Methyl viologen</td>
			<td style="width:101px;"></td>
			<td style="width:119px;"></td>
			<td style="width:167px;">1910-42-5</td>
		</tr>
	</tbody>
</table>

epr monitored redox titration of the cofactors of saccharomyces cerevisiae nar1

Electron Paramagnetic Resonance (EPR) monitored redox titrations are a powerful method to determine the midpoint potential of cofactors in proteins and to identify and quantify the cofactors in their detectable redox state.
The technique is complementary to direct electrochemistry (voltammetry) approaches, as it does not offer information on electron transfer rates, but does establish the identity and redox state of the cofactors in the protein under study. The technique is widely applicable to any protein containing an electron paramagnetic resonance (EPR) detectable cofactor.
A typical titration requires 2 ml protein with a cofactor concentration in the range of 1-100 &#181;M. The protein is titrated with a chemical reductant (sodium dithionite) or oxidant (potassium ferricyanide) in order to poise the sample at a certain potential. A platinum wire and a Ag/AgCl reference electrode are connected to a voltmeter to measure the potential of the protein solution. A set of 13 different redox mediators is used to equilibrate between the redox cofactors of the protein and the electrodes. Samples are drawn at different potentials and the Electron Paramagnetic Resonance spectra, characteristic for the different redox cofactors in the protein, are measured. The plot of the signal intensity versus the sample potential is analyzed using the Nernst equation in order to determine the midpoint potential of the cofactor.

The redox titration of the iron-sulfur cluster containing protein Nar1 from Saccharomyces cerevisiae resulted in the identification of three different cofactors: Nar1: a [3Fe-4S] cluster, a [4Fe-4S] cluster and a mononuclear Fe center (Figure 1). The EPR signals are characterized by their g-values: for the [3Fe-4S]+ gz 2.01, gcrossover 2.00 (Figure 1B); for the [4Fe-4S]+, gz 2.02 gy 1.93, gx 1.82 (<stro...

Watch this Scientific Journal Video about EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1 at JoVE.com

EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1

The goal of this protocol is to use electron paramagnetic resonance (EPR) monitored redox titrations to identify different cofactors of Saccharomyces cerevisiae Nar1. Redox titrations offer a very robust way to obtain midpoint potentials of different redox active cofactors in enzymes and proteins.

EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1

Electron Paramagnetic Resonance (EPR) monitored redox titrations are a powerful method to determine the midpoint potential of cofactors in proteins and to ...

epr-monitored-redox-titration-cofactors-saccharomyces-cerevisiae

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13.4K Views.  Delft University of Technology. The goal of this protocol is to use electron paramagnetic resonance (EPR) monitored redox titrations to identify different cofactors of Saccharomyces cerevisiae Nar1. Redox titrations offer a very robust way to obtain midpoint potentials of different redox active cofactors in enzymes and proteins.

Video: EPR Monitored Redox Titration of the Cofactors of Saccharomyces cerevisiae Nar1

Dissection of Saccharomyces Cerevisiae Asci

Yeast is a highly tractable model system that is used to study many different cellular processes. The common laboratory strain Saccharomyces cerevisiae exists in either a haploid or diploid state. The ability to combine alleles from two haploids and the ability to introduce modifications to the genome requires the production and dissection of asci. Asci production from haploid cells begins with the mating of two yeast haploid strains with compatible mating types to produce a diploid strain. This can be accomplished in a number of ways either on solid medium or in liquid. It is advantageous to select for the diploids in medium that selectively promotes their growth compared to either of the haploid strains. The diploids are then allowed to sporulate on nutrient-poor medium to form asci, a bundle of four haploid daughter cells resulting from meiotic reproduction of the diploid. A mixture of vegetative cells and asci is then treated with the enzyme zymolyase to digest away the membrane sac surrounding the ascospores of the asci. Using micromanipulation with a microneedle under a dissection microscope one can pick up individual asci and separate and relocate the four ascopores. Dissected asci are grown for several days and tested for the markers or alleles of interest by replica plating onto appropriate selective media.

Dissection of Saccharomyces Cerevisiae Asci

Micromanipulation of yeast cells is needed for meiotic genetic analysis or to select diploid zygotes. These micromanipulations are carried out using the microneedle of a dissection microscope. The microneedle is used to relocate cells and is controlled by a micromanipulator which are available with various degrees of automation.

Yeast is a highly tractable model system that is used to study many different cellular processes. The common laboratory strain Saccharomyces cerevisiae ...

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground using a cryolysis procedure in a ball mill grinder and the resulting grindate brought into solution by urea solubilization. This procedure allows for the lysis of the cells in a metabolically inactive state, preserving phosphorylation and preventing reorientation of the phosphoproteome during cell lysis.  Following reduction, alkylation, trypsin digestion of the proteins, the samples are desalted on C18 columns and the sample complexity reduced by fractionation using hydrophilic interaction chromatography (HILIC). HILIC columns preferentially retain hydrophilic molecules which is well suited for phosphoproteomics.  Phosphorylated peptides tend to elute later in the chromatographic profile than the non phosphorylated counterparts. After fractionation, phosphopeptides are enriched using immobilized metal chromatography, which relies on charge-based affinities for phosphopeptide enrichment. At the end of this procedure the samples are ready to be quantitatively analyzed by mass spectrometry.

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

Description of a quantitative phosphorylation procedure using cryolysis, urea solubilziation, HILIC fractionation and IMAC enrichment of phosphorylated peptides.

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground ...

Quantitation and Analysis of the Formation of HO-Endonuclease Stimulated Chromosomal Translocations by Single-Strand Annealing in Saccharomyces cerevisiae

Genetic variation is frequently mediated by genomic rearrangements that arise through interaction between dispersed repetitive elements present in every eukaryotic genome. This process is an important mechanism for generating diversity between and within organisms1-3. The human genome consists of approximately 40% repetitive sequence of retrotransposon origin, including a variety of LINEs and SINEs4. Exchange events between these repetitive elements can lead to genome rearrangements, including translocations, that can disrupt gene dosage and expression that can result in autoimmune and cardiovascular diseases5, as well as cancer in humans6-9.
Exchange between repetitive elements occurs in a variety of ways. Exchange between sequences that share perfect (or near-perfect) homology occurs by a process called homologous recombination (HR). By contrast, non-homologous end joining (NHEJ) uses little-or-no sequence homology for exchange10,11. The primary purpose of HR, in mitotic cells, is to repair double-strand breaks (DSBs) generated endogenously by aberrant DNA replication and oxidative lesions, or by exposure to ionizing radiation (IR), and other exogenous DNA damaging agents. 
In the assay described here, DSBs are simultaneously created bordering recombination substrates at two different chromosomal loci in diploid cells by a galactose-inducible HO-endonuclease (Figure 1). The repair of the broken chromosomes generates chromosomal translocations by single strand annealing (SSA), a process where homologous sequences adjacent to the chromosome ends are covalently joined subsequent to annealing. One of the substrates, his3-&Delta;3', contains a 3' truncated HIS3 allele and is located on one copy of chromosome XV at the native HIS3 locus. The second substrate, his3-&Delta;5', is located at the LEU2 locus on one copy of chromosome III, and contains a 5' truncated HIS3 allele. Both substrates are flanked by a HO endonuclease recognition site that can be targeted for incision by HO-endonuclease. HO endonuclease recognition sites native to the MAT locus, on both copies of chromosome III, have been deleted in all strains. This prevents interaction between the recombination substrates and other broken chromosome ends from interfering in the assay. The KAN-MX-marked galactose-inducible HO endonuclease expression cassette is inserted at the TRP1 locus on chromosome IV. The substrates share 311 bp or 60 bp of the HIS3 coding sequence that can be used by the HR machinery for repair by SSA. Cells that use these substrates to repair broken chromosomes by HR form an intact HIS3 allele and a tXV::III chromosomal translocation that can be selected for by the ability to grow on medium lacking histidine (Figure 2A). Translocation frequency by HR is calculated by dividing the number of histidine prototrophic colonies that arise on selective medium by the total number of viable cells that arise after plating appropriate dilutions onto non-selective medium (Figure 2B). A variety of DNA repair mutants have been used to study the genetic control of translocation formation by SSA using this system12-14.

Quantitation and Analysis of the Formation of HO-Endonuclease Stimulated Chromosomal Translocations by Single-Strand Annealing in Saccharomyces cerevisiae

The HO-stimulated translocation assay monitors single-strand annealing following the creation of DNA double-strand breaks at multiple loci in diploid Saccharomyces cerevisiae. This mechanism may model genome rearrangements in somatic cells of higher eukaryotes following exposure to high doses of ionizing radiation.

Genetic variation is frequently mediated by genomic rearrangements that arise through interaction between dispersed repetitive elements present in every ...

Expression and Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein in Saccharomyces cerevisiae

The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel, that when mutated, can give rise to cystic fibrosis in humans.There is therefore considerable interest in this protein, but efforts to study its structure and activity have been hampered by the difficulty of expressing and purifying sufficient amounts of the protein1-3. Like many 'difficult' eukaryotic membrane proteins, expression in a fast-growing organism is desirable, but challenging, and in the yeast S. cerevisiae, so far low amounts were obtained and rapid degradation of the recombinant protein was observed 4-9. Proteins involved in the processing of recombinant CFTR in yeast have been described6-9 .In this report we describe a methodology for expression of CFTR in yeast and its purification in significant amounts. The protocol describes how the earlier proteolysis problems can be overcome and how expression levels of CFTR can be greatly improved by modifying the cell growth conditions and by controlling the induction conditions, in particular the time period prior to cell harvesting. The reagants associated with this protocol (murine CFTR-expressing yeast cells or yeast plasmids) will be distributed via the US Cystic Fibrosis Foundation, which has sponsored the research. An article describing the design and synthesis of the CFTR construct employed in this report will be published separately (Urbatsch, I.; Thibodeau, P. et al., unpublished). In this article we will explain our method beginning with the transformation of the yeast cells with the CFTR construct - containing yeast plasmid (Fig. 1). The construct has a green fluorescent protein (GFP) sequence fused to CFTR at its C-terminus and follows the system developed by Drew et al. (2008)10. The GFP allows the expression and purification of CFTR to be followed relatively easily. The JoVE visualized protocol finishes after the preparation of microsomes from the yeast cells, although we include some suggestions for purification of the protein from the microsomes. Readers may wish to add their own modifications to the microsome purification procedure, dependent on the final experiments to be carried out with the protein and the local equipment available to them. The yeast-expressed CFTR protein can be partially purified using metal ion affinity chromatography, using an intrinsic polyhistidine purification tag. Subsequent size-exclusion chromatography yields a protein that appears to be &gt;90% pure, as judged by SDS-PAGE and Coomassie-staining of the gel.

Expression and Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein in Saccharomyces cerevisiae

Attempts to express the cystic fibrosis transmembrane conductance regulator (CFTR) in Saccharomyces cerevisiae have, until now, yielded relatively low amounts of protein. This protocol and the associated reagents distributed via the Cystic Fibrosis Foundation should allow the preparation of milligram amounts of this 'difficult' eukaryotic membrane protein.

The  cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride  channel, that when mutated, can give rise to cystic fibrosis in  ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must be maintained to avoid deleterious consequences 1. External or internal factors that disrupt this balance can lead to protein aggregation, toxicity and cell death. In humans this is a major contributing factor to the symptoms associated with neurodegenerative disorders such as Huntington's, Parkinson's, and Alzheimer's diseases 10. It is therefore essential that the proteins involved in maintenance of proteostasis be identified in order to develop treatments for these debilitating diseases. This article describes techniques for monitoring in vivo protein folding at near-real time resolution using the model protein firefly luciferase fused to green fluorescent protein (FFL-GFP). FFL-GFP is a unique model chimeric protein as the FFL moiety is extremely sensitive to stress-induced misfolding and aggregation, which inactivates the enzyme 12. Luciferase activity is monitored using an enzymatic assay, and the GFP moiety provides a method of visualizing soluble or aggregated FFL using automated microscopy. These coupled methods incorporate two parallel and technically independent approaches to analyze both refolding and functional reactivation of an enzyme after stress. Activity recovery can be directly correlated with kinetics of disaggregation and re-solubilization to better understand how protein quality control factors such as protein chaperones collaborate to perform these functions. In addition, gene deletions or mutations can be used to test contributions of specific proteins or protein subunits to this process. In this article we examine the contributions of the protein disaggregase Hsp104 13, known to partner with the Hsp40/70/nucleotide exchange factor (NEF) refolding system 5, to protein refolding to validate this approach.

Coupled Assays for Monitoring Protein Refolding in Saccharomyces cerevisiae

This article describes the use of a firefly luciferase-GFP fusion protein to investigate in vivo protein folding in Saccharomyces cerevisiae. Using this reagent, refolding of a model heat-denatured protein can be monitored simultaneously by fluorescence microscopy and an enzymatic assay to probe the roles of proteostasis network components in protein quality control.

Proteostasis, defined as the combined processes of protein folding/biogenesis, refolding/repair, and degradation, is a delicate cellular balance that must ...

Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein Expressed in Saccharomyces cerevisiae

Defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein cause cystic fibrosis (CF), an autosomal recessive disease that currently limits the average life expectancy of sufferers to &#60;40 years of age. The development of novel drug molecules to restore the activity of CFTR is an important goal in the treatment CF, and the isolation of functionally active CFTR is a useful step towards achieving this goal.
We describe two methods for the purification of CFTR from a eukaryotic heterologous expression system, S. cerevisiae. Like prokaryotic systems, S. cerevisiae can be rapidly grown in the lab at low cost, but can also traffic and posttranslationally modify large membrane proteins. The selection of detergents for solubilization and purification is a critical step in the purification of any membrane protein. Having screened for the solubility of CFTR in several detergents, we have chosen two contrasting detergents for use in the purification that allow the final CFTR preparation to be tailored to the subsequently planned experiments.
In this method, we provide comparison of the purification of CFTR in dodecyl-&#946;-D-maltoside (DDM) and 1-tetradecanoyl-sn-glycero-3-phospho-(1&#39;-rac-glycerol) (LPG-14). Protein purified in DDM by this method shows ATPase activity in functional assays. Protein purified in LPG-14 shows high purity and yield, can be employed to study post-translational modifications, and can be used for structural methods such as small-angle X-ray scattering and electron microscopy. However it displays significantly lower ATPase activity.

Purification of the Cystic Fibrosis Transmembrane Conductance Regulator Protein Expressed in Saccharomyces cerevisiae

Heterologous expression and purification of the cystic fibrosis transmembrane conductance regulator (CFTR) are significant challenges and limiting factors in the development of drug therapies for cystic fibrosis. This protocol describes two methods for the isolation of milligram quantities of CFTR suitable for functional and structural studies.&#160;

Defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein cause cystic fibrosis (CF), an autosomal recessive disease that ...

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

mRNA steady state levels vary depending on environmental conditions. Regulation of the steady state accumulation levels of an mRNA ensures that the correct amount of protein is synthesized for the cell&#8217;s specific growth conditions. One approach for measuring mRNA decay rates is inhibiting transcription and subsequently monitoring the disappearance of the already present mRNA. The rate of mRNA decay can then be quantified, and an accurate half-life can be determined utilizing several techniques. In S. cerevisiae, protocols that measure mRNA half-lives have been developed and include inhibiting transcription of mRNA using strains that harbor a temperature sensitive allele of RNA polymerase II, rpb1-1. Other techniques for measuring mRNA half-lives include inhibiting transcription with transcriptional inhibitors such as thiolutin or 1,10-phenanthroline, or alternatively, by utilizing mRNAs that are under the control of a regulatable promoter such as the galactose inducible promoter and the TET-off system. Here, we describe measurement of S. cerevisiae mRNA decay rates using the temperature sensitive allele of RNA polymerase II. This technique can be used to measure mRNA decay rates of individual mRNAs or genome-wide.

Measurement of mRNA Decay Rates in Saccharomyces cerevisiae Using rpb1-1 Strains

The steady state level of specific mRNAs is determined by the rate of synthesis and decay of the mRNA. Genome-wide mRNA degradation rates or the decay rates of specific mRNAs can be measured by determining mRNA half-lives. This protocol focuses on measurement of mRNA decay rates in Saccharomyces cerevisiae.

mRNA steady state levels vary depending on environmental conditions. Regulation of the steady state accumulation levels of an mRNA ensures that the ...

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described.

Rapid Identification of Chemical Genetic Interactions in Saccharomyces cerevisiae

Here we present a cost-effective method for defining chemical-genetic interactions in budding yeast. The approach is built on fundamental techniques in yeast molecular biology and is well suited for the mechanistic interrogation of small to medium collections of chemicals and other media environments.

Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. ...

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

Directed evolution in Saccharomyces cerevisiae offers many attractive advantages when designing enzymes for biotechnological applications, a process that involves the construction, cloning and expression of mutant libraries, coupled to high frequency homologous DNA recombination in vivo. Here, we present a protocol to create and screen mutant libraries in yeast based on the example of a fungal aryl-alcohol oxidase (AAO) to enhance its total activity. Two protein segments were subjected to focused-directed evolution by random mutagenesis and in vivo DNA recombination. Overhangs of ~50 bp flanking each segment allowed the correct reassembly of the AAO-fusion gene in a linearized vector giving rise to a full autonomously replicating plasmid. Mutant libraries enriched with functional AAO variants were screened in S. cerevisiae supernatants with a sensitive high-throughput assay based on the Fenton reaction. The general process of library construction in S. cerevisiae described here can be readily applied to evolve many other eukaryotic genes, avoiding extra PCR reactions, in vitro DNA recombination and ligation steps.

Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening

We present a detailed protocol to construct and screen mutant libraries for directed evolution campaigns in Saccharomyces cerevisiae.

Directed evolution in Saccharomyces cerevisiae offers many attractive advantages when designing enzymes for biotechnological applications, a process that ...