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 ...

This method can help answer key questions in the drug screening field, such elucidating the effect of small-molecule inhibitors on very low concentrations for protein-protein interactions. The main advantage of this technique is that it is calibration-free, it can be implemented in any confocal microscope, and utilizes very small amounts of labeled proteins. The implications of this technique extend towards development of cancer drugs, small-molecule inhibitors, and various fusion inhibitors because it provides quantitative information on protein-protein interactions.Though this method can provide insight into protein interactions and aggregations in vitro, it can also be applied to other systems, such as live cell protein dynamics and cell-cell interactions. To begin, transform pLysS cells with a pET-22b vector containing monomerized human FKBP12 and N-terminal His6 and mVenus tags. After the cells have recovered from being incubated and heat-shocked, plate them onto LB agar supplemented with antibiotics.Transfer the transformed colonies into a 100-milliliter LB starter culture, and grow for 16 to 20 hours at 37 degrees Celsius with shaking. Following incubation, dilute the dense starter culture one to 100 in LB medium in two 500-milliliter batches. Then, grow for two to three hours to an optical density at 600 nanometers of 0.6 to 0.8.After cooling the cultures on ice, induce protein production with 250-micromolar IPTG. Grow the cultures for 16 to 20 hours at 21 degrees Celsius and 200 rpm. Then, harvest cells by centrifugation at 2, 000 g for 20 minutes.Remove the supernatant, and resuspend the pellet in 40 milliliters of IMAC buffer A supplemented with EDTA-free protease inhibitors. Now, sonicate the cells at 500 watts, 20 kilohertz, and 40%amplitude at nine seconds on, 11 seconds off for 15 minutes on ice. Following sonication, harvest the soluble material by centrifugation at 20, 000 g for an hour at four degrees Celsius.Transfer soluble lysate to a conical flask, and add two milliliters of TALON resin. Allow the suspension to incubate for one hour with 105 rpm rotation. Now, harvest the resin, and wash it with 250 milliliters of IMAC buffer A followed by 500 milliliters of IMAC buffer B.Elute His6-tagged protein using IMAC buffer C.Inject the eluate onto a pre-equilibrated size-exclusion column, and collect the FKBP12 peak, which elutes at approximately 87.7 milliliters.Assess the purity of the protein via SDS-PAGE, and pool and concentrate as required. To set up the multiwell plate array, first prepare a solution of 100-nanomolar purified FKBP12 in the same buffer used for size-exclusion chromatography. Sonicate and centrifuge with a quick spin of 13, 000 rpm to prevent the formation of aggregates.Now, pipette 100 to 200 microliters of the diluted protein into an eight-well observation chamber with a glass bottom. Add the BB dimerizer to final concentrations of 10, 20, 40, 80, 100, 150, 300, and 500 nanomolar. As a reference, prepare a solution of 100-nanomolar mVenus alone to evaluate potential aggregation and precipitation effects and to recover a brightness value for the monomer with the same acquisition settings.Any light scanning microscope confocal system equipped with digital detectors or well-characterized analog detectors and capable of keeping a constant dwell time for every pixel acquired can be used. Select the collar correction water immersion objective designed for fluorescence correlation spectroscopy. Now, add a drop of water to the collar correction water immersion objective.Mount the eight-well observation chamber into the stage. Set the excitation beam path by turning on the 514-nanometer laser and setting it at 20 to 100 nanowatts power at the exit of the objective. Turn on one HyD detector.Detectors capable of photon-counting are preferable. Select the emission window from 520 to 560 nanometers. For the acquisition mode, use 16 by 16 pixels.Set the pixel dwell time such that the frame time is longer than the protein diffusion and the pixel dwell time is much shorter. This corresponded to setting the dwell time to approximately 13 microseconds for the system used in this demonstration. Set the pinhole at one Airy unit for the corresponding emission of approximately 545 nanometers.Select the xy time acquisition mode, and select the number of frames to be acquired per acquisition and well. Now, set the pixel size at approximately 120 nanometers. If the system is equipped with high-throughput mode, introduce the coordinates of each well and the number of acquisitions per well to automate the process.If the system is equipped with a perfusion system, load the BB solution and program the perfusion to start right after the 5, 000th frame to evaluate the kinetics of dimerization while acquiring 10, 000 images. Select the correct well, and focus on the solution. Then, start the acquisition, and save the resulting stack of images in TIFF format.Sequences of 20, 000 images of purified FKBP12 mVenus in 100-nanometer solution were acquired as specified in the protocol section. The intensity of the first frame is shown together with the mean intensity profile of the detrended image. The brightness without and with smooth filtering is also shown.After 10, 000 frames were acquired, the homodimerizer drug BB was added to the solution while acquiring. Each consecutive series of 5, 000 frames was analyzed. The mean brightness five minutes after BB addition was 1.010, which is a twofold increase, indicating an FKBP12 dimer.The kinetics of the process shows a delay between BB addition and full FKBP12 dimerization of approximately two minutes. A key aspect to evaluate protein-protein interactions in vitro is the production and purification of your labeled protein. Be sure you have small amounts of the labeled protein of interest and that your protein is not aggregating per your analysis.Following this procedure, other methods like surface plasmon resonance or fluorescence correlation spectroscopy can be performed in order to answer additional questions, like dissociation constants or diffusion coefficients. After its development, this technique paved the way for researchers in the field of biophysics to explore in detail protein-protein interactions in live cells. Don't forget that working with reagents for protein purification can be extremely hazardous, and precautions, such as safety glasses, gloves, should always be taken while performing this procedure.

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Biochemistry

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

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

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

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

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

Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092

Development of new antimicrobials and vaccines for Streptococcus pneumoniae (pneumococcus) are necessary to halt the rapid rise in multiple resistant strains. Carbohydrate substrate binding proteins (SBPs) represent viable targets for the development of protein-based vaccines and new antimicrobials because of their extracellular localization and the centrality of carbohydrate import for pneumococcal metabolism, respectively. Described here is a rationalized integrated protocol to carry out a comprehensive characterization of SP0092, which can be extended to other carbohydrate SBPs from the pneumococcus and other bacteria. This procedure can aid the structure-based design of inhibitors for this class of proteins. Presented in the first part of this manuscript are protocols for biochemical analysis by thermal shift assay, multi angle light scattering (MALS), and size exclusion chromatography (SEC), which optimize the stability and homogeneity of the sample directed to crystallization trials and so enhance the probability of success. The second part of this procedure describes the characterization of the SBP crystals using a tunable wavelength anomalous diffraction synchrotron beamline, and data collection protocols for measuring data that can be used to resolve the crystallized protein structure.

A streamlined protocol for performing an extensive biochemical and structural characterization of a carbohydrate substrate binding protein from Streptococcus pneumoniae is presented.

Development of new antimicrobials and vaccines for Streptococcus pneumoniae (pneumococcus) are necessary to halt the rapid rise in multiple resistant ...

Quantification of Hypopigmentation Activity In Vitro

This study presents laboratory methods for the quantification of hypopigmentation activity in vitro. Melanin, the major pigment in melanocytes, is synthesized in response to multiple cellular and environmental factors. Melanin protects skin cells from ultraviolet damage, but also has biophysical and biochemical functions. Excessive production or accumulation of melanin in melanocytes can cause dermatological problems, such as freckles, dark spots, melasma, and moles. Therefore, the control of melanogenesis with hypopigmentation agents is important in individuals with clinical or cosmetic needs. Melanin is primarily synthesized in the melanosomes of melanocytes in a complex biochemical process called melanogenesis, which is influenced by extrinsic and intrinsic factors, such as hormones, inflammation, age, and ultraviolet light exposure. We describe three methods to determine the hypopigmentation activity of chemicals or natural substances in melanocytes: measurement of the 1) cellular tyrosinase activity and 2) melanin content, and 3) staining and quantifying cellular melanin with image analysis.
In melanogenesis, tyrosinase catalyzes the rate-limiting step that converts L-tyrosine into 3,4-dihydroxyphenylalanine (L-DOPA) and then into dopaquinone. Therefore, the inhibition of tyrosinase is a primary hypopigmentation mechanism. In cultured melanocytes, tyrosinase activity can be quantified by adding L-DOPA as a substrate and measuring dopaquinone production by spectrophotometry. Melanogenesis can also be measured by quantifying the melanin content. The melanin-containing cellular fraction is extracted with NaOH and melanin is quantified spectrophotometrically. Finally, the melanin content can be quantified by image analysis following Fontana-Masson staining of melanin. Although the results of these in vitro assays may not always be reproduced in human skin, these methods are widely used in melanogenesis research, especially as the initial step to identify potential hypopigmentation activity. These methods can also be used to assess melanocyte activity, growth, and differentiation. Consistent results with the three different methods ensure the validity of the effects.

We describe three experimental methods for evaluating the hypopigmentation activity of chemicals in vitro: quantification of 1) cellular tyrosinase activity and 2) melanin content, and 3) measurement of melanin by cellular melanin staining and image analysis.

This study presents laboratory methods for the quantification of hypopigmentation activity in vitro. Melanin, the major pigment in melanocytes, is ...

Analysis of Protein Folding, Transport, and Degradation in Living Cells by Radioactive Pulse Chase

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and the degradation of target proteins in live cells. By using short (pulse) radiolabeling times (&lt;30 min) and tightly controlled chase times, it is possible to label only a small fraction of the total protein pool and follow its folding. When combined with nonreducing/reducing SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoprecipitation with (conformation-specific) antibodies, folding processes can be examined in great detail. This system has been used to analyze the folding of proteins with a huge variation in properties such as soluble proteins, single and multi-pass transmembrane proteins, heavily N- and O-glycosylated proteins, and proteins with and without extensive disulfide bonding. Pulse-chase methods are the basis of kinetic studies into a range of additional features, including co- and posttranslational modifications, oligomerization, and polymerization, essentially allowing the analysis of a protein from birth to death. Pulse-chase studies on protein folding are complementary with other biochemical and biophysical methods for studying proteins in vitro by providing increased temporal resolution and physiological information. The methods as described within this paper are adapted easily to study the folding of almost any protein that can be expressed in mammalian or insect-cell systems.

Here we describe a protocol for a general pulse-chase method that allows the kinetic analysis of folding, transport, and degradation of proteins to be followed in live cells.

Radioactive pulse-chase labeling is a powerful tool for studying the conformational maturation, the transport to their functional cellular location, and ...

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, we developed IDBac&#8212;a low-cost and high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bioinformatics pipeline. IDBac software is designed for non-experts, is freely available, and capable of analyzing a few to thousands of bacterial colonies. Here, we present procedures for the preparation of bacterial colonies for MALDI-TOF MS analysis, MS instrument operation, and data processing and visualization in IDBac. In particular, we instruct users how to cluster bacteria into dendrograms based on protein MS fingerprints and interactively create Metabolite Association Networks (MANs) from specialized metabolite data.

IDBac is an open-source mass spectrometry-based bioinformatics pipeline that integrates data from both intact protein and specialized metabolite spectra, collected on cell material scraped from bacterial colonies. The pipeline allows researchers to rapidly organize hundreds to thousands of bacterial colonies into putative taxonomic groups, and further differentiate them based on specialized metabolite production.

In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, ...

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Dynamic protein-protein interactions control cellular behavior, from motility to DNA replication to signal transduction. However, monitoring dynamic interactions among multiple proteins in a protein interaction network is technically difficult. Here, we present a protocol for Quantitative Multiplex Immunoprecipitation (QMI), which allows quantitative assessment of fold changes in protein interactions based on relative fluorescence measurements of Proteins in Shared Complexes detected by Exposed Surface epitopes (PiSCES). In QMI, protein complexes from cell lysates are immunoprecipitated onto microspheres, and then probed with a labeled antibody for a different protein in order to quantify the abundance of PiSCES. Immunoprecipitation antibodies are conjugated to different MagBead spectral regions, which allows a flow cytometer to differentiate multiple parallel immunoprecipitations and simultaneously quantify the amount of probe antibody associated with each. QMI does not require genetic tagging and can be performed using minimal biomaterial compared to other immunoprecipitation methods. QMI can be adapted for any defined group of interacting proteins, and has thus far been used to characterize signaling networks in T cells and neuronal glutamate synapses. Results have led to new hypothesis generation with potential diagnostic and therapeutic applications. This protocol includes instructions to perform QMI, from the initial antibody panel selection through to running assays and analyzing data. The initial assembly of a QMI assay involves screening antibodies to generate a panel, and empirically determining an appropriate lysis buffer. The subsequent reagent preparation includes covalently coupling immunoprecipitation antibodies to MagBeads, and biotinylating probe antibodies so they can be labeled by a streptavidin-conjugated fluorophore. To run the assay, lysate is mixed with MagBeads overnight, and then beads are divided and incubated with different probe antibodies, and then a fluorophore label, and read by flow cytometry. Two statistical tests are performed to identify PiSCES that differ significantly between experimental conditions, and results are visualized using heatmaps or node-edge diagrams.

Quantitative Multiplex Immunoprecipitation (QMI) uses flow cytometry for sensitive detection of differences in the abundance of targeted protein-protein interactions between two samples. QMI can be performed using a small amount of biomaterial, does not require genetically engineered tags, and can be adapted for any previously defined protein interaction network.

Dynamic protein-protein interactions control cellular behavior, from motility to DNA replication to signal transduction. However, monitoring dynamic ...

Absolute Quantification of Cell-Free Protein Synthesis Metabolism by Reversed-Phase Liquid Chromatography-Mass Spectrometry

Cell-free protein synthesis (CFPS) is an emerging technology in systems and synthetic biology for the in vitro production of proteins. However, if CFPS is going to move beyond the laboratory and become a widespread and standard just in time manufacturing technology, we must understand the performance limits of these systems. Toward this question, we developed a robust protocol to quantify 40 compounds involved in glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, energy metabolism and cofactor regeneration in CFPS reactions. The method uses internal standards tagged with 13C-aniline, while compounds in the sample are derivatized with 12C-aniline. The internal standards and sample were mixed and analyzed by reversed-phase liquid chromatography-mass spectrometry (LC/MS). The co-elution of compounds eliminated ion suppression, allowing the accurate quantification of metabolite concentrations over 2-3 orders of magnitude where the average correlation coefficient was 0.988. Five of the forty compounds were untagged with aniline, however, they were still detected in the CFPS sample and quantified with a standard curve method. The chromatographic run takes approximately 10 min to complete. Taken together, we developed a fast, robust method to separate and accurately quantify 40 compounds involved in CFPS in a single LC/MS run. The method is a comprehensive and accurate approach to characterize cell-free metabolism, so that ultimately, we can understand and improve the yield, productivity and energy efficiency of cell-free systems.

Here, we present a robust protocol to quantify 40 compounds involved in central carbon and energy metabolism in cell-free protein synthesis reactions. The cell-free synthesis mixture is derivatized with aniline for effective separation using reversed-phase liquid chromatography and then quantified by mass spectrometry using isotopically labelled internal standards.

Cell-free protein synthesis (CFPS) is an emerging technology in systems and synthetic biology for the in vitro production of proteins. However, if CFPS is ...

Quantification of Humic and Fulvic Acids in Humate Ores, DOC, Humified Materials and Humic Substance-Containing Commercial Products

The purpose of this method is to provide an accurate and precise concentration of humic (HA) and/or fulvic acids (FA) in soft coals, humic ores and shales, peats, composts and humic substance-containing commercial products. The method is based on the alkaline extraction of test materials, using 0.1 N NaOH as an extractant, and separation of the alkaline soluble humic substances (HS) from nonsoluble products by centrifugation. The pH of the centrifuged alkaline extract is then adjusted to pH 1 with conc. HCl, which results in precipitation of the HA. The precipitated HA are separated from the fulvic fraction (FF) (the fraction of HS that remains in solution,) by centrifugation. The HA is then oven or freeze dried and the ash content of the dried HA determined. The weight of the pure (i.e., ash-free) HA is then divided by the weight of the sample and the resulting fraction multiplied by 100 to determine the % HA in the sample. To determine the FA content, the FF is loaded onto a hydrophobic DAX-8 resin, which adsorbs the FA fraction also referred to as the hydrophobic fulvic acid (HFA). The remaining non-fulvic acid fraction, also called the hydrophilic fulvic fraction (HyFF) is then removed by washing the resin with deionized H2O until all nonabsorbed material is completely removed. The FA is then desorbed with 0.1 N NaOH. The resulting Na-fulvate is then protonated by passing it over a strong H+-exchange resin. The resulting FA is oven or freeze dried, the ash content determined and the concentration in the sample calculated as described above for HA.

This method provides a gravimetric quantification of humic substances (e.g., humic and fulvic acids) on an ash-free basis, in dry and liquid materials from soft coals (i.e., oxidized and non-oxidized lignite and sub-bituminous coal), humate ores and shales, peats, composts and commercial fertilizers and soil amendments.

The purpose of this method is to provide an accurate and precise concentration of humic (HA) and/or fulvic acids (FA) in soft coals, humic ores and ...

Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox

The smfBox is a recently developed cost-effective, open-source instrument for single-molecule F&#246;rster Resonance Energy Transfer (smFRET), which makes measurements on freely diffusing biomolecules more accessible. This overview includes a step-by-step protocol for using this instrument to make measurements of precise FRET efficiencies in duplex DNA samples, including details of the sample preparation, instrument setup and alignment, data acquisition, and complete analysis routines. The presented approach, which includes how to determine all the correction factors required for accurate FRET-derived distance measurements, builds on a large body of recent collaborative work across the FRET Community, which aims to establish standard protocols and analysis approaches. This protocol, which is easily adaptable to a range of biomolecular systems, adds to the growing efforts in democratising smFRET for the wider scientific community.

This article provides step-by-step instructions for making fully-corrected accurate FRET measurements on individual, freely diffusing biomolecules using the open-source, inexpensive smfBox, from switch on, through alignment and focusing, to data collection and analysis.

The smfBox is a recently developed cost-effective, open-source instrument for single-molecule F&#246;rster Resonance Energy Transfer (smFRET), which makes ...

Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot

Mass spectrometry-based shotgun proteomics experiments require multiple sample preparation steps, including enzymatic protein digestion and clean-up, which can take up significant person-hours of bench labor and present a source of batch-to-batch variability. Lab automation with pipetting robots can reduce manual work, maximize throughput, and increase research reproducibility. Still, the steep starting prices of standard automation stations make them unaffordable for many academic laboratories. This article describes a proteomics sample preparation workflow using an affordable, open-source automation system (The Opentrons OT-2), including instructions for setting up semi-automated protein reduction, alkylation, digestion, and clean-up steps; as well as accompanying open-source Python scripts to program the OT-2 system through its application programming interface.

Detailed protocol and three Python scripts are provided for operating an open-source robotic liquid handling system to perform semi-automated protein sample preparation for mass spectrometry experiments, covering detergent removal, protein digestion, and peptide desalting steps.

Mass spectrometry-based shotgun proteomics experiments require multiple sample preparation steps, including enzymatic protein digestion and clean-up, ...