This work was funded by NIH grant #DA15169 to H.E.M.

Procedure Overview:
Using this approach, cell surface proteins are covalently labeled with biotin on available extracellular lysine residues using a membrane impermeant, disulfide-coupled biotinylation reagent (sulfo-NHS-SS-biotin) under trafficking restrictive conditions (i.e. low temperature) (see Fig. 1 for illustration). One set of cells is shifted to trafficking permissive conditions (37&deg;C) and biotinylated proteins internalize. The other set of cells are kept at low temperature as controls for 1) the total surface protein at time=0, and 2) stripping control. Following a short period of internalization, cells are shifted back to low temperature to stop internalization, and any residual surface biotin is stripped off by treating cells with a reducing agent, which cleaves the disulfide-coupled biotin. Biotinylated proteins that arose from the cell surface and were internalized are protected from the stripping step, and will be the only biotinylated proteins that remain. Following cell lysis, biotinylated proteins are isolated by streptavidin affinity chromatography and the protein of interest is detected by quantitative immunoblotting. To determine the endocytic rate, the amount of internalized protein is compared to the total surface control labeled at time=0. We have successfully used this approach to measure the internalization rate of the neuronal norepinephrine1 and dopamine1-4 transporters.
Detailed Protocol:
Day 1:
<ol>
	<li>Plate cells in 6 well plates such that they will be ~80% confluent on Day 2. Alternatively, if transfected cells are being used, transfect at a density such that they will be ~80% confluent at the time the internalization rate will be measured. If cells are not strongly adherent, tissue culture ware should be treated with a cell adhesion substrate (e.g. poly-D-lysine) to prevent cell loss during the extensive wash steps.</li>
<li>For each protein being tested, plate 2 wells on one plate to be used as the total surface protein (t=0) and stripping controls. On a second plate, plate one well for each internalization condition being tested (i.e. basal endocytic rate vs. drug-treated).</li>
<li>Prepare the following solutions and store at the indicated temperatures for use on Day 2:<ul>
<li>PBS2+: Phosphate buffered saline (pH 7.4) supplemented with 1.5 mM MgCl2, 0.2 mM CaCl2, (4&deg;C)</li>
<li>Biotinylation Quench Solution: PBS2+ supplemented with 100 mM glycine, (4&deg;C)</li>
<li>NT buffer: 150 mM NaCl, 1.0 mM EDTA, 0.2% BSA, 20 mM Tris, pH 8.6, (4&deg;C)</li>
<li>RIPA buffer: 10 mM Tris, pH 7.4, 150 mM NaCl, 1.0 mM EDTA, 0.1% SDS, 1.0% Triton X 100, 1.0% sodium deoxycholate, (4&deg;C)</li>
<li>Sulfo-NHS-SS-biotin stock solution: Dissolve in dimethylsulfoxide (DMSO) to 200 mg/ml, (-20&deg;C)</li>
<li>Tris(2-Carboxyethyl) phosphine Hydrochloride (TCEP) stock solution: 500 mM in H2O, (-20&deg;C, covered in foil to block light)</li>
</ul>
</li>
</ol>
Day 2:
<ol>
<li>Prepare PBS2+ supplemented with 0.18g/ml glucose, 0.2% IgG/protease-free bovine serum albumin (PBS2+/g/BSA). Pre-warm this solution to 37&deg;C in water bath.</li>
<li>Thaw out the sulfo-NHS-SS-biotin stock solution on the bench top to melt the DMSO. Immediately prior to use, prepare fresh sulfo-NHS-SS-biotin solution (2.5 mg/ml in ice cold PBS2+, sufficient for 0.75 ml/well). Vortex the solution vigorously to solubilize the DMSO. Note that the NHS-biotin reagent is easily hydrolyzed in aqueous solution. Therefore, all solutions should be prepared immediately prior to use.</li>
<li>Biotinylation: Place plates on an ice bath in the cold room and rinse 3 x 2 ml with ice cold PBS2+. Be certain that plates are slightly angled to allow for complete drainage and removal of the buffer solution. Add 0.75 ml/well of the fresh sulfo-NHS-SS-biotin solution to each well. Incubate x 15', 4&deg;C on the ice bath with vigorous shaking. After the incubation is complete, prepare another fresh sulfo-NHS-SS-biotin solution. Replace the old solution with the fresh solution and incubate x 15', 4&deg;C.</li>
<li>Quenching: It is critical that all non-reacting NHS-biotin molecules are quenched, so that they will not react with and biotinylate intracellular proteins once the cells are lysed. Wash cells 3 x 2 ml with quenching solution and incubate twice in 2 ml quench solution x 15', 4&deg;C with gentle shaking.</li>
<li>Internalization: If drug treatments are being tested, add appropriate drug concentration to PBS2+/g/BSA. Keep control plate at 4&deg;C and bring internalization plate out of the cold room. Wash 3 x 2 ml with pre-warmed PBS2+/g/BSA (+/- drugs) and leave in same solutions (2 ml/well). Fill any empty wells with pre-warmed solution to ensure even temperature across the plate. Transfer the cells to a 37&deg;C incubator for 10'. Immediately prior to end of 37&deg;C incubation, prepare fresh 50 mM TCEP solution in NT buffer to be used for stripping step and store on ice. Prepare sufficient amount for 1.0 ml/well.</li>
<li>Stripping: Immediately transfer plate(s) to ice bath and return to cold room. Rapidly wash cells with ice cold NT buffer, 3 x 2 ml to stop endocytosis. Also wash strip control wells 3 x 2 ml with NT buffer. Add 1.0 ml fresh stripping solution to each well. Incubate on ice, 15', 4&deg;C with gentle shaking. Replace wells with fresh stripping solution and incubate an additional 15', 4&deg;C on ice.</li>
<li>Lysis: Wash all wells that were exposed to stripping solution, 3 x 2 ml NT buffer. Then wash all wells (including total controls) with 3 x 2 ml PBS2+. Lyse in 300&mu;l/well RIPA buffer (or other lysis buffer compatible for the protein of interest) containing fresh protease inhibitors (1.0 mM PMSF, 1.0 &mu;g/ml each leupeptin, aprotinin and pepstatin). Lyse by shaking x 20', 4&deg;C. Transfer to microfuge tubes and clear cellular debris by centrifuging 18,000 x g, 10', 4&deg;C.</li>
<li>Protein concentration determination: Use a protein assay compatible with your lysis conditions (e.g. DC protein assay, Bio-Rad) to determine the protein concentration of the lysates as compared to a standard BSA curve.</li>
<li>Streptavidin affinity chromatography: Prepare microfuge tubes with equivalent amounts of protein for each sample. Add lysis buffer to bring final volume of each sample to 200&mu;l. Vortex the streptavidin agarose beads vigorously to bring to an even suspension. Using a 200&mu;l pipettor with the tip cut off, pipette beads into each tube. Recommended 20&mu;l beads/50 &mu;g lysate. Incubate overnight, 4&deg;C on a tube rotator.</li>
</ol>
Day 3:
<ol>
<li>Bead washing: Centrifuge samples, 18,000 x g, 2' to collect beads. Aspirate off lysate, being careful not to approach bead pellet with aspirator. Use a plastic pipette tip on the end of the aspirator for better control. Add 0.75 ml lysis buffer to each tube, and vortex to wash beads. Centrifuge samples, 18,000 x g, 2' to collect beads and repeat aspiration and washing twice (three washes in total). After the final wash, aspirate as much of the buffer as possible without disturbing the bead pellet. Tipping the tube toward the aspirator assists with this step.</li>
<li>Sample elution: Add 20-25&mu;l 2x Laemmli sample buffer (reducing) to each tube. The reducing agent will cleave the NHS-SS-biotin disulfide bond, releasing the isolated proteins into solution. Most membrane proteins are highly vulnerable to aggregation when boiled, and should not be heated prior to loading on gels for SDS-PAGE. Determine heat sensitivity of your protein of interest prior to performing these experiments. If protein cannot tolerate boiling/heating, incubate on a rotator, 30', room temperature prior to analyzing by SDS-PAGE. This is sufficient to cleave the disulfide bond and elute the proteins.</li>
<li>SDS-PAGE and immunoblotting: Separate proteins by SDS-PAGE. For each sample, it is easiest to run the samples in the following order: total surface (time=0), strip, internalization condition#1, Condition#2, etc. Transfer to membrane for immunoblotting and blot with appropriate antibody for your protein of interest. Capture immunoreactive bands using a CCD-camera gel documentation system, being certain that there are no saturated pixels. Quantify each band density using gel analysis/densitometry software.</li>
</ol>
Representative Results:
A representative immunoblot result is shown in Figure 2A. The strongest signal is in the "total" lane (T), which is total amount of surface protein prior to internalization. The "strip" control (S) should ideally be close to blank, which demonstrates that the strip was efficient for the experiment. The strip efficiency is calculated by comparing the density of the "strip" lane to that of the "total" lane (e.g. protein that was biotinylated in parallel with the strip, but was neither warmed to 37&deg;C nor exposed to stripping solution). The following formula is used: [1-(strip/total)]*100%
Using this formula, the strip in Figure 2 was 99.8% efficient. Finally, you will see bands of lesser intensity than the total in the internalization lane(s) (I). In the example (Figure 2), cells treated were treated with either vehicle or 1&mu;M phorbol myristate acetate (PMA) during a 10' internalization and dopamine transporter internalization rates were measured for a 10' initial internalization period. The internalization rate is calculated as follows: 
internalized/total*100
As seen in Figure 2B, 10.4% surface DAT internalized over 10' under vehicle-treated conditions. PMA treatment increased DAT internalization rates to 23.2% of total surface DAT.
<img src="/files/ftp_upload/1669/1669fig1.jpg" alt="Figure 1" /> Figure 1. Protocol illustration. Cells are biotinylated at 4&deg;C to exclusively label the surface population, and are shifted to 37&deg;C to initiate internalization. Following internalization, cells are rapidly chilled to stop endocytic processes and residual surface biotin is stripped by treating cells with a reducing agent. The only biotinylated proteins that remain are those that arose from the surface at t=0 and were internalized, thus protecting them from the stripping treatment. Biotinylated proteins are isolated by batch affinity chromatography with streptavidin beads and the protein of interest is detected by immunoblotting.
<img src="/files/ftp_upload/1669/1669fig2.jpg" alt="Figure 2" /> Figure 2. PKC activation increases the DAT endocytic rate. Internalization assay. PC12 cells stably expressing DAT were biotinylated, 4&deg;C as described in "Detailed Protocol". Cells were rapidly warmed to 37&deg;C &plusmn;1 &mu;M PMA and incubated 10', 37&deg;C. Residual biotin was stripped by reducing, cells were lysed and biotinylated proteins were isolated by streptavidin affinity chromatography. (A) Representative immunoblot showing total surface DAT at t=0 (T), strip control (S), and internalized DAT (I) under the indicated conditions. (B) Bands were captured with a CCD camera and quantified with Quantity Data software (Bio-Rad). Data are expressed as % total DAT internalized/10 min.
<img src="/files/ftp_upload/1669/1669fig3.jpg" alt="Figure 3" /> Figure 3. Example immunoblot depicting a poor biotin strip. Internalization assay. PC12 cells stably expressing DAT were biotinylated, 4&deg;C as described in "Detailed Protocol". Cells were rapidly warmed to 37&deg;C and incubated 10', 37&deg;C. Residual biotin was stripped by reducing, cells were lysed and biotinylated proteins were isolated by streptavidin affinity chromatography. The immunoblot shows total surface DAT at t=0 (T), strip control (S), and internalized DAT (I). Note the visible band in the strip control lane, indicative of poor strip efficiency.

<ol>
	<li>Holton, K. L., Loder, M. K., Melikian, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nonclassical+distinct+endocytic+signals+dictate+constitutive+and+PKC-regulated+neurotransmitter+transporter+internalization.">Nonclassical distinct endocytic signals dictate constitutive and PKC-regulated neurotransmitter transporter internalization.</a> Nat Neurosci. 8, 881-888 (2005).</li><li>Boudanova, E., Navaroli, D. M., Melikian, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Amphetamine-induced+decreases+in+dopamine+transporter+surface+expression+are+protein+kinase+C-independent.">Amphetamine-induced decreases in dopamine transporter surface expression are protein kinase C-independent.</a> Neuropharmacology. 54, 605-612 (2008).</li><li>Boudanova, E., Navaroli, D. M., Stevens, Z., Melikian, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dopamine+transporter+endocytic+determinants:+carboxy+terminal+residues+critical+for+basal+and+PKC-stimulated+internalization.">Dopamine transporter endocytic determinants: carboxy terminal residues critical for basal and PKC-stimulated internalization.</a> Mol Cell Neurosci. 39, 211-217 (2008).</li><li>Loder, M. K., Melikian, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+dopamine+transporter+constitutively+internalizes+and+recycles+in+a+protein+kinase+C-regulated+manner+in+stably+transfected+PC12+cell+lines.">The dopamine transporter constitutively internalizes and recycles in a protein kinase C-regulated manner in stably transfected PC12 cell lines.</a> J Biol Chem. 278, 22168-22174 (2003).</li></ol>

Common problems: The most common problem that arises in these experiments is poor strip efficiency. The efficiency of the strip is critical in being able to interpret the results. Unless the strip was highly efficient, it is not possible to conclude that any biotinylated proteins in the internalization lanes were, in fact, internalized from the surface. Strips &ge;90% efficiency are optimal, and we discard any results if the strip falls below this level. An example of a poor strip is shown in Figure 3. Note t...

measuring plasma membrane protein endocytic rates by reversible biotinylation

Plasma membrane proteins are a large, diverse group of proteins comprised of receptors, ion channels, transporters and pumps.  Activity of these proteins is responsible for a variety of key cellular events, including nutrient delivery, cellular excitability, and chemical signaling.  Many plasma membrane proteins are dynamically regulated by endocytic trafficking, which modulates protein function by altering protein surface expression.  The mechanisms that facilitate protein endocytosis are complex and are not fully understood for many membrane proteins.  In order to fully understand the mechanisms that control the endocytic trafficking of a given protein, it is critical that the protein s endocytic rate be precisely measured.  For many receptors, direct endocytic rate measurements are frequently achieved utilizing labeled receptor ligands.  However, for many classes of membrane proteins, such as transporters, pumps and ion channels, there is no convenient ligand that can be used to measure the endocytic rate.  In the present report, we describe a reversible biotinylation method that we employ to measure the dopamine transporter (DAT) endocytic rate.  This method provides a straightforward approach to measuring internalization rates, and can be easily employed for trafficking studies of most membrane proteins.

Watch this Scientific Journal Video about Measuring Plasma Membrane Protein Endocytic Rates by Reversible Biotinylation at JoVE.com

Measuring Plasma Membrane Protein Endocytic Rates by Reversible Biotinylation

Regulated endocytosis governs the cell surface expression levels of the majority of membrane proteins. Here we utilize reducible, membrane impermeant biotinylation reagents to measure the endocytic rate of the dopamine transporter (DAT), a polytopic membrane protein. The method facilitates a straightforward approach to measuring the endocytic rate of most plasma membrane proteins.

Plasma membrane proteins are a large, diverse group of proteins comprised of receptors, ion channels, transporters and pumps.  Activity of these proteins ...

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Research

JoVE Journal

Biology

16.9K Görüntüleme.  University of Massachusetts Medical School. Düzenlenmiş endositoz, hücre zarı proteinleri çoğunluğu yüzey ekspresyon düzeyleri yönetir. Burada, dopamin taşıyıcısı (DAT), polytopic membran proteini endositik hızını ölçmek için indirgenebilir, Membran geçirgenliği olmayan biyotinilasyon reaktifleri kullanmaktadır. Bu yöntem çoğu plazma membran proteinlerinin endositik oranını ölçmek için basit bir yaklaşımdır kolaylaştırır.

Video: Measuring Plasma Membrane Protein Endocytic Rates by Reversible Biotinylation

Measuring Near Plasma Membrane and Global Intracellular Calcium Dynamics in Astrocytes

The brain contains glial cells.  Astrocytes, a type of glial cell, have long been known to provide a passive supportive role to neurons. However, increasing evidence suggests that astrocytes may also actively participate in brain function through functional interactions with neurons.  However, many fundamental aspects of astrocyte biology remain controversial, unclear and/or experimentally unexplored. One important issue is the dynamics of intracellular calcium transients in astrocytes. This is relevant because calcium is well established as an important second messenger and because it has been proposed that astrocyte calcium elevations can trigger the release of transmitters from astrocytes. However, there has not been any detailed or satisfying description of near plasma membrane calcium signaling in astrocytes. Total internal reflection fluorescence (TIRF) microscopy is a powerful tool to analyze physiologically relevant signaling events within about 100 nm of the plasma membrane of live cells. Here, we use TIRF microscopy and describe how to monitor near plasma membrane and global intracellular calcium dynamics almost simultaneously. The further refinement and systematic application of this approach has the potential to inform about the precise details of astrocyte calcium signaling. A detailed understanding of astrocyte calcium dynamics may provide a basis to understand if, how, when and why astrocytes and neurons undergo calcium-dependent functional interactions.

We describe how to measure near membrane and global intracellular calcium dynamics in cultured astrocytes using total internal reflection and epifluorescence microscopy.

The brain contains glial cells.  Astrocytes, a type of glial cell, have long been known to provide a passive supportive role to neurons. However, ...

Measuring the Induced Membrane Voltage with Di-8-ANEPPS

Placement of a cell into an external electric field causes a local charge redistribution inside and outside of the cell in the vicinity of the cell membrane, resulting in a voltage across the membrane. This voltage, termed the induced membrane voltage (also induced transmembrane voltage, or induced transmembrane potential difference) and denoted by &Delta;&Phi;, exists only as long as the external field is present. If the resting voltage is present on the membrane, the induced voltage superimposes (adds) onto it. By using one of the potentiometric fluorescent dyes, such as di-8-ANEPPS, it is possible to observe the variations of &Delta;&Phi; on the cell membrane and to measure its value noninvasively. di-8-ANEPPS becomes strongly fluorescent when bound to the lipid bilayer of the cell membrane, with the change of the fluorescence intensity proportional to the change of &Delta;&Phi;. This video shows the protocol for measuring &Delta;&Phi; using di-8-ANEPPS and also demonstrates the influence of cell shape on the amplitude and spatial distribution of &Delta;&Phi;.

External electric field induces a voltage on the membrane of a cell, termed the induced membrane voltage (&Delta;&Phi;). By using the potentiometric dye di-8-ANEPPS, it is possible to measure the &Delta;&Phi; noninvasively. This video shows the protocol for measuring &Delta;&Phi; using di-8-ANEPPS.

Placement of a cell into an external electric field causes a local charge redistribution inside and outside of the cell in the vicinity of the cell ...

Quantitative Measurement of GLUT4 Translocation to the Plasma Membrane by Flow Cytometry

Glucose is the main source of energy for the body, requiring constant regulation of its blood concentration. Insulin release by the pancreas induces glucose uptake by insulin-sensitive tissues, most notably the brain, skeletal muscle, and adipocytes. Patients suffering from type-2 diabetes and/or obesity often develop insulin resistance and are unable to control their glucose homeostasis. New insights into the mechanisms of insulin resistance may provide new treatment strategies for type-2 diabetes.
The GLUT family of glucose transporters consists of thirteen members distributed on different tissues throughout the body1. Glucose transporter type 4 (GLUT4) is the major transporter that mediates glucose uptake by insulin sensitive tissues, such as the skeletal muscle. Upon binding of insulin to its receptor, vesicles containing GLUT4 translocate from the cytoplasm to the plasma membrane, inducing glucose uptake. Reduced GLUT4 translocation is one of the causes of insulin resistance in type-2 diabetes2,3.
The translocation of GLUT4 from the cytoplasm to the plasma membrane can be visualized by immunocytochemistry, using fluorophore-conjugated GLUT4-specific antibodies.
Here, we describe a technique to quantify total amounts of GLUT4 translocation to the plasma membrane of cells during a chosen duration, using flow cytometry. This protocol is rapid (less than 4 hours, including incubation with insulin) and allows the analysis of as few as 3,000 cells or as many as 1 million cells per condition in a single experiment. It relies on anti-GLUT4 antibodies directed to an external epitope of the transporter that bind to it as soon as it is exposed to the extracellular medium after translocation to the plasma membrane.

This protocol describes a rapid technique to quantify the translocation of GLUT4 from the cytoplasm to the plasma membrane of cells by flow cytometry.

Glucose is the main source of energy for the body, requiring constant regulation of its blood concentration. Insulin release by the pancreas induces ...

Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing (MTT)

Our goal is to obtain a comprehensive description of molecular processes occurring at cellular membranes in different biological functions. We aim at characterizing the complex organization and dynamics of the plasma membrane at single-molecule level, by developing analytic tools dedicated to Single-Particle Tracking (SPT) at high density: Multiple-Target Tracing (MTT)1. Single-molecule videomicroscopy, offering millisecond and nanometric resolution1-11, allows a detailed representation of membrane organization12-14 by accurately mapping descriptors such as cell receptors localization, mobility, confinement or interactions.
We revisited SPT, both experimentally and algorithmically. Experimental aspects included optimizing setup and cell labeling, with a particular emphasis on reaching the highest possible labeling density, in order to provide a dynamic snapshot of molecular dynamics as it occurs within the membrane. Algorithmic issues concerned each step used for rebuilding trajectories: peaks detection, estimation and reconnection, addressed by specific tools from image analysis15,16. Implementing deflation after detection allows rescuing peaks initially hidden by neighboring, stronger peaks. Of note, improving detection directly impacts reconnection, by reducing gaps within trajectories. Performances have been evaluated using Monte-Carlo simulations for various labeling density and noise values, which typically represent the two major limitations for parallel measurements at high spatiotemporal resolution.
The nanometric accuracy17 obtained for single molecules, using either successive on/off photoswitching or non-linear optics, can deliver exhaustive observations. This is the basis of nanoscopy methods17 such as STORM18, PALM19,20, RESOLFT21 or STED22,23, which may often require imaging fixed samples. The central task is the detection and estimation of diffraction-limited peaks emanating from single-molecules. Hence, providing adequate assumptions such as handling a constant positional accuracy instead of Brownian motion, MTT is straightforwardly suited for nanoscopic analyses. Furthermore, MTT can fundamentally be used at any scale: not only for molecules, but also for cells or animals, for instance. Hence, MTT is a powerful tracking algorithm that finds applications at molecular and cellular scales.

Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT

Multiple-Target Tracing is a homemade algorithm developed for tracking individually labeled molecules within the plasma membrane of living cells. Efficiently detecting, estimating and tracing molecules over time at high-density provide a user-friendly, comprehensive tool to investigate nanoscale membrane dynamics.

Our goal is to obtain a comprehensive description of molecular processes occurring at cellular membranes in different biological functions. We aim at ...

Harvesting and Cryo-cooling Crystals of Membrane Proteins Grown in Lipidic Mesophases for Structure Determination by Macromolecular Crystallography

An important route to understanding how proteins function at a mechanistic level is to have the structure of the target protein available, ideally at atomic resolution. Presently, there is only one way to capture such information as applied to integral membrane proteins (Figure 1), and the complexes they form, and that method is macromolecular X-ray crystallography (MX). To do MX diffraction quality crystals are needed which, in the case of membrane proteins, do not form readily. A method for crystallizing membrane proteins that involves the use of lipidic mesophases, specifically the cubic and sponge phases1-5, has gained considerable attention of late due to the successes it has had in the G protein-coupled receptor field6-21 (<a href="http://www.mpdb.tcd.ie" target="_blank">www.mpdb.tcd.ie</a>). However, the method, henceforth referred to as the in meso or lipidic cubic phase method, comes with its own technical challenges. These arise, in part, due to the generally viscous and sticky nature of the lipidic mesophase in which the crystals, which are often micro-crystals, grow. Manipulating crystals becomes difficult as a result and particularly so during harvesting22,23. Problems arise too at the step that precedes harvesting which requires that the glass sandwich plates in which the crystals grow (Figure 2)24,25 are opened to expose the mesophase bolus, and the crystals therein, for harvesting, cryo-cooling and eventual X-ray diffraction data collection.
The cubic and sponge mesophase variants (Figure 3) from which crystals must be harvested have profoundly different rheologies4,26. The cubic phase is viscous and sticky akin to a thick toothpaste. By contrast, the sponge phase is more fluid with a distinct tendency to flow. Accordingly, different approaches for opening crystallization wells containing crystals growing in the cubic and the sponge phase are called for as indeed different methods are required for harvesting crystals from the two mesophase types. Protocols for doing just that have been refined and implemented in the Membrane Structural and Functional Biology (MS&amp;FB) Group, and are described in detail in this JoVE article (Figure 4). Examples are given of situations where crystals are successfully harvested and cryo-cooled. We also provide examples of cases where problems arise that lead to the irretrievable loss of crystals and describe how these problems can be avoided. In this article the Viewer is provided with step-by-step instructions for opening glass sandwich crystallization wells, for harvesting and for cryo-cooling crystals of membrane proteins growing in cubic and in sponge phases.

Herein is described procedures implemented in the Caffrey Membrane Structural and Functional Biology Group to harvest and cryo-cool membrane protein crystals grown in lipidic cubic and sponge phases for use in structure determination using macromolecular X-ray crystallography.

An important route to understanding how proteins function at a mechanistic level is to have the structure of the target protein available, ideally at ...

Real-time Analyses of Retinol Transport by the Membrane Receptor of Plasma Retinol Binding Protein

Vitamin A is essential for vision and the growth/differentiation of almost all human organs. Plasma retinol binding protein (RBP) is the principle and specific carrier of vitamin A in the blood. Here we describe an optimized technique to produce and purify holo-RBP and two real-time monitoring techniques to study the transport of vitamin A by the high-affinity RBP receptor STRA6. The first technique makes it possible to produce a large quantity of high quality holo-RBP (100%-loaded with retinol) for vitamin A transport assays. High quality RBP is essential for functional assays because misfolded RBP releases vitamin A readily and bacterial contamination in RBP preparation can cause artifacts. Real-time monitoring techniques like electrophysiology have made critical contributions to the studies of membrane transport. The RBP receptor-mediated retinol transport has not been analyzed in real time until recently. The second technique described here is the real-time analysis of STRA6-catalyzed retinol release or loading. The third technique is real-time analysis of STRA6-catalyzed retinol transport from holo-RBP to cellular retinol binding protein I (CRBP-I). These techniques provide high sensitivity and resolution in revealing RBP receptor's vitamin A uptake mechanism.

Here we describe an optimized technique to produce high-quality vitamin A/RBP complex and two real-time monitoring techniques to study vitamin A transport by STRA6, the RBP receptor.

Vitamin A is essential for vision and the growth/differentiation of almost all human organs.  Plasma retinol binding protein (RBP) is the principle and ...

Imaging Plasma Membrane Deformations With pTIRFM

To gain novel insights into the dynamics of exocytosis, our group focuses on the changes in lipid bilayer shape that must be precisely regulated during the fusion of vesicle and plasma membranes. These rapid and localized changes are achieved by dynamic interactions between lipids and specialized proteins that control membrane curvature. The absence of such interactions would not only have devastating consequences for vesicle fusion, but a host of other cellular functions that involve control of membrane shape. In recent years, the identity of a number of proteins with membrane-shaping properties has been determined. What remains missing is a roadmap of when, where, and how they act as fusion and content release progress.
Our understanding of the molecular events that enable membrane remodeling has historically been limited by a lack of analytical methods that are sensitive to membrane curvature or have the temporal resolution to track rapid changes. PTIRFM satisfies both of these criteria. We discuss how pTIRFM is implemented to visualize and interpret rapid, submicron changes in the orientation of chromaffin cell membranes during dense core vesicle (DCV) fusion. The chromaffin cells we use are isolated from bovine adrenal glands. The membrane is stained with a lipophilic carbocyanine dye,1,1&#39;-dioctadecyl-3,3,3&#39;,3&#39;-tetramethylindodicarbocyanine, 4-chlorobenzenesulfonate, or&#160;diD. DiD intercalates in the membrane plane with a &#34;fixed&#34; orientation and is therefore sensitive to the polarization of the evanescent field. The diD-stained cell membrane is sequentially excited with orthogonal polarizations of a 561&#160;nm laser (p-pol, s-pol). A 488&#160;nm laser is used to visualize vesicle constituents and time the moment of fusion. Exocytosis is triggered by locally perfusing cells with a depolarizing KCl solution. Analysis is performed offline using custom-written software to understand how diD emission intensity changes relate to fusion pore dilation.

Polarization-based Total Internal Reflection Fluorescence Microscopy (pTIRFM) enables real-time detection of cell membrane dynamics. This article describes the implementation of pTIRFM for the study of membrane remodeling during regulated exocytosis. The technique is generalizable to other processes in cell biology that directly or indirectly involve changes in membrane shape.

To gain novel insights into the dynamics of exocytosis, our group focuses on the changes in lipid bilayer shape that must be precisely regulated during ...

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation.

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

A streamlined approach to screening for the expression of recombinant membrane proteins in Escherichia coli based on fusion to green fluorescent protein is presented.

The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and ...

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Membrane protein transport on the single protein level still evades detailed analysis, if the substrate translocated is non-electrogenic. Considerable efforts have been made in this field, but techniques enabling automated high-throughput transport analysis in combination with solvent-free lipid bilayer techniques required for the analysis of membrane transporters are rare. This class of transporters however is crucial in cell homeostasis and therefore a key target in drug development and methodologies to gain new insights desperately needed.
The here presented manuscript describes the establishment and handling of a novel biochip for the analysis of membrane protein mediated transport processes at single transporter resolution. The biochip is composed of microcavities enclosed by nanopores that is highly parallel in its design and can be produced in industrial grade and quantity. Protein-harboring liposomes can directly be applied to the chip surface forming self-assembled pore-spanning lipid bilayers using SSM-techniques (solid supported lipid membranes). Pore-spanning parts of the membrane are freestanding, providing the interface for substrate translocation into or out of the cavity space, which can be followed by multi-spectral fluorescent readout in real-time. The establishment of standard operating procedures (SOPs) allows the straightforward establishment of protein-harboring lipid bilayers on the chip surface of virtually every membrane protein that can be reconstituted functionally. The sole prerequisite is the establishment of a fluorescent read-out system for non-electrogenic transport substrates.
High-content screening applications are accomplishable by the use of automated inverted fluorescent microscopes recording multiple chips in parallel. Large data sets can be analyzed using the freely available custom-designed analysis software. Three-color multi spectral fluorescent read-out furthermore allows for unbiased data discrimination into different event classes, eliminating false positive results.
The chip technology is currently based on SiO2 surfaces, but further functionalization using gold-coated chip surfaces is also possible.

The presented protocol describes the analysis of membrane protein mediated transport on the single transporter level using pore-spanning solvent-free lipid bilayers. This is achieved by the creation of bulk produced nanopore array chips, combined with highly parallel data acquisition and analysis, enabling the future establishment of membrane protein effector screenings.

Membrane protein transport on the single protein level still evades detailed analysis, if the substrate translocated is non-electrogenic. Considerable ...

Determination of Plasma Membrane Partitioning for Peripherally-associated Proteins

This method provides a fast approach for the determination of plasma membrane partitioning of any fluorescently-tagged peripherally-associated protein using the profiles of fluorescence intensity across the plasma membrane. Measured fluorescence profiles are fitted by a model for membrane and cytoplasm fluorescence distribution along a line applied perpendicularly to the cell periphery. This model is constructed from the fluorescence intensity values in reference cells expressing a fluorescently-tagged marker for cytoplasm and with FM 4-64-labeled plasma membrane. The method can be applied to various cell types and organisms; however, only plasma membranes of non-neighboring cells can be evaluated. This fast microscopy-based method is suitable for experiments, where subtle and dynamic changes of plasma membrane-associated markers are expected and need to be quantified, e.g., in the analysis of mutant versions of proteins, inhibitor treatments, and signal transduction observations. The method is implemented in a multi-platform R package that is coupled with an ImageJ macro that serves as a user-friendly interface.

Here, we present a protocol to perform a quantitative analysis of the level of plasma-membrane association for fluorescently-tagged peripherally-associated protein. The method is based on the computational decomposition of membrane and cytoplasmic component of signal observed in cells labeled with plasma membrane fluorescent marker.

This method provides a fast approach for the determination of plasma membrane partitioning of any fluorescently-tagged peripherally-associated protein ...