We gratefully acknowledge the technical support of Sini Miettinen, Minna P&#246;ll&#228;nen and Taru Rautavesi. We thank Helka Nurkkala for providing HEK 293 cells expressing twin-Strep-tagged GFP and Pekka Evij&#228;rvi for providing sound recording equipment. This work was funded by the Academy of Finland, grant numbers 138329, 134684 and 258978.

1. Cross-linking of Strep-Tactin Polymethacrylate Resin with Bis(sulfosuccinimidyl) Suberate (BS3)
<ol>
	<li>Equilibrate one sealed microtube containing 2 mg of BS3 cross-linker to room temperature. CAUTION: BS3 is a hazardous substance. Wear protective gloves and goggles.</li>
	<li>Resuspend Strep-Tactin polymethacrylate resin (50% suspension in 100 mM Tris-HCl, pH 8.0; 1 mM EDTA; 150 mM NaCl) by brief vigorous shaking and immediately transfer 600 &#181;l of the suspension to a spin column using a pipette tip with the end cut off.</li>
	<li>Centrifuge at 1,500 x g for 30 sec at room temperature. Discard the flow-through and add 450 &#181;l of phosphate buffered saline (PBS) to the column.</li>
	<li>Repeat the previous step 2 more times to completely replace Tris buffer with PBS and leave the resin in 430 &#181;l of PBS adjusted to pH 8.0 after the last centrifugation.</li>
	<li>Puncture the foil of the microtube with BS3 with a pipette tip containing 100 &#181;l of ultrapure water. Dissolve the BS3 powder in water by gently pipetting up and down and immediately add 20 &#181;l of the solution to the spin column. The final concentration of BS3 in the cross-linking reaction is ~1.2 mM.</li>
	<li>Rotate the column for 30 min at room temperature. Check that the resin is mixed properly with the BS3 solution.</li>
	<li>To quench the reaction, add 6 &#181;l of 3M Tris-HCl, pH 7.5 and rotate the column for another 15 min at room temperature.</li>
	<li>Centrifuge at 1,500 x g for 30 sec at room temperature. Discard the flow-through and resuspend the cross-linked resin in 450 &#181;l of Tris buffered saline with Tween 20 (TBST). Repeat the centrifugation and wash steps two more times. At the last step, resuspend the resin in 450 &#181;l of TBS.</li>
	<li>Transfer the resin suspension to a fresh tube using a pipette tip with the end cut off. Resuspend the resin left in the column with another 450 &#181;l of TBS and transfer to the same tube. Repeat the last step once more to ensure maximum transfer of the resin from the column to the tube.</li>
	<li>Let the tube stand for 10 min at room temperature and adjust the volume to 600 &#181;l by removing excess TBS. The resin is ready for immediate use (recommended) or can be stored at 4&#160;&#176;C, without freezing.</li>
</ol>
2. Binding of the Twin-Strep-tagged Bait Protein and Associated Complexes to the Cross-linked Strep-Tactin Polymethacrylate Resin
<ol>
	<li>Centrifuge 1 ml of the bait protein sample in binding buffer at 17,000 x g for 10 min at 4&#160;&#176;C and transfer the supernatant to a fresh tube.</li>
	<li>To minimize binding of endogenous biotinylated proteins to the Strep-Tactin resin, add avidin to a final concentration of 100 &#181;g/ml and rotate for 15 min at 4&#160;&#176;C.
	<ol>
		<li>If the cross-linked resin from step 1.10 has been stored for an extended period of time at 4&#160;&#176;C, collect the resin by centrifugation at 400 x g for 1 min at 4&#160;&#176;C, discard the supernatant and wash the resin with 1 ml of TBST. Repeat the centrifugation and wash steps two more times, first with TBST and then with TBS. Centrifuge the tube at 400 x g for 1 min at 4&#160;&#176;C and adjust to the original volume by removing excess TBS.</li>
	</ol>
	</li>
	<li>Resuspend the cross-linked Strep-Tactin resin by vortexing. Immediately add 50 &#181;l of the resin suspension to the tube containing the bait protein sample using a cut pipette tip and rotate for another 30 min at 4&#160;&#176;C.</li>
	<li>While waiting, set thermomixer to 55&#160;&#176;C and preheat 500 &#181;l of elution buffer for use in step 3.1.</li>
	<li>Centrifuge at 400 x g for 1 min at 4&#160;&#176;C. Discard the supernatant and wash the resin on a rotator for 5 min at 4&#160;&#176;C with 1 ml of pre-chilled wash buffer #1. Repeat the centrifugation and wash steps three times. At the last step, resuspend the resin in 250 &#181;l of wash buffer #2.</li>
	<li>Transfer the resin suspension to a fresh spin column. Resuspend the resin remaining in the tube in another 250 &#181;l of wash buffer #2 and transfer to the same column.</li>
	<li>Centrifuge at 400 x g for 3 min at 4&#160;&#176;C, discard the flow-through and transfer the column to a fresh dolphin-nose 2 ml tube. Proceed immediately to the elution step below.</li>
</ol>
3. Elution of Specific Protein Complexes
<ol>
	<li>Add 150 &#181;l of preheated elution buffer from step 2.4 to the spin column.</li>
	<li>Incubate in thermomixer for 5 min at 55&#160;&#176;C, shaking at 1,400 rpm.</li>
	<li>Centrifuge at 1,500 x g for 1 min at room temperature.</li>
	<li>Discard the column and store the purified target proteins at &#8804; -20&#160;&#176;C.</li>
</ol>
<table border="0" cellpadding="0" cellspacing="0" width="598">
	<tbody>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">Phosphate buffered saline (PBS)</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Na2HPO4</td>
			<td style="width:299px;">10 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">KH2PO4</td>
			<td style="width:299px;">2mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaCl</td>
			<td style="width:299px;">137 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">KCl</td>
			<td style="width:299px;">2.7 mM</td>
		</tr>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">pH adjusted to 7.4 unless stated otherwise (pH 8.0 in section 1.4)</td>
		</tr>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">Tris buffered saline (TBS)</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Tris-HCl, pH 7.4</td>
			<td style="width:299px;">50 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaCl</td>
			<td style="width:299px;">150 mM</td>
		</tr>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">Tris buffered saline with Tween 20 (TBST)</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Tris-HCl, pH 7.4</td>
			<td style="width:299px;">50 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaCl</td>
			<td style="width:299px;">150 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Tween 20</td>
			<td style="width:299px;">0.1% (v/v)</td>
		</tr>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">Binding buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Tris-HCl, pH 8.0</td>
			<td style="width:299px;">25 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaCl</td>
			<td style="width:299px;">550 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaF</td>
			<td style="width:299px;">5 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">EDTA</td>
			<td style="width:299px;">0.5 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Glycerol</td>
			<td style="width:299px;">10% (v/v)</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">PMSF</td>
			<td style="width:299px;">0.1 mM</td>
		</tr>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">Wash buffer #1</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Tris-HCl, pH 8.0</td>
			<td style="width:299px;">25 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaCl</td>
			<td style="width:299px;">500 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaF</td>
			<td style="width:299px;">5 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">EDTA</td>
			<td style="width:299px;">0.4 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Igepal CA-630</td>
			<td style="width:299px;">0.2% (v/v)</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Glycerol</td>
			<td style="width:299px;">5% (v/v)</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">PMSF</td>
			<td style="width:299px;">0.1 mM</td>
		</tr>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">Wash buffer #2</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Tris-HCl, pH 8.0</td>
			<td style="width:299px;">25 mM</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">NaCl</td>
			<td style="width:299px;">150 mM</td>
		</tr>
		<tr height="20">
			<td colspan="2" height="20" style="height:20px;width:597px;">Elution buffer</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:299px;">Tris-HCl, pH 8.0</td>
			<td style="width:299px;">25 mM</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:299px;">SDS</td>
			<td style="width:299px;">1% (w/v)</td>
		</tr>
	</tbody>
</table>
Table 1. Buffers used in the present study.

<ol>
	<li>Voss, S., Skerra, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutagenesis+of+a+flexible+loop+in+streptavidin+leads+to+higher+affinity+for+the+Strep-tag+II+peptide+and+improved+performance+in+recombinant+protein+purification.">Mutagenesis of a flexible loop in streptavidin leads to higher affinity for the Strep-tag II peptide and improved performance in recombinant protein purification.</a> Protein Eng. 10 (8), 975-982 (1997).</li><li>Schmidt, T. G., Skerra, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Strep-tag+system+for+one-step+purification+and+high-affinity+detection+or+capturing+of+proteins.">The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins.</a> Nat. Protoc. 2 (6), 1528-1535 (2007).</li><li>Junttila, M. R., Saarinen, S., Schmidt, T., Kast, J., Westermarck, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-step+Strep-tag+purification+for+the+isolation+and+identification+of+protein+complexes+from+mammalian+cells.">Single-step Strep-tag purification for the isolation and identification of protein complexes from mammalian cells.</a> Proteomics. 5 (5), 1199-1203 (2005).</li><li>Hafren, A., Hofius, D., Ronnholm, G., Sonnewald, U., Makinen, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HSP70+and+its+cochaperone+CPIP+promote+potyvirus+infection+in+Nicotiana+benthamiana+by+regulating+viral+coat+protein+functions.">HSP70 and its cochaperone CPIP promote potyvirus infection in Nicotiana benthamiana by regulating viral coat protein functions.</a> Plant Cell. 22 (2), 523-535 (2010).</li><li>Jaskiewicz, M., Peterhansel, C., Conrath, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+histone+modifications+in+plant+leaves.">Detection of histone modifications in plant leaves.</a> J. Vis. Exp. (55), (2011).</li><li>Witte, C. P., Noel, L. D., Gielbert, J., Parker, J. E., Romeis, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+one-step+protein+purification+from+plant+material+using+the+eight-amino+acid+StrepII+epitope.">Rapid one-step protein purification from plant material using the eight-amino acid StrepII epitope.</a> Plant Mol. Biol. 55 (1), 135-147 (2004).</li><li>Werner, A. K., Sparkes, I. A., Romeis, T., Witte, C. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification,+biochemical+characterization,+and+subcellular+localization+of+allantoate+amidohydrolases+from+Arabidopsis+and+soybean.">Identification, biochemical characterization, and subcellular localization of allantoate amidohydrolases from Arabidopsis and soybean.</a> Plant Physiol. 146 (2), 418-430 (2008).</li><li>Panwar, P., Deniaud, A., Pebay-Peyroula, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Contamination+from+an+affinity+column:+an+encounter+with+a+new+villain+in+the+world+of+membrane-protein+crystallization.">Contamination from an affinity column: an encounter with a new villain in the world of membrane-protein crystallization.</a> Acta Crystallogr. D. Biol. Crystallogr. 68 (10), 1272-1277 (2012).</li><li>Hendrickson, W. A., 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=Crystal+structure+of+core+streptavidin+determined+from+multiwavelength+anomalous+diffraction+of+synchrotron+radiation.">Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation.</a> Proc. Natl. Acad. Sci. U. S. A. 86 (7), 2190-2194 (1989).</li><li>Bernot, K. M., Lee, C. H., Coulombe, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+small+surface+hydrophobic+stripe+in+the+coiled-coil+domain+of+type+I+keratins+mediates+tetramer+stability.">A small surface hydrophobic stripe in the coiled-coil domain of type I keratins mediates tetramer stability.</a> J. 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No conflicts of interest declared.

The above protocol can be used to purify any twin-Strep-tagged bait protein of interest and its associated complexes in any suitable buffer that does not contain biotin or strong denaturants. In the current version of the protocol, binding and washing are performed under relatively stringent conditions in the presence of high salt and non-ionic detergent. Although this results in less background, fragile protein complexes may dissociate under these conditions. To preserve such lower affinity complexes, salt concentration...

In recent years, Strep-tag technology has become widely used in many areas of biomedical research, including proteomics and structural biology. This protein purification technology, which relies on the fusion of recombinant proteins to a short Strep-tag peptide, has matured with the advent of affinity matrices carrying Strep-Tactin, a genetically engineered variant of streptavidin with improved peptide-binding capacity.1,2 Fusion proteins containing two copies of Strep-tag II, designated twin-Strep-tag or SIII-tag, exhibit a higher affinity for Strep-Tactin matrices than those containing only a single Strep-tag, ensuring more efficient purification of the recombinant proteins and their associated binding partners. However, the higher affinity of twin-Strep-tagged proteins to Strep-Tactin also has its downside. Competitive elution of such proteins with excess biotin may be incomplete, leading to decreased target protein yield. A more efficient alternative is elution with SDS, but it leads to undesired sample contamination with Strep-Tactin released from the resin, making the assay incompatible with proteomic analysis. This paper presents a technique to overcome this limitation by first stabilizing the resin-coupled tetramer of Strep-Tactin by chemical cross-linking and then using SDS to elute twin-Strep-tagged proteins and their associated complexes from the resulting cross-linked resin. Thus, sufficient protein yield can be achieved without sample contamination with Strep-Tactin, thereby allowing further analysis by mass spectrometry.
The method is suitable for purification of any recombinant fusion protein with a surface-exposed SIII-tag3 or twin-Strep-tag (amino acid sequence WSHPQFEK(GGGS)3 WSHPQFEK and SAWSHPQFEK(GGGS)2 GGSAWSHPQFEK, respectively). The protein can be of animal, plant or bacterial origin and can be isolated from either total cell lysate or enriched organelle fraction. As an example, we describe here the purification of an SIII-tagged protein VPg-Pro of Potato Virus A (PVA)4 from the nuclear fraction of PVA-infected Nicotiana benthamiana plants. The nuclear fraction was isolated as previously described5, with the following modifications: cells were not treated with formaldehyde, sodium butyrate was substituted in all buffers with 5 mM sodium fluoride, complete protease inhibitor was substituted with PMSF, Triton X-100 concentration in extraction buffer #2 was lowered to 0.3% (v/v) and the nuclear pellet obtained by centrifugation through sucrose cushion (extraction buffer #3) was resuspended in 1.45 ml of pre-chilled binding buffer and rotated for 1.5 hours at 4&#160;&#176;C. The resulting nuclear extract containing the SIII-tagged bait protein and associated complexes (bait protein sample) was processed according to the protocol described below (see section 2).

<table border="0" cellpadding="0" cellspacing="0" width="606">
	<tbody>
		<tr>
			<td>Bis(sulfosuccinimidyl) suberate (BS3), No-Weigh format, 8 x 2mg</td>
			<td>Pierce/Thermo Scientific</td>
			<td>21585</td>
			<td><a href="http://www.fishersci.com">www.fishersci.com CAUTION: Hazardous substance. Causes serious respiratory, skin and eye irritation. Wear protective gloves and eye protection.</a></td>
		</tr>
		<tr>
			<td>Strep-Tactin MacroPrep resin (50% suspension)</td>
			<td>IBA</td>
			<td>2-1505</td>
			<td><a href="http://www.iba-lifesciences.com/">www.iba-lifesciences.com</a></td>
		</tr>
		<tr>
			<td>Spin-X centrifuge tube filter, cellulose acetate membrane, pore size 0.45 &#956;m, non-sterile</td>
			<td>Costar (Corning)</td>
			<td>8163</td>
			<td><a href="http://www.corning.com/lifesciences/">www.corning.com/lifesciences/</a></td>
		</tr>
		<tr>
			<td>Dolphin-nose tubes</td>
			<td>Costar (Corning)</td>
			<td>3213</td>
			<td><a href="http://www.corning.com/lifesciences/">www.corning.com/lifesciences/</a></td>
		</tr>
		<tr>
			<td>Avidin&#160;</td>
			<td>IBA</td>
			<td>2-0204</td>
			<td><a href="http://www.iba-lifesciences.com/">www.iba-lifesciences.com</a></td>
		</tr>
	</tbody>
</table>

one-step purification of twin-strep-tagged proteins and their complexes on strep-tactin resin cross-linked with bis(sulfosuccinimidyl) suberate (bs3)

Affinity purification of Strep-tagged fusion proteins on resins carrying an engineered streptavidin (Strep-Tactin) has become a widely used method for isolation of protein complexes under physiological conditions. Fusion proteins containing two copies of Strep-tag II, designated twin-Strep-tag or SIII-tag, have the advantage of higher affinity for Strep-Tactin compared to those containing only a single Strep-tag, thus allowing more efficient protein purification. However, this advantage is offset by the fact that elution of twin-Strep-tagged proteins with biotin may be incomplete, leading to low protein recovery. The recovery can be dramatically improved by using denaturing elution with sodium dodecyl sulfate (SDS), but this leads to sample contamination with Strep-Tactin released from the resin, making the assay incompatible with downstream proteomic analysis. To overcome this limitation, we have developed a method whereby resin-coupled tetramer of Strep-Tactin is first stabilized by covalent cross-linking with Bis(sulfosuccinimidyl) suberate (BS3) and the resulting cross-linked resin is then used to purify target protein complexes in a single batch purification step. Efficient elution with SDS ensures good protein recovery, while the absence of contaminating Strep-Tactin allows downstream protein analysis by mass spectrometry. As a proof of concept, we describe here a protocol for purification of SIII-tagged viral protein VPg-Pro from nuclei of virus-infected N. benthamiana plants using the Strep-Tactin polymethacrylate resin cross-linked with BS3. The same protocol can be used to purify any twin-Strep-tagged protein of interest and characterize its physiological binding partners.

The purification procedure is schematically illustrated in Figure 1, together with a representation of problems associated with other existing purification methods.
<img alt="Figure 1" fo:content-width="5.5in" src="/files/ftp_upload/51536/51536fig1highres.jpg" width="650" /> 
Figure 1. Schematic representation of the purification procedure. The workflow includes stabilization of the resin-coupled Strep-Tactin tetramer...

Watch this Scientific Journal Video about One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bissulfosuccinimidyl Suberate BS3 at JoVE.com

One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bissulfosuccinimidyl Suberate BS3

A method is described for efficient purification of twin-Strep-tagged fusion proteins and their specific complexes on modified streptavidin (Strep-Tactin) resin covalently cross-linked with Bis(sulfosuccinimidyl) suberate (BS3). The method has the advantages of fast speed, good target protein recovery and high purity, and is compatible with subsequent analysis by mass spectrometry.

One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bis(sulfosuccinimidyl) Suberate (BS3)

Affinity purification of Strep-tagged fusion proteins on resins carrying an engineered streptavidin (Strep-Tactin) has become a widely used method for ...

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JoVE Journal

Biology

18.6K Views.  University of Helsinki. A method is described for efficient purification of twin-Strep-tagged fusion proteins and their specific complexes on modified streptavidin (Strep-Tactin) resin covalently cross-linked with Bis(sulfosuccinimidyl) suberate (BS3). The method has the advantages of fast speed, good target protein recovery and high purity, and is compatible with subsequent analysis by mass spectrometry.

Video: One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bissulfosuccinimidyl Suberate BS3

Purification and Visualization of Influenza A Viral Ribonucleoprotein Complexes

The influenza A viral genome consists of eight negative-sense, single stranded RNA molecules, individually packed with multiple copies of the influenza A nucleoprotein (NP) into viral ribonulceoprotein particles (vRNPs). The influenza vRNPs are enclosed within the viral envelope. During cell entry, however, these vRNP complexes are released into the cytoplasm, where they gain access to the host nuclear transport machinery. In order to study the nuclear import of influenza vRNPs and the replication of the influenza genome, it is useful to work with isolated vRNPs so that other components of the virus do not interfere with these processes. Here, we describe a procedure to purify these vRNPs from the influenza A virus. The procedure starts with the disruption of the influenza A virion with detergents in order to release the vRNP complexes from the enveloped virion. The vRNPs are then separated from the other components of the influenza A virion on a 33-70% discontinuous glycerol gradient by velocity sedimentation. The fractions obtained from the glycerol gradient are then analyzed on via SDS-PAGE after staining with Coomassie blue. The peak fractions containing NP are then pooled together and concentrated by centrifugation. After concentration, the integrity of the vRNPs is verified by visualization of the vRNPs by transmission electron microscopy after negative staining. The glycerol gradient purification is a modification of that from Kemler et al. (1994)1, and the negative staining has been performed by Wu et al. (2007).2

The genome of the influenza A virus consists of eight separate complexes of RNA and proteins, termed viral ribonucleoprotein complexes (vRNPs). This paper describes the glycerol gradient purification and transmission electron microscopy visualization of influenza A vRNPs.

The influenza A viral genome consists of eight negative-sense, single stranded RNA molecules, individually packed with multiple copies of the influenza A ...

Identification of protein complexes with quantitative proteomics in S. cerevisiae

Lipids are the building blocks of cellular membranes that function as barriers and in compartmentalization of cellular processes, and recently, as important intracellular signalling molecules. However, unlike proteins, lipids are small hydrophobic molecules that traffic primarily by poorly described nonvesicular routes, which are hypothesized to occur at membrane contact sites (MCSs). MCSs are regions where the endoplasmic reticulum (ER) makes direct physical contact with a partnering organelle, e.g., plasma membrane (PM). The ER portion of ER-PM MCSs is enriched in lipid-synthesizing enzymes, suggesting that lipid synthesis is directed to these sites and implying that MCSs are important for lipid traffic. Yeast is an ideal model to study ER-PM MCSs because of their abundance, with over 1000 contacts per cell, and their conserved nature in all eukaryotes. Uncovering the proteins that constitute MCSs is critical to understanding how lipids traffic is accomplished in cells, and how they act as signaling molecules. We have found that an ER called Scs2p localize to ER-PM MCSs and is important for their formation. We are focused on uncovering the molecular partners of Scs2p. Identification of protein complexes traditionally relies on first resolving purified protein samples by gel electrophoresis, followed by in-gel digestion of protein bands and analysis of peptides by mass spectrometry. This often limits the study to a small subset of proteins. Also, protein complexes are exposed to denaturing or non-physiological conditions during the procedure. To circumvent these problems, we have implemented a large-scale quantitative proteomics technique to extract unbiased and quantified data. We use stable isotope labeling with amino acids in cell culture (SILAC) to incorporate staple isotope nuclei in proteins in an untagged control strain. Equal volumes of tagged culture and untagged, SILAC-labeled culture are mixed together and lysed by grinding in liquid nitrogen. We then carry out an affinity purification procedure to pull down protein complexes. Finally, we precipitate the protein sample, which is ready for analysis by high-performance liquid chromatography/ tandem mass spectrometry. Most importantly, proteins in the control strain are labeled by the heavy isotope and will produce a mass/ charge shift that can be quantified against the unlabeled proteins in the bait strain. Therefore, contaminants, or unspecific binding can be easily eliminated. By using this approach, we have identified several novel proteins that localize to ER-PM MCSs. Here we present a detailed description of our approach. 

Here we describe a new quantitative proteomics technique for identifying protein complexes in Saccharomyces cerevisiae. In this study, we have used the SILAC method together with affinity purification followed by tandem mass spectrometry to identify with high specificity the binding partners of an ER protein, Scs2p.

Lipids are the building blocks of cellular membranes that function as barriers and in compartmentalization of cellular processes, and recently, as ...

Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents (Methanol, Ethanol or 2-Propanol) and acetic acid are used for fixation, staining and destaining of proteins in a gel after SDS-PAGE. To speed up the procedure, heating the staining solution in the microwave oven for a short time is frequently used. This usually results in evaporation of toxic or hazardous Methanol, Ethanol or 2-Propanol and a strong smell of acetic acid in the lab which should be avoided due to safety considerations. In a protocol originally published in two patent applications by E.M. Wondrak (US2001046709 (A1), US6319720 (B1)), an alternative composition of the staining solution is described in which no organic solvent or acid is used. The CBB is dissolved in bidistilled water (60-80mg of CBB G-250 per liter) and 35 mM HCl is added as the only other compound in the staining solution. The CBB staning of the gel is done after SDS-PAGE and thorough washing of the gel in bidistilled water. By heating the gel during the washing and staining steps, the process can be finished faster and no toxic or hazardous compunds are evaporating. The staining of proteins occurs already within 1 minute after heating the gel in staining solution and is fully developed after 15-30 min with a slightly blue background that is destained completely by prolonged washing of the stained gel in bidistilled water, without affecting the stained protein bands.

A short protocol for protein staining with Coomassie Brilliant Blue (CBB) G-250 in polyacrylamide gels is described without using organic solvents or acetic acid as in the classical staining procedures with CBB.

In classical protein staining protocols using Coomassie Brilliant Blue (CBB), solutions with high contents of toxic and flammable organic solvents ...

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System 

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers. Genetic studies in mammalian systems have been limited due to the lack of readily available tools including defined mutant genetic cell lines, regulatory expression systems, and appropriate selectable markers. To circumvent these difficulties, model genetic systems in lower eukaryotes have become an attractive choice for the study of functionally conserved DNA repair proteins and pathways. We have developed a model yeast system to study the poorly defined genetic functions of the Werner syndrome helicase-nuclease (WRN) in nucleic acid metabolism. Cellular phenotypes associated with defined genetic mutant backgrounds can be investigated to clarify the cellular and molecular functions of WRN through its catalytic activities and protein interactions. The human WRN gene and associated variants, cloned into DNA plasmids for expression in yeast, can be placed under the control of a regulatory plasmid element. The expression construct can then be transformed into the appropriate yeast mutant background, and genetic function assayed by a variety of methodologies. Using this approach, we determined that WRN, like its related RecQ family members BLM and Sgs1, operates in a Top3-dependent pathway that is likely to be important for genomic stability. This is described in our recent publication [1] at <a href="http://www.impactaging.com">www.impactaging.com</a>. Detailed methods of specific assays for genetic complementation studies in yeast are provided in this paper.

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System

Genetic studies in yeast can be employed to investigate the molecular and cellular functions of human genes in cellular DNA metabolism. Methods are described for the genetic characterization of the human WRN gene product defective in the premature aging disorder Werner syndrome in functionally conserved pathways using yeast as a tractable model system.

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers.  Genetic studies in mammalian ...

One-step Metabolomics: Carbohydrates, Organic and Amino Acids Quantified in a Single Procedure

Every infant born in the US is now screened for up to 42 rare genetic disorders called "inborn errors of metabolism". The screening method is based on tandem mass spectrometry and quantifies acylcarnitines as a screen for organic acidemias and also measures amino acids. All states also perform enzymatic testing for carbohydrate disorders such as galactosemia. Because the results can be non-specific, follow-up testing of positive results is required using a more definitive method. The present report describes the "urease" method of sample preparation for inborn error screening. Crystalline urease enzyme is used to remove urea from body fluids which permits most other water-soluble metabolites to be dehydrated and derivatized for gas chromatography in a single procedure. Dehydration by evaporation in a nitrogen stream is facilitated by adding acetonitrile and methylene chloride. Then, trimethylsilylation takes place in the presence of a unique catalyst, triethylammonium trifluoroacetate. Automated injection and chromatography is followed by macro-driven custom quantification of 192 metabolites and semi-quantification of every major component using specialized libraries of mass spectra of TMS derivatized biological compounds. The analysis may be performed on the widely-used Chemstation platform using the macros and libraries available from the author. In our laboratory, over 16,000 patient samples have been analyzed using the method with a diagnostic yield of about 17%--that is, 17% of the samples results reveal findings that should be acted upon by the ordering physician. Included in these are over 180 confirmed inborn errors, of which about 38% could not have been diagnosed using previous methods.

The urease method of sample preparation for GC/MS analysis of intermediary metabolites is presented by its inventor. The method allows one-step follow-up of newborn screening for inborn errors by tandem mass spectrometry by quantifying carbohydrates, organic and amino acids all in a single process.

Every infant born in the US is now screened for up to 42 rare genetic disorders called "inborn errors of metabolism". The screening method is based on ...

Preparation, Purification, and Characterization of Lanthanide Complexes for Use as Contrast Agents for Magnetic Resonance Imaging

Polyaminopolycarboxylate-based ligands are commonly used to chelate lanthanide ions, and the resulting complexes are 
useful as contrast agents for magnetic resonance imaging (MRI). Many commercially available ligands are especially useful because they contain 
functional groups that allow for fast, high-purity, and high-yielding conjugation to macromolecules and biomolecules via amine-reactive 
activated esters and isothiocyanate groups or thiol-reactive maleimides. While metalation of these ligands is considered common 
knowledge in the field of bioconjugation chemistry, subtle differences in metalation procedures must be taken into account when 
selecting metal starting materials. Furthermore, multiple options for purification and characterization exist, and selection of the most 
effective procedure partially depends on the selection of starting materials. These subtle differences are often neglected in published 
protocols. Here, our goal is to demonstrate common methods for metalation, purification, and characterization of lanthanide complexes 
that can be used as contrast agents for MRI (Figure 1). We expect that this publication will enable biomedical scientists to incorporate 
lanthanide complexation reactions into their repertoire of commonly used reactions by easing the selection of starting materials and 
purification methods.

We demonstrate the metalation, purification, and characterization of lanthanide complexes. The complexes described here can be conjugated to macromolecules to enable tracking of these molecules using magnetic resonance imaging.

Polyaminopolycarboxylate-based ligands are commonly used to chelate lanthanide ions, and the resulting complexes are 
useful as contrast agents for ...

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems1, 2. Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria1-6. In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes1, 2, 7. Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast8, 9, and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system10. Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits).
Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking.

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Affinity purification of tagged proteins in combination with mass spectrometry (APMS) is a powerful method for the systematic mapping of protein interaction networks and for investigating the mechanistic basis of biological processes. Here, we describe an optimized sequential peptide affinity (SPA) APMS procedure developed for the bacterium Escherichia coli that can be used to isolate and characterize stable multi-protein complexes to near homogeneity even starting from low copy numbers per cell.

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the ...

Formulations for Freeze-drying of Bacteria and Their Influence on Cell Survival

Cellular water can be removed to reversibly inactivate microorganisms to facilitate storage. One such method of removal is freeze-drying, which is considered a gentle dehydration method. To facilitate cell survival during drying, the cells are often formulated beforehand. The formulation forms a matrix that embeds the cells and protects them from various harmful stresses imposed on the cells during freezing and drying. We present here a general method to evaluate the survival rate of cells after freeze-drying and we illustrate it by comparing the results obtained with four different formulations: the disaccharide sucrose, the sucrose derived polymer Ficoll PM400, and the respective polysaccharides hydroxyethyl cellulose (HEC) and hydroxypropyl methyl cellulose (HPMC), on two strains of bacteria, P. putida KT2440 and A. chlorophenolicus A6. In this work we illustrate how to prepare formulations for freeze-drying and how to investigate the mechanisms of cell survival after rehydration by characterizing the formulation using of differential scanning calorimetry (DSC), surface tension measurements, X-ray analysis, and electron microscopy and relating those data to survival rates. The polymers were chosen to get a monomeric structure of the respective polysaccharide resembling sucrose to a varying degrees. Using this method setup we showed that polymers can support cell survival as effectively as disaccharides if certain physical properties of the formulation are controlled1.

Freeze-drying is often an easy and convenient way to obtain dry products of viable bacterial cells. An issue of the process is cell survival. We detail here a procedure to investigate how cell survival during freeze-drying is influenced by the properties of the formulation used.

Cellular water can be removed to reversibly inactivate microorganisms to facilitate storage. One such method of removal is freeze-drying, which is ...

High-throughput Purification of Affinity-tagged Recombinant Proteins

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide- and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain- or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity.
In order to attribute the different phenotypes to the nature of the mutation - rather than to fluctuating experimental conditions - it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates1-5.
Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex6-8. TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase9-11. This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex4,5,12 . We exploited the high-throughput purification method to generate single, double and triple substitution and deletions mutations within the TFIIB linker and to subsequently analyse them in functional assays for their stimulation effect on the catalytic activity of RNA polymerase4. Altogether, we generated, purified and analysed 381 mutants - a task which would have been time-consuming and laborious to perform manually. We produced and assayed the proteins in multiplicates which allowed us to appreciate any experimental variations and gave us a clear idea of the reproducibility of our results.
This method serves as a generic protocol for the purification of His-tagged proteins and has been successfully used to purify other recombinant proteins. It is currently optimised for the purification of 24 proteins but can be adapted to purify up to 96 proteins.

We describe a method for the affinity-tagged purification of recombinant proteins using liquid-handling robotics. This method is generally applicable to the small-scale purification of soluble His-tagged proteins in a high-throughput format.

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further ...

Purification of Transcripts and Metabolites from Drosophila Heads

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. Although fruit flies provide obvious experimental advantages, research on neurodegenerative diseases has mostly relied on traditional techniques, including genetic interaction, histology, immunofluorescence, and protein biochemistry. These techniques are effective for mechanistic, hypothesis-driven studies, which lead to a detailed understanding of the role of single genes in well-defined biological problems. However, neurodegenerative diseases are highly complex and affect multiple cellular organelles and processes over time. The advent of new technologies and the omics age provides a unique opportunity to understand the global cellular perturbations underlying complex diseases. Flexible model organisms such as Drosophila are ideal for adapting these new technologies because of their strong annotation and high tractability. One challenge with these small animals, though, is the purification of enough informational molecules (DNA, mRNA, protein, metabolites) from highly relevant tissues such as fly brains. Other challenges consist of collecting large numbers of flies for experimental replicates (critical for statistical robustness) and developing consistent procedures for the purification of high-quality biological material. Here, we describe the procedures for collecting thousands of fly heads and the extraction of transcripts and metabolites to understand how global changes in gene expression and metabolism contribute to neurodegenerative diseases. These procedures are easily scalable and can be applied to the study of proteomic and epigenomic contributions to disease.

Purification of Transcripts and Metabolites from Drosophila Heads

We describe here the procedures for the extraction and purification of mRNA and metabolites from Drosophila heads. We are applying these techniques to better understand the cellular perturbations underlying neuronal degeneration. These methodologies can be easily scaled and adapted for other "omic" projects.

For the last decade, we have tried to understand the molecular and cellular mechanisms of neuronal degeneration using Drosophila as a model organism. ...