Name: calibration-free in vitro quantification of protein homo-oligomerization using commercial instrumentation and free, open source brightness analysis software
Uploaded: 2018-07-17T15:30:00
Description: Watch this Scientific Journal Video about Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software a

This work has been supported by Wellcome Trust grant 105278/Z/14/2 to R.N. The Wellcome Trust Centre for Human Genetics is funded by Wellcome Trust Core Award 203852/Z/16/2. Work in the C.S. group is supported by Cancer Research UK (C20724/A14414), and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant 647278.

1. FKBP12 F36V -mVenus Purification
<ol>
	<li>Transform (DE3) pLysS cells with pET22b vector containing monomerized human FKBP12F36V12 and N-terminal His6 and mVenus tags (vector available on request). Plate cells onto LB agar supplemented with 50 &#181;g/mL Ampicillin and 34 &#181;g/mL Chloramphenicol.</li>
	<li>Transfer transformed colonies into 100 mL LB starter culture and grow for 16 - 20 hours at 37 &#176;C with shaking.</li>
	<li>Dilute dense starter culture (OD600 &#62;1) 1:100 in LB med...

<ol>
	<li>Voith von Voithenberg, L., Lamb, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+pair+forster+resonance+energy+transfer:+A+versatile+tool+to+investigate+protein+conformational+dynamics.">Single pair forster resonance energy transfer: A versatile tool to investigate protein conformational dynamics.</a> BioEssays. 40, (2018).</li><li>Padilla-Parra, S., Auduge, N., Coppey-Moisan, M., Tramier, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+FRET+analysis+by+fast+acquisition+time+domain+FLIM+at+high+spatial+resolution+in+living+cells.">Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells.</a> Biophysical Journal. 95, 2976-2988 (2008).</li><li>Padilla-Parra, S., Auduge, N., Coppey-Moisan, M., Tramier, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dual-color+fluorescence+lifetime+correlation+spectroscopy+to+quantify+protein-protein+interactions+in+live+cell.">Dual-color fluorescence lifetime correlation spectroscopy to quantify protein-protein interactions in live cell.</a> Microscopy Research and Technique. 74, 788-793 (2011).</li><li>Muller, J. D., Chen, Y., Gratton, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+correlation+spectroscopy.">Fluorescence correlation spectroscopy.</a> Methods in Enzymology. 361, 69-92 (2003).</li><li>Tramier, M., Coppey-Moisan, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+anisotropy+imaging+microscopy+for+homo-FRET+in+living+cells.">Fluorescence anisotropy imaging microscopy for homo-FRET in living cells.</a> Methods in Cell Biology. 85, 395-414 (2008).</li><li>Digman, M. A., Dalal, R., Horwitz, A. F., Gratton, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+the+number+of+molecules+and+brightness+in+the+laser+scanning+microscope.">Mapping the number of molecules and brightness in the laser scanning microscope.</a> Biophysical Journal. 94, 2320-2332 (2008).</li><li>Nolan, R., Iliopoulou, M., Alvarez, L., Padilla-Parra, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detecting+protein+aggregation+and+interaction+in+live+cells:+A+guide+to+number+and+brightness.">Detecting protein aggregation and interaction in live cells: A guide to number and brightness.</a> Methods. , (2017).</li><li>Dalal, R. B., Digman, M. A., Horwitz, A. F., Vetri, V., Gratton, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+particle+number+and+brightness+using+a+laser+scanning+confocal+microscope+operating+in+the+analog+mode.">Determination of particle number and brightness using a laser scanning confocal microscope operating in the analog mode.</a> Microscopy Research and Technique. 71, 69-81 (2008).</li><li>Nolan, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=nandb-number+and+brightness+in+R+with+a+novel+automatic+detrending+algorithm.">nandb-number and brightness in R with a novel automatic detrending algorithm.</a> Bioinformatics. , (2017).</li><li>Hur, K. H., 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=Quantitative+Measurement+of+Brightness+from+Living+Cells+in+the+Presence+of+Photodepletion.">Quantitative Measurement of Brightness from Living Cells in the Presence of Photodepletion.</a> PLoS One. 9, (2014).</li><li>Amara, J. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+versatile+synthetic+dimerizer+for+the+regulation+of+protein-protein+interactions.">A versatile synthetic dimerizer for the regulation of protein-protein interactions.</a> Proceedings of the National Academy of Sciences of the United States of America. 94, 10618-10623 (1997).</li><li>Clackson, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Redesigning+an+FKBP-ligand+interface+to+generate+chemical+dimerizers+with+novel+specificity.">Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity.</a> Proceedings of the National Academy of Sciences of the United States of America. 95, 10437-10442 (1998).</li><li>Rollins, C. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+ligand-reversible+dimerization+system+for+controlling+protein-protein+interactions.">A ligand-reversible dimerization system for controlling protein-protein interactions.</a> Proceedings of the National Academy of Sciences of the United States of America. 97, 7096-7101 (2000).</li><li>Schindelin, J., Rueden, C. T., Hiner, M. C., Eliceiri, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ImageJ+ecosystem:+An+open+platform+for+biomedical+image+analysis.">The ImageJ ecosystem: An open platform for biomedical image analysis.</a> Molecular Reproduction and Development. 82, 518-529 (2015).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=R:+A+Language+and+Environment+for+Statistical+Computing.">R: A Language and Environment for Statistical Computing.</a> R Core. , (2017).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RStudio:+Integrated+Development+Environment+for+R.">RStudio: Integrated Development Environment for R.</a> R Team. , (2016).</li><li>. nandb R package Available from: <a target="_blank" href="https://CRAN.R-project.org/package=nandb">https://CRAN.R-project.org/package=nandb</a> (2017)</li><li>Jung, G., Wiehler, J., Zumbusch, 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+photophysics+of+green+fluorescent+protein:+influence+of+the+key+amino+acids+at+positions+65,+203,+and+222.">The photophysics of green fluorescent protein: influence of the key amino acids at positions 65, 203, and 222.</a> Biophysical Journal. 88, 1932-1947 (2005).</li><li>Shaner, N. 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N&#38;B is a technique to detect multimerization using commercial light scanning confocal microscopes equipped with digital detectors. This approach is quite attractive compared to single point FCS, FCCS, and smFRET because it is calibration free and the brightness calculation is straightforward and concentration independent6. It is of major importance, however, to correct for bleaching and long-term intensity fluctuations before performing brightness calculations9; a sligh...

Protein-protein Interactions In Vitro
Traditionally, crystallography and nuclear magnetic resonance experiments combined with cryo-electron microscopy (cryoEM) are the technologies chosen to accurately describe the three-dimensional architecture of proteins and to infer their function by scrutinizing their high resolution structural details. Proteins, however, are not static structures and can undergo a variety of conformational changes and vibrations in time and space. This is why structural information from crystallographic or CryoEM data needs to be complemented with other techniques (e.g., molecular dynamics simulations and single molecule techniques): the function of a protein is related to its conformational changes and interactions, and this information is not present in a static structure. In order to probe for intra-molecular dynamics, techniques based on single molecule Forster Resonance Energy Transfer (smFRET) are very effective1. These approaches are able to assess different subpopulations of molecules in complex media. This is very important, as these changes are rapid and occur during the acquisition of the data (i.e.,&#160;nanosecond to second range).
Two main approaches are commonly employed to detect and quantify these changes: proteins in solution and surface-immobilization. For the detection of inter-molecular interactions and in particular, the process of dimerization induced by ligands, smFRET is not always the best tool. Indeed, FRET depends not only on the distance (&#8776;10 nm) but also on the orientation of the two dipoles (donor and acceptor, &#967;2) and the overlap of the donor emission with the acceptor&#39;s absorption spectra2, but perhaps this last condition is less important provided that the experimentalist can chose the right FRET couple. A particular disadvantage of smFRET for probing homo-dimerization comes from the labeling of the protein of interest: for hetero smFRET, dimerization can only be detected up to 50% (i.e.,&#160;hetero-FRET will only be able to detect donor-acceptor and acceptor-donor homo-dimers but not donor-donor or acceptor-acceptor, which is the other 50% of the dimers). The use of fluorescence correlation spectroscopy (FCS) and derivatives (FCCS, etc.3) to ascertain protein diffusion constants and binding constants in vitro is another alternative. These approaches are not able to fully quantify homo-dimerization either, as in FCS one measures concentration and diffusion, and the radius and diffusion coefficient of a diffusing particle are very poorly dependent on the molecular weight; for example a 10-fold increase in the molecular weight will only imply a 2.15 fold change in the diffusion coefficient4. In the case of two-color FCS or FCCS, only 50% of homo-dimers will be seen for the same reason as above. The most practical and quantitative approaches to detect homo-dimerization in vitro and in vivo are homo-FRET5 and number and brightness (N&#38;B)6. Given the fact that homo-FRET requires specific instrumentation recovery of the anisotropy value (i.e.,&#160;optical elements/analyzers to recover the parallel and perpendicular polarization), N&#38;B is presented here as a favorable technique to detect protein homo-dimerization and aggregation. It can be employed both in vitro and in vivo with a commercial set-up.
Number and Brightness
N&#38;B has been recently reviewed7. That review focused on the application of the technique in live cells. It is worthwhile to reproduce the mathematical formalism here as these equations will be applied to the data collected in vitro. First, it is necessary to define some terms and mathematical quantities:
<ul>
	<li>An entity is a set of molecules which are bound together.</li>
	<li>The brightness &#949; of an entity is the number of photons it emits per unit time (per frame).</li>
	<li>n is the number of entities present.</li>
	<li>For a given pixel over the course of an image series, &#60;I&#62; is its mean intensity and &#963;2 is the variance in its intensity.</li>
</ul>
Then, with photon-counting detectors and assuming mobile entities and no background,
<img alt="Equation 1" src="/files/ftp_upload/58157/58157eq1.jpg" /> 
<img alt="Equation 2" src="/files/ftp_upload/58157/58157eq2.jpg" />
where N is the apparent number and B is the apparent brightness. This results in
<img alt="Equation 3" src="/files/ftp_upload/58157/58157eq3.jpg" /> 
<img alt="Equation 4" src="/files/ftp_upload/58157/58157eq4.jpg" />
Dalal et al.8 showed that with analog equipment, one needs three correction terms: the S factor, the background offset, and the readout noise &#963;02. Then, again assuming mobile entities,
<img alt="Equation 5" src="/files/ftp_upload/58157/58157eq5.jpg" /> 
<img alt="Equation 6" src="/files/ftp_upload/58157/58157eq6.jpg" />
giving
<img alt="Equation 7" src="/files/ftp_upload/58157/58157eq7.jpg" /> 
<img alt="Equation 8" src="/files/ftp_upload/58157/58157eq8.jpg" />
Note that the above equation for is different that given in Dalal et al.8 and a subsequent review.7 In Dalal et al. the S in the denominator was omitted due to a typo and this error was reproduced in the review. The equation above is the correct one. Instructions for measuring S, offset and &#963;02&#160;- together with an explanation of their meaning - are given by Dalal et al.8
The brightness&#160;&#949; is proportional to the oligomeric state of the diffusing entities:&#160;&#949; will be twice as big for dimers as it is for monomers, three times as big for trimers as it is for monomers, twice as big for hexamers as it is for trimers and so on. In this way, measuring the brightness &#949;, one can quantify any type of multimerization.
If there are a mixture of oligomeric states present, number and brightness is not capable of recovering the individual oligomeric states present. This is a limitation of the technique.
Detrend algorithm and nandb software
The importance of correcting for photobleaching has been previously stressed9. Photobleaching inevitably occurs during light microscopy experiments in time-lapse mode; both in live cells and in vitro. Many approaches have been described in the literature to correct for bleaching7. The exponential filtering technique with automatic choice of detrending parameter T&#160;is the current best. It is integrated into the free, open source software nandb9. Indeed, software that requires the user to manually choose their detrending parameter can lead to incorrect results because this parameter choice will likely be arbitrary and incorrect. The automatic algorithm inspects the data and determines the appropriate parameter for it, without the need for user intervention9. Even with the best choice of smoothing parameter, detrending has its limitations and works well only with photobleaching percentages lower than 25%, as shown with simulations9. Interestingly, when using the automatic detrending routine, its accuracy is such that one can work with low brightness values (even B &#60;1.01), and hence low intensities, and still be precise enough to quantify homo-dimerization.
Photobleaching also causes another problem: the presence of photobleached fluorophores in a multimer complex. This makes e.g., a trimer appear like a dimer when one of the three units in the trimer is non-fluorescent. Hur and Mueller10 showed how to correct for this and this correction was also stressed in a subsequent review7. The nandb software includes this correction9.
The FKBP12F36V system
FKBP12F36V is a protein which does not naturally oligomerize but is known to dimerize upon the addition of the AP20187 drug (colloquially known as the BB dimerizing ligand)11,12. This makes it an ideal test case for number and brightness: with labelled FKBP12F36V, a doubling of oligomeric state should be observed upon addition of BB.

<table border="0" cellpadding="0" cellspacing="0" style="width:997px;" width="997">
	<tbody>
		<tr height="40">
			<td height="40" style="height:40px;width:331px;">RosettaTM (DE3) pLysS cells</td>
			<td style="width:123px;">Novagen</td>
			<td style="width:344px;">70956-3</td>
			<td style="width:200px;"></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Ampicillin</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:344px;">PubChem Substance ID 329824407</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Chloramphenicol</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td>PubChem Substance ID: 24892250</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">LB starter culture</td>
			<td style="width:123px;">QIAGEN</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">LB medium</td>
			<td style="width:123px;">QIAGEN</td>
			<td height="40" style="height:40px;width:344px;&quot;">https://www.sigmaaldrich.com/content/dam/sigma-aldrich/head/search/external-link-icon.gif</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">IPTG</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:344px;">PubChem Substance ID 329815691</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">IMAC buffer</td>
			<td>Medicago</td>
			<td>09-1010-10</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">EDTA-free protease inhibitors&#160;</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td>11873580001</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">TALON resin</td>
			<td>Clonetech</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Nickel sepharose</td>
			<td style="width:123px;">GE Healthcare</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">S200 16/60 column</td>
			<td style="width:123px;">GE Healthcare</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Glass bottom 8 well observation dish</td>
			<td>Ibidi</td>
			<td>80827</td>
			<td></td>
		</tr>
	</tbody>
</table>

calibration-free in vitro quantification of protein homo-oligomerization using commercial instrumentation and free, open source brightness analysis software

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

Detrending and monomeric brightness
Once the data has been acquired, one can start the brightness calculations to determine the oligomeric state of the protein of interest in the solution. Even if the effect of bleaching in solution may not be as drastic as it can be in vivo, the intensity trace will still probably not have stationary mean, possibly due to photophysical effects related to the fluorophor...

Watch this Scientific Journal Video about Calibration-free In Vitro Quantification of Protein Homo-oligomerization Using Commercial Instrumentation and Free, Open Source Brightness Analysis Software a

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

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

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

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

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