The experiments were performed at the Light Microscopy Technology Platform (LiMiTec) of the Faculty of Biology, Bielefeld University. This work has been funded by Bielefeld University.

NOTE: For the following protocol, transient transfection of protoplasts was performed, as described previously12. A brief description is given below.
1. Transient transfection of protoplasts
<ol>
	<li>Cut ~4 g of healthy leaves of Arabidopsis thaliana ecotype Columbia into 1 mm slices and transfer them to 20 mL of enzyme solution (1.5% cellulase; 0.4% macerozyme; 0.1% bovine serum albumin Fraction V; 0.4 M mannitol; 20 mM KCl; 20 mM 2-(N-morpholino)ethanesulfonic acid (MES), pH 5.7; 10 mM CaCl2).</li>
	<li>Vacuum-infiltrate the leaf slices followed by an incubation with agitation for 2 h at room temperature. Harvest the cells by centrifugation for 3 min at 100 &#215; g.</li>
	<li>Wash the protoplasts with W5-solution (154 mM NaCl; 125 mM CaCl2; 5 mM KCl; 2 mM MES, pH 5.7) and resuspend them in MMG solution (0.4 M mannitol; 15 mM MgCl2; 4 mM MES, pH 5.7).</li>
	<li>Perform the transfection in an 8-well slide by osmotic shock in the presence of polyethyleneglycol (PEG) 4000. Mix 20 &#181;L of the protoplast suspension with 5 &#181;L of plasmid DNA (5 &#181;g/&#181;L) and 25 &#181;L of PEG solution (0.2 M mannitol, 0.1 M CaCl2, 40% PEG 4000).</li>
	<li>Reverse the osmotic shock by gentle readjustment of the osmotic conditions. 
	&#8203;NOTE: Besides the sample of interest, the expression of donor alone and acceptor alone is required to determine the spectral bleed-through of the donor and the acceptor, respectively. A fusion protein of the donor and the acceptor must be expressed too for calibration purposes. The fluorescent protein expression was under the control of a cauliflower mosaic virus 35S promoter (pCaMV35S). For all measurements, two confocal laser scanning microscopes (LSM1 and LSM2) were used. LSM1 has two types of detectors: for FRET measurements, the donor signal was detected by a GaAsP-detector, while FRET and acceptor emission were recorded with a photomultiplier. LSM2 has two photomultipliers, which were used for the detection of donor, FRET, and acceptor emission.</li>
</ol>
2. Laser-adjustment
NOTE: Here, 458 nm and 514 nm lines of an argon-ion laser have been applied for FRET analysis between enhanced cyan fluorescent protein (ECFP)- and enhanced yellow fluorescent protein (EYFP)-labeled proteins. For reproducible data acquisition, both lines were adjusted to similar intensity. This was achieved by either a transmission photomultiplier or the reflection mode.
<ol>
	<li>Laser adjustment with a transmission photomultiplier
	<ol>
		<li>Use an empty well for adjustment.</li>
		<li>Choose line-scanning mode and histogram view.</li>
		<li>Decrease the laser intensity to the minimum, and adjust the detector gain to detectable background noise.</li>
		<li>Increase the laser intensity in steps of 0.5% and record the corresponding signal.</li>
		<li>Apply the routine for both laser lines.</li>
	</ol>
	</li>
	<li>Laser adjustment with reflection mode
	<ol>
		<li>Use an empty well for adjustment.</li>
		<li>Apply a reflection filter, switch on the reflection mode, if available.</li>
		<li>Ensure that the detector wavelength range covers the wavelength of the laser.</li>
		<li>Choose the line-scanning mode and histogram view.</li>
		<li>Decrease the laser intensity to the minimum, and adjust the detector gain to detectable background noise.</li>
		<li>Move the objective to the lowest position.</li>
		<li>Move the objective up until the reflection of the coverslip is visible.</li>
		<li>Increase the laser intensity in steps of 0.5% and record the corresponding signal.</li>
		<li>Apply the routine for both laser lines.</li>
	</ol>
	</li>
	<li>Data evaluation
	<ol>
		<li>Tabulate the data and sort the data by signal intensities.</li>
		<li>Plot the signal intensities against the relative laser power.</li>
		<li>Choose laser intensities that result in similar signal intensity.</li>
	</ol>
	</li>
</ol>
3. Adjustment of photomultipliers
NOTE: After laser adjustment, the photomultipliers were adjusted to individual gains to obtain similar sensitivity. This calibration was done with the 514 nm laser line, which is in the center of the wavelength range of interest.
<ol>
	<li>Use an empty well for adjustment.</li>
	<li>Apply a reflection filter, and switch to reflection mode if available.</li>
	<li>Ensure that the detector wavelength range covers the wavelength of the laser (514 nm).</li>
	<li>Choose the line scanning mode and histogram view.</li>
	<li>Decrease detector gain to half the maximum, and adjust the laser intensity to detectable background noise.</li>
	<li>Move the objective to the lowest position.</li>
	<li>Move the objective up until the reflection of the coverslip is visible.</li>
	<li>Increase the detector gain in steps of 50 to 100 V and record the corresponding signal.</li>
	<li>Apply steps 3.1 to 3.8 for both detectors.</li>
	<li>Data evaluation
	<ol>
		<li>Plot the intensity against the detector gain for each detector.</li>
		<li>Choose the individual detector gains to obtain similar sensitivity.</li>
	</ol>
	</li>
</ol>
4. FRET image acquisition
NOTE: Start with the sample of interest for setting up image acquisition.
<ol>
	<li>Choose the appropriate filters/dichroic mirrors, e.g., a double dichroic mirror MBS 458/514 for the FRET-pair ECFP/EYFP. Use the same dichroic mirror for all channels to enable line-by-line scanning. Select a water immersion objective for the imaging of living cells. Choose 12 bit- or 16-bit scanning and moderate scanning speed.</li>
	<li>Define the detection range, preferably 470-510 nm for donor detection and 530-600 nm for acceptor/FRET detection in the case of ECFP/EYFP. When using a 445 nm or 440 nm diode laser, use 450 to 510 nm as the detection range. In the case of an acousto-optic beam splitter (AOBS), define donor detection in the range of 450 to 500 nm to prevent unwanted acceptor detection.</li>
	<li>Apply the detector setting according to 3.10.2.</li>
	<li>Apply the laser setting according to 2.3.2. Revise the laser intensity based on the obtained laser power table, if required. Ensure that the signal-to-noise ratio covers the entire dynamic range of the detectors (intensity ranging from 0 to 4095 for 12-bit scanning).</li>
	<li>Keep laser intensities and detector gains constant. Use the pinhole diameter for fine-tuning. 
	NOTE: Keep in mind that changes in the pinhole diameter affect spatial resolution.</li>
	<li>Perform the measurements (take images of at least 20 cells).</li>
</ol>
5. Determination of crosstalk corrections
NOTE: Cells expressing only the donor or the acceptor are required to determine donor spectral bleed-through (DSBT) and acceptor spectral bleed-through (ASBT), respectively. Keep the same settings described in section 4.
<ol>
	<li>Perform FRET measurements with cells expressing the donor fluorophore.</li>
	<li>Perform FRET measurements with cells expressing the acceptor fluorophore.</li>
</ol>
6. Calibration of the measurements according to Beemiller et al.13
NOTE: Cells expressing a donor-acceptor fusion of known FRET efficiency are required. Here, an ECFP-5 aa-EYFP-fusion with a FRET efficiency of 0.46 has been used4. Keep the same settings described in section 4.
<ol>
	<li>Perform FRET measurements with cells expressing the donor-acceptor fusion</li>
</ol>
7. Data evaluation
<ol>
	<li>Obtain line profiles of the cells, ensuring that each profile contains no more than one cell. Save the profiles as text files.</li>
	<li>Import the text files into a spreadsheet using the text file import option in the Data section.</li>
	<li>Read out the maximum values by applying the Max function.</li>
	<li>List the obtained values in a table, have a column each for donor emission ID, FRET emission IF, acceptor emission IA, and at least four data sets: donor only, acceptor only, donor-acceptor fusion, and measurement. 
	NOTE: Excitation of the donor also results in direct excitation of the acceptor and causes ASBT that is described by the &#945; value.</li>
	<li>Calculate the ASBT &#945; values with the acceptor-only dataset using equation (1). 
	<img alt="Equation 1" src="/files/ftp_upload/62758/62758eq01.jpg" /> (1) 
	NOTE: Use the median of all &#945;-values in the following equations. The donor shows a broad emission spectrum that results in emission crosstalk with the sensitized emission of the acceptor. This DSBT is given by the &#946; value.</li>
	<li>Calculate the donor spectral bleed-through &#946; values with the donor-only dataset using equation (2). 
	<img alt="Equation 2" src="/files/ftp_upload/62758/62758eq02.jpg" /> (2) 
	NOTE: Use the median of all &#946; values in the following equations. The calibration factor &#958; describes the linear relationship of FRET-derived donor quenching and sensitized emission of the acceptor. Use the medians of 7.5 and 7.6 in the following equations.</li>
	<li>Calculate the calibration factors &#958; with the donor-acceptor fusion dataset and its FRET efficiency E (0.46) using equation (3). 
	<img alt="Equation 3" src="/files/ftp_upload/62758/62758eq03.jpg" /> (3) 
	NOTE: Use the median of all &#958; values in the following equations.</li>
	<li>Calculate the FRET efficiencies of the protein pair of interest using equations (4) and (5). 
	<img alt="Equation 4" src="/files/ftp_upload/62758/62758eq04.jpg" /> (4) 
	<img alt="Equation 5" src="/files/ftp_upload/62758/62758eq05.jpg" /> (5)</li>
	<li>Estimate the effects of expression strength and/or donor-acceptor ratio: plot the sum of ID, IF, and IA against the FRET efficiencies. Perform a linear regression; note that the steeper the graph and the higher R2 is, the higher is the impact of the expression level or the greater is the difference of donor and acceptor abundance.</li>
</ol>

<ol>
	<li>Lakowicz, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Principles of Fluorescent Spectroscopy. Third Edition. , (2006).</li><li>Clegg, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=F&#246;rster+resonance+energy+transfer-+FRET+what+it+is,+why+do+it,+and+how+it's+done.">F&#246;rster resonance energy transfer- FRET what it is, why do it, and how it's done.</a> Laboratory Techniques in Biochemistry and Molecular Biology. 33, 1-57 (2009).</li><li>Vogel, S. S., Nguyen, T. A., vander Meer, B. W., Blank, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+impact+of+heterogeneity+and+dark+acceptor+states+on+FRET:+implications+for+using+fluorescent+protein+donors+and+acceptors.">The impact of heterogeneity and dark acceptor states on FRET: implications for using fluorescent protein donors and acceptors.</a> PLoS ONE. 7, 49593 (2012).</li><li>M&#252;ller, S. M., Galliardt, H., Schneider, J., Barisas, B. G., Seidel, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantification+of+F&#246;rster+resonance+energy+transfer+by+monitoring+sensitized+emission+in+living+plant+cells.">Quantification of F&#246;rster resonance energy transfer by monitoring sensitized emission in living plant cells.</a> Frontiers in Plant Science. 4, 413 (2013).</li><li>Gadella, T. W. J., vander Krogt, G. N., Bisseling, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GFP-based+FRET-microscopy+in+living+plant+cells.">GFP-based FRET-microscopy in living plant cells.</a> Trends in Plant Science. 4, 287-291 (1999).</li><li>Van Rheenen, J., Langeslag, M., Jalink, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Correcting+confocal+acquisition+to+optimize+imaging+of+fluorescence+resonance+energy+transfer+by+sensitized+emission.">Correcting confocal acquisition to optimize imaging of fluorescence resonance energy transfer by sensitized emission.</a> Biophysical Journal. 86, 2517-2529 (2004).</li><li>Seidel, T., Golldack, D., Dietz, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+of+C-termini+of+V-ATPase+subunits+by+in+vivo-FRET+measurements.">Mapping of C-termini of V-ATPase subunits by in vivo-FRET measurements.</a> FEBS Letters. 579, 4374-4382 (2005).</li><li>Seidel, T., Schnitzer, D., Golldack, D., Sauer, M., Dietz, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organelle-specific+iso-enzymes+of+plant+V-ATPase+as+revealed+by+in+vivo-FRET.">Organelle-specific iso-enzymes of plant V-ATPase as revealed by in vivo-FRET.</a> BMC Cell Biology. 9, 28 (2008).</li><li>Schnitzer, D., Seidel, T., Sander, T., Golldack, D., Dietz, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cellular+energization+state+affects+peripheral+stalk+stability+of+plant+vacuolar+H+-ATPase+and+impairs+vacuolar+acidification.">The cellular energization state affects peripheral stalk stability of plant vacuolar H+-ATPase and impairs vacuolar acidification.</a> Plant Cell Physiology. 52, 946-956 (2011).</li><li>Roshchina, V. 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D., Swanson, J. 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+phosphatidylinositol-3-kinase-dependent+signal+transition+regulates+ARF1+and+ARF6+during+FC&#947;+receptor-mediated+phagocytosis.">A phosphatidylinositol-3-kinase-dependent signal transition regulates ARF1 and ARF6 during FC&#947; receptor-mediated phagocytosis.</a> PLoS Biology. 4, 162 (2006).</li><li>Lambert, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FPbase:+a+community-editable+fluorescent+protein+database.">FPbase: a community-editable fluorescent protein database.</a> Nature Methods. 16, 277-278 (2019).</li></ol>

We ensure that all authors have disclosed any and all conflicts of interest and have no competing financial interests.

Donor quenching and sensitized acceptor emission are characterized by a linear relationship that allows for either donor- or acceptor-based calculation of FRET. The corresponding factors of linearity are called either G factor (donor to acceptor) or xi (acceptor to donor), which are reciprocal values4. Measuring FRET between fluorescent proteins by fluorescence microscopy often requires corrections for DSBT and ASBT due to the broad absorption and emission spectra of the fluorescent proteins. Howe...

F&#246;rster resonance energy transfer ((F)RET) is typically observed by fluorescence spectroscopy, although the process itself is not limited to occur between fluorophores. The underlying dipole-dipole coupling simply requires a light-emitting donor molecule and a light-absorbing acceptor. This is derived from the required spectral overlap integral J of the normalized donor emission and acceptor absorbance spectra1. However, because RET competes with fluorescence, the energy transfer becomes measurable by alterations in fluorescence emission: RET induces donor quenching and sensitized acceptor emission.
Fluorophore-based RET has been termed fluorescence resonance energy transfer (FRET) to separate it from bioluminescence resonance energy transfer (BRET). RET depends strongly on the distance between donor and acceptor, which is widely in the range of 0.5-10 nm2 and thus, in the same range as the dimensions of proteins and their complexes. Second, RET depends on the dipole-dipole orientation kappa squared. Combined with the fact that rotational freedom of protein-bound fluorophores can be neglected due to the molecular weight and the slow rotational relaxation, RET allows for the analysis of conformational alterations3.
The so-called F&#246;rster radius is based on the spectral overlap integral and the wavelength range of the overlap, so that red light-absorbing chromophores result in longer F&#246;rster radii than blue light-absorbing dyes. As the dynamic range of FRET measurements is limited by 0.5 &#215; R0 and 1.5 &#215; R0, the FRET pair ECFP-EYFP has a dynamic range of 2.5-7.3 nm due to its R0 of 4.9 nm4.
The brightness of a fluorophore is given by the product of its molar extinction coefficient and its quantum yield. For FRET measurements, it is advantageous to choose fluorophores of nearly similar brightness. This enhances the detection of donor quenching and sensitized acceptor emission. It also favors the calibration of the microscopy system. Looking at the frequently used FRET pairs of cyan and fluorescent proteins, the lower brightness of the cyan fluorescent proteins becomes obvious (Figure 1A).
However, the lifetime of the acceptor must be lower than the lifetime of the donor, ensuring the availability of the acceptor for energy transfer. If the lifetime of the acceptor exceeds the lifetime of the donor, the acceptor might still be in the excited state when the donor is excited again. Advanced cyan fluorescent proteins such as mTurquoise show an extended lifetime and thus contribute to an increased probability of FRET (Figure1B). The probability of FRET also depends on the molar extinction coefficient of the acceptor.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>8-well slides</td>
			<td>Ibidi</td>
			<td>80821</td>
			<td></td>
		</tr>
		<tr>
			<td>Immersion oil Immersol&#160; W2010</td>
			<td>Zeiss</td>
			<td>444969-0000-000</td>
			<td>refraction index of water</td>
		</tr>
		<tr>
			<td>LSM 1: AxioObserver with LSM 780 scan head, confocal laser scanning microscope</td>
			<td>Zeiss</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>LSM 2: AxioObserver with LSM 5 scan head, confocal laser scanning microscope</td>
			<td>Zeiss</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

f&#246;rster resonance energy transfer measurements in living plant cells

Sensitized emission-based F&#246;rster resonance energy transfer (FRET) experiments are easily done but depend on the microscopic setup. Confocal laser scanning microscopes have become a workhorse for biologists. Commercial systems offer high flexibility in laser power adjustment and detector sensitivity and often combine different detectors to obtain the perfect image. However, the comparison of intensity-based data from different experiments and setups is often impossible due to this flexibility. Biologist-friendly procedures are of advantage and allow for simple and reliable adjustment of laser and detector settings. 
Furthermore, as FRET experiments in living cells are affected by the variability in protein expression and donor-acceptor ratios, protein expression levels must be considered for data evaluation. Described here is a simple protocol for reliable and reproducible FRET measurements, including routines for the estimation of protein expression and adjustment of laser intensity and detector settings. Data evaluation will be performed by calibration with a fluorophore fusion of known FRET efficiency. To improve simplicity, correction factors have been compared that have been obtained in cells and by measuring recombinant fluorescent proteins.

Adjustment of the confocal laser-scanning microscope 
The laser adjustment revealed a linear increase of emission with increasing laser intensity (Figure 2 and Table 1). As expected for argon-ion lasers, the emission of the 514 nm line was much higher than the emission of the 458 nm line, as evidenced by a steeper slope. For subsequent experiments, laser power of 4.5% and 6.5% was chosen for the 514 nm line and the 458 nm line, respectively. This result...

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F&#246;rster Resonance Energy Transfer Measurements in Living Plant Cells

A protocol is provided for setting up a standard confocal laser-scanning microscope for in vivo F&#246;rster resonance energy transfer measurements, followed by data evaluation.

Sensitized emission-based F&#246;rster resonance energy transfer (FRET) experiments are easily done but depend on the microscopic setup. Confocal laser ...

frster-resonance-energy-transfer-measurements-in-living-plant-cells

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Biochemistry

2.7K Views.  Bielefeld University. A protocol is provided for setting up a standard confocal laser-scanning microscope for in vivo Förster resonance energy transfer measurements, followed by data evaluation.

Video: Förster Resonance Energy Transfer Measurements in Living Plant Cells

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from the oxidation of reduced compounds such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH2). The complete annotation of the Arabidopsis thaliana genome has established it as the most widely used plant model system, and thus the need to purify mitochondria from a variety of organs (leaf, root, or flower) is necessary to fully utilize the tools that are now available for Arabidopsis to study mitochondrial biology. Mitochondria are isolated by homogenization of the tissue using a variety of approaches, followed by a series of differential centrifugation steps producing a crude mitochondrial pellet that is further purified using continuous colloidal density gradient centrifugation. The colloidal density material is subsequently removed by multiple centrifugation steps. Starting from 100 g of fresh leaf tissue, 2 - 3 mg of mitochondria can be routinely obtained. Respiratory experiments on these mitochondria display typical rates of 100 - 250 nmol O2 min-1 mg total mitochondrial protein-1 (NADH-dependent rate) with the ability to use various substrates and inhibitors to determine which substrates are being oxidized and the capacity of the alternative and cytochrome terminal oxidases. This protocol describes an isolation method of mitochondria from Arabidopsis thaliana leaves using continuous colloidal density gradients and an efficient respiratory measurements of purified plant mitochondria.

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

As mitochondria are only a small percentage of the plant cell, they need to be purified for a range of studies. Mitochondria can be isolated from a variety of plant organs by homogenization, followed by differential and density gradient centrifugation to obtain a highly purified mitochondrial fraction.

Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from ...

Modifying Baculovirus Expression Vectors to Produce Secreted Plant Proteins in Insect Cells

It has been a challenge for scientists to express recombinant secretory eukaryotic proteins for structural and biochemical studies. The baculovirus-mediated insect cell expression system is one of the systems used to express recombinant eukaryotic secretory proteins with some post-translational modifications. The secretory proteins need to be routed through the secretory pathways for protein glycosylation, disulfide bonds formation, and other post-translational modifications. To improve the existing insect cell expression of secretory plant proteins, a baculovirus expression vector is modified by the addition of either a GP67 or a hemolin signal peptide sequence between the promoter and multiple-cloning sites. This newly designed modified vector system successfully produced a high yield of soluble recombinant secreted plant receptor proteins of Arabidopsis thaliana. Two of the expressed plant proteins, the extracellular domains of Arabidopsis TDR and PRK3 plasma membrane receptors, were crystallized for X-ray crystallographic studies. The modified vector system is an improved tool that can potentially be used for the expression of recombinant secretory proteins in the animal kingdom as well.

Here, we present the protocols for utilizing the insect cell and baculovirus protein expression system to produce large quantities of plant secreted proteins for protein crystallization. A baculovirus expression vector has been modified with either GP67 or insect hemolin signal peptide for plant protein secretion expression in insect cells.

It has been a challenge for scientists to express recombinant secretory eukaryotic proteins for structural and biochemical studies. The ...

Isolation of Physiologically Active Thylakoids and Their Use in Energy-Dependent Protein Transport Assays

Chloroplasts are the organelles in green plants responsible for carrying out numerous essential metabolic pathways, most notably photosynthesis. Within the chloroplasts, the thylakoid membrane system houses all the photosynthetic pigments, reaction center complexes, and most of the electron carriers, and is responsible for light-dependent ATP synthesis. Over 90% of chloroplast proteins are encoded in the nucleus, translated in the cytosol, and subsequently imported into the chloroplast. Further protein transport into or across the thylakoid membrane utilizes one of four translocation pathways. Here, we describe a high-yield method for isolation of transport-competent thylakoids from peas (Pisum sativum), along with transport assays through the three energy-dependent cpTat, cpSec1, and cpSRP-mediated pathways. These methods enable experiments relating to thylakoid protein localization, transport energetics, and the mechanisms of protein translocation across biological membranes.

We present protocols herein for high-yield isolation of physiologically active thylakoids and protein transport assays for the chloroplast twin arginine translocation (cpTat), secretory (cpSec1), and signal recognition particle (cpSRP) pathways.

Chloroplasts are the organelles in green plants responsible for carrying out numerous essential metabolic pathways, most notably photosynthesis. Within ...

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 In Vitro Fluorescence Resonance Energy Transfer to Study the Dynamics Of Protein Complexes at a Millisecond Time Scale

Proteins are the primary operators of biological systems, and they usually interact with other macro- or small molecules to carry out their biological functions. Such interactions can be highly dynamic, meaning the interacting subunits are constantly associated and dissociated at certain rates. While measuring the binding affinity using techniques such as quantitative pull-down reveals the strength of the interaction, studying the binding kinetics provides insights on how fast the interaction occurs and how long each complex can exist. Furthermore, measuring the kinetics of an interaction in the presence of an additional factor, such as a protein exchange factor or a drug, helps reveal the mechanism by which the interaction is regulated by the other factor, providing important knowledge for the advancement of biological and medical research. Here, we describe a protocol for measuring the binding kinetics of a protein complex that has a high intrinsic association rate and can be dissociated quickly by another protein. The method uses fluorescence resonance energy transfer to report the formation of the protein complex in vitro, and it enables monitoring the fast association and dissociation of the complex in real time on a stopped-flow fluorimeter. Using this assay, the association and dissociation rate constants of the protein complex are quantified.

Protein-protein interactions are critical for biological systems, and studies of the binding kinetics provide insights into the dynamics and function of protein complexes. We describe a method that quantifies the kinetic parameters of a protein complex using fluorescence resonance energy transfer and the stopped-flow technique. &#160;

Proteins are the primary operators of biological systems, and they usually interact with other macro- or small molecules to carry out their biological ...

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

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

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

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

Single Molecule Fluorescence Energy Transfer Study of Ribosome Protein Synthesis

The ribosome is a large ribonucleoprotein complex that assembles proteins processively along mRNA templates. The diameter of the ribosome is approximately 20 nm to accommodate large tRNA substrates at the A-, P- and E-sites. Consequently, the ribosome dynamics are naturally de-phased quickly. Single molecule method can detect each ribosome separately and distinguish inhomogeneous populations, which is essential to reveal the complicated mechanisms of multi-component systems. We report the details of a smFRET method based on the Nikon Ti2 inverted microscope to probe the ribosome dynamics between the ribosomal protein L27 and tRNAs. The L27 is labeled at its unique Cys 53 position and reconstituted into a ribosome that is engineered to lack L27. The tRNA is labeled at its elbow region. As the tRNA moves to different locations inside the ribosome during the elongation cycle, such as pre- and post- translocation, the FRET efficiencies and dynamics exhibit differences, which have suggested multiple subpopulations. These subpopulations are not detectable by ensemble methods. The TIRF-based smFRET microscope is built on a manual or motorized inverted microscope, with home-built laser illumination. The ribosome samples are purified by ultracentrifugation, loaded into a home-built multi-channel sample cell and then illuminated via an evanescent laser field. The reflection laser spot can be used to achieve feedback control of perfect focus. The fluorescence signals are separated by a motorized filter-turret and collected by two digital CMOS cameras. The intensities are retrieved via the NIS-Elements software.

Single molecule fluorescence energy transfer is a method that tracks the tRNA dynamics during ribosomal protein synthesis. By tracking individual ribosomes, inhomogeneous populations are identified, which shed light on mechanisms. This method can be used to track biological conformational changes in general to reveal dynamic-function relationships in many other complexed biosystems. Single molecule methods can observe non-rate limiting steps and low-populated key intermediates, which are not accessible by conventional ensemble methods due to the average effect.

The ribosome is a large ribonucleoprotein complex that assembles proteins processively along mRNA templates. The diameter of the ribosome is approximately ...

Pure Shift Nuclear Magnetic Resonance: a New Tool for Plant Metabolomics

Nuclear Magnetic Resonance (NMR) is one of the most powerful tools used in metabolomics. It stands as a highly accurate and reproducible method that not only provides quantitative data but also permits structural identification of the metabolites present in complex mixtures.
Metabolic profiling by 1H NMR has proven useful in the study of various types of plant scenarios, which include the evaluation of crop&#160;conditions, harvest and post- harvest treatments, metabolic phenotyping, metabolic pathways, gene regulation, identification of biomarkers, chemotaxonomy, quality control, denomination of origin, among others. However, signal overlapping of the large number of resonances with expanded J-coupling multiplicities complicates the spectra analysis and its interpretation, and represents a limitation for classical 1H NMR profiling.
In the last decade, novel NMR broadband homonuclear decoupling techniques through which multiplet signals collapse into single resonance lines - commonly called Pure Shift methods - have been developed to overcome the spectra resolution problem inherent to 1H NMR classical spectra.
Here a step-by-step protocol of the plant extract preparation and the procedure to record optimal Pure Shift PSYCHE and SAPPHIRE-PSYCHE spectra in three different plant matrices - Vanilla plant&#160;leaves, potato tubers (S. tuberosum), and Cape gooseberries (P. peruviana) - is presented. The effect of the gain in resolution in metabolic identification, correlation analysis and multivariate analyses, as compared against classical spectra, is discussed.

This paper presents the use of PSYCHE and SAPPHIRE-PSYCHE in the metabolic profiling of plants and includes detailed procedures for sample preparation and optimal Pure Shift NMR spectra recording. Examples through which the gain in resolution achieved by homonuclear decoupling allows a more comprehensive understanding of the system are discussed.

Nuclear Magnetic Resonance (NMR) is one of the most powerful tools used in metabolomics. It stands as a highly accurate and reproducible method that not ...

Time-resolved F&#246;rster Resonance Energy Transfer Assays for Measurement of Endogenous Phosphorylated STAT Proteins in Human Cells

The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway plays a crucial role in mediating cellular responses to cytokines and growth factors. STAT proteins are activated by tyrosine phosphorylation mediated mainly by JAKs. The abnormal activation of STAT signaling pathways is implicated in many human diseases, especially cancer and immune-related conditions. Therefore, the ability to monitor STAT protein phosphorylation within the native cell signaling environment is important for both academic and drug discovery research. The traditional assay formats available to quantify phosphorylated STAT proteins include western blotting and the enzyme-linked immunosorbent assay (ELISA). These heterogeneous methods are labor-intensive, low-throughput, and often not reliable (specific) in the case of western blotting. Homogeneous (no-wash) methods are available but remain expensive. 
Here, detailed protocols are provided for the sensitive, robust, and cost-effective measurement in a 384-well format of endogenous levels of phosphorylated STAT1 (Y701), STAT3 (Y705), STAT4 (Y693), STAT5 (Y694/Y699), and STAT6 (Y641) in cell lysates from adherent or suspension cells using the novel THUNDER time-resolved F&#246;rster resonance energy transfer (TR-FRET) platform. The workflow for the cellular assay is simple, fast, and designed for high-throughput screening (HTS). The assay protocol is flexible, uses a low-volume sample (15 &#181;L), requires only one reagent addition step, and can be adapted to low-throughput and high-throughput applications. Each phospho-STAT sandwich immunoassay is validated under optimized conditions with known agonists and inhibitors and generates the expected pharmacology and Z'-factor values. As TR-FRET assays are ratiometric and require no washing steps, they provide much better reproducibility than traditional approaches. Together, this suite of assays provides new cost-effective tools for a more comprehensive analysis of specific phosphorylated STAT proteins following cell treatment and the screening and characterization of specific and selective modulators of the JAK/STAT signaling pathway.

Time-resolved F&#246;rster resonance energy transfer cell-based assay protocols are described for the simple, specific, sensitive, and robust quantification of endogenous phosphorylated signal transducer and activator of transcription (STAT) 1/3/4/5/6 proteins in cell lysates in a 384-well format.

The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway plays a crucial role in mediating cellular responses to ...

F&#246;rster Resonance Energy Transfer Mapping: A New Methodology to Elucidate Global Structural Features

F&#246;rster resonance energy transfer (FRET) is an established fluorescence-based method used to successfully measure distances in and between biomolecules in vitro as well as within cells. In FRET, the efficiency of energy transfer, measured by changes in fluorescence intensity or lifetime, relates to the distance between two fluorescent molecules or labels. Determination of dynamics and conformational changes from the distances are just some examples of applications of this method to biological systems. Under certain conditions, this methodology can add to and enhance existing X-ray crystal structures by providing information regarding dynamics, flexibility, and adaptation to binding surfaces. We describe the use of FRET and associated distance determinations to elucidate structural properties, through the identification of a binding site or the orientations of dimer subunits. Through judicious choice of labeling sites, and often employment of multiple labeling strategies, we have successfully applied these mapping methods to determine global structural properties in a protein-DNA complex and the SecA-SecYEG protein translocation system. In the SecA-SecYEG system, we have used FRET mapping methods to identify the preprotein-binding site and determine the local conformation of the bound signal sequence region. This study outlines the steps for performing FRET mapping studies, including identification of appropriate labeling sites, discussion of possible labels including non-native amino acid residues, labeling procedures, how to perform measurements, and interpreting the data.

The study details the methodology of FRET mapping including the selection of labeling sites, choice of dyes, acquisition, and data analysis. This methodology is effective at determining binding sites, conformational changes, and dynamic motions in protein systems and is most useful if performed in conjunction with existing 3-D structural information.