Name: PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions (Video) | JoVE Journal
Uploaded: 2017-07-27T13:00:00.000+00:00
Duration: 10 min 58 s
Description: Learn label-free protein-phosphoinositide interaction analysis using the PIP-on-a-chip microfluidic assay. This method enables quantitative assessment of membrane binding in physiologically relevant conditions without detergents.

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D.S. and C.E.C. were supported, in part, by grant AI053531 (NIAID, NIH); S.S and P.S.C. were supported by grant N00014-14-1-0792 (ONR).

The authors have nothing to disclose.

Each PIP variant, albeit at low concentrations, is present on the cytosolic surface of specific organelles where they contribute to the establishment of a unique physical composition and functional specificity of the organellar membrane1. One of the most important uses of PIPs is as a specific docking platform for the multitude of proteins requiring specific subcellular localization and/or activation6,7. Due to their role in cellular physi...

Myriad interactions and biochemical processes take place on two-dimensionally fluid membrane surfaces. Membrane-enclosed organelles in eukaryotic cells are unique not only in biochemical processes and their associated proteome but also in their lipid composition. One exceptional class of phospholipids is phosphoinositides (PIPs). Even though they comprise only 1% of the cellular lipidome, they play a crucial role in signal transduction, autophagy, and membrane trafficking, among others1,2,3,4. Dynamic phosphorylation of the inositol head group by cellular PIP kinases gives rise to seven PIP headgroups that are mono-, bis-, or tris-phosphorylated5. Additionally, PIPs define the subcellular identity of membranes and serve as specialized membrane docking sites for proteins/enzymes containing one or more phosphoinositide-binding domains, for example, Pleckstrin Homology (PH), Phox Homology (PX), and epsin N-terminal Homology (ENTH)6,7. One of the best-studied PIP-binding domains is phospholipase C (PLC)-&#948;1 PH domain that specifically interacts with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) within a high nanomolar-low micromolar range affinity8,9,10,11.
A variety of qualitative and quantitative in vitro methods have been developed and used to study the mechanism, thermodynamics, and specificity of these interactions. Among the most commonly used PIP-binding assays are surface plasmon resonance (SPR), isothermal calorimetry (ITC), nuclear magnetic resonance (NMR) spectroscopy, liposome flotation/sedimentation assay, and lipid-blots (Fat-blots/PIP-strips)12,13. Even though these are extensively utilized, they all have many disadvantages. For example, SPR, ITC, and NMR require large amounts of sample, expensive instrumentation, and/or trained personnel12,13. Some assay formats such as antibody-based lipid-blots utilize water soluble forms of PIPs and present them in a nonphysiological manner12,14,15,16. In addition, lipid-blots cannot be quantitated reliably and they have often resulted in false positive/negative observations12,17,18. To overcome these challenges and improve upon the current tool set, a new label-free method was established based on a supported lipid bilayer (SLB) in the context of a microfluidic platform, which was successfully applied to the study of protein-PIP interactions (Figure 1)19.
The strategy employed for detecting protein-PIP interactions is based on pH modulation sensing. This involves a pH-sensitive dye that has ortho-Sulforhodamine B (oSRB) directly conjugated to phosphatidylethanolamine lipid head group20. The oSRB-POPE probe (Figure 2A) is highly fluorescent at low pH and quenched at high pH with a pKa around 6.7 within 7.5 mol% PI(4,5)P2-containing SLBs (Figure 5B). PLC-&#948;1 PH domain has been used extensively for validating protein-PIP-binding methodologies due to its high specificity towards PI(4,5)P2 (Figure 5A)21,22,23,24,25.Hence, we reasoned that the PLC-&#948;1 PH domain can be used to test its binding to PI(4,5)P2 through the PIP-on-a-chip assay. The PH domain construct used in this study has a net positive charge (pI 8.4), and thus attracts OH- ions (Figure 5C). Upon binding to PI(4,5)P2-containing SLBs, the PH domain brings the OH- ions to the membrane surface, which in turn modulates the interfacial potential and shifts the protonation state of oSRB-POPE (Figure 5C)26. As a function of the PH domain concentration, the fluorescence is quenched (Figure 6A). Finally, the normalized data is fit to a binding isotherm to determine the affinity of the PH domain-PI(4,5)P2 interaction (Figure 6B, 6C).
In this study, a detailed protocol is provided to perform protein binding to PIP-containing SLBs within a microfluidic platform. This protocol takes the reader from assembling the microfluidic device and vesicle preparation to SLB formation and protein binding. In addition, directions for data analysis to extract affinity information for the PLC-&#948;1 PH domain-PI(4,5)P2 interaction are provided.

<table><tbody><tr><td>&lt;strong&gt;Coverslip&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Glass Coverslips: Rectangles</td><td>Fisher Scientific</td><td>12-544B</td><td>22 x 40 x 0.16 - 0.19 mm, No. 1 1/2; Borosilicate Glass</td></tr><tr><td>7X Cleaning Solution</td><td>MP Biomedicals</td><td>976670</td><td>Detergent</td></tr><tr><td>PYREX Crystallizing Dish</td><td>Corning</td><td>3140-190</td><td>Borosilicate glass dish with a flat bottom; Diameter x Height (190 x 100 mm); Distributor: VWR (89090-700)</td></tr><tr><td>Sentry Xpress 2.0</td><td>Paragon Industries</td><td>SC-2</td><td>Kiln</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;PDMS&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Sylgard 184 Silicone Elastomer Kit</td><td>Dow Corning</td><td>4019862</td><td>Polydimethylsiloxane (PDMS); Distributor: Ellsworth Adhesives</td></tr><tr><td>PYREX Desiccator</td><td>VWR</td><td>89134-402</td><td>Vacuum Rated</td></tr><tr><td>Biopsy punch</td><td>Harris</td><td>15110-10</td><td>Harris Uni-Core; 1.0 mm diameter; Miltex Biopsy Punch with Plunger (Cat. No. 15110-10) can be used as an alternative</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Device&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Plasma Cleaning System</td><td>PlasmaEtch</td><td>PE25-JW</td><td>2-stage Direct Drive Oil Vacuum Pump, O2 service (Krytox Charged)</td></tr><tr><td>Digital Hot Plate</td><td>Benchmark</td><td>H3760-H</td><td>Purchased through Denville Scientific (Cat. No. 1005640)</td></tr><tr><td>Frosted Micro Slides</td><td>VWR</td><td>48312-003</td><td>Frosted, Selected, and Precleaned; Made of Swiss Glass; Thickness: 1 mm; Dimensions: 75 x 25 mm; GR 144</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Mold&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>AutoCAD</td><td>Autodesk</td><td>v.2016</td><td>Drafting software for the photomask design</td></tr><tr><td>Photomask</td><td>CAD/Art Services</td><td>N/A</td><td>Design with black background and clear features was printed at 20k dpi resolution on a transparent mask (5 x 7 in) by CAD/Art Services</td></tr><tr><td>Silicone Wafers</td><td>University Wafer</td><td>1575</td><td>Prime Grade, Single Side Polished; 100 mm (4 inch) Diameter; 525 um Thickness</td></tr><tr><td>SU-8 50</td><td>MicroChem Corp.</td><td>N/A</td><td>Negative Tone Photoresist; Penn State Nanofabrication Facility Property</td></tr><tr><td>SU-8 Developer</td><td>MicroChem Corp.</td><td>N/A</td><td>Penn State Nanofabrication Facility Property</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;SUV&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine</td><td>Avanti Polar Lipids</td><td>850457C</td><td>POPC</td></tr><tr><td>L-&amp;alpha;-phosphatidylinositol-4-phosphate</td><td>Avanti Polar Lipids</td><td>840045X</td><td>PI4P</td></tr><tr><td>L-&amp;alpha;-phosphatidylinositol-4,5-bisphosphate</td><td>Avanti Polar Lipids</td><td>840046X</td><td>PI(4,5)P2</td></tr><tr><td>1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine</td><td>Avanti Polar Lipids</td><td>850757C</td><td>POPE; Required for the synthesis of oSRB-POPE</td></tr><tr><td>Lissamine Rhodamine B Sulfonyl Chloride (mixed isomers)</td><td>ThermoFisher Scientific</td><td>L-20</td><td>Required for the synthesis of oSRB-POPE</td></tr><tr><td>pH Sensitive Fluorescent Lipid Probe (oSRB-POPE)</td><td>In-house</td><td>N/A</td><td>In-house Synthesis (Huang D. et al. 2013)</td></tr><tr><td>Glass Scintillation Vial</td><td>VWR</td><td>66022-065</td><td>20 mL volume capacity</td></tr><tr><td>Aquasonic 250D</td><td>VWR</td><td>N/A</td><td>Ultrasonic Water Bath</td></tr><tr><td>Nuclepore Track-Etched Membranes</td><td>Whatman</td><td>110605</td><td>Polycarbonate Membrane; Diameter: 25 mm; Pore Size: 0.1 um; Distributor: Sigma-Aldrich</td></tr><tr><td>Chloroform</td><td>VWR</td><td>CX1054-6</td><td>HPLC grade</td></tr><tr><td>LIPEX Extruder</td><td>Transferra Nanosciences</td><td>T.001</td><td>LIPEX 10 mL Thermobarrel Extruder</td></tr><tr><td>Viscotek 802 DLS</td><td>Malvern Instruments</td><td>N/A</td><td>Dynamic Light Scattering; Penn State X-Ray Crystallography Facility Property</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Data Analysis&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>GraphPad Prism</td><td>GraphPad Software</td><td>v.6</td><td>Curve-fitting software for data analysis</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Microscope&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Axiovert 200M Epifluorescence Microscope</td><td>Carl Zeiss Microscopy</td><td>N/A</td><td>Microscope</td></tr><tr><td>AxioCam MRm Camera</td><td>Carl Zeiss Microscopy</td><td>N/A</td><td>Camera</td></tr><tr><td>X-Cite 120</td><td>Excelitas Technologies</td><td>N/A</td><td>Light Source</td></tr><tr><td>Alexa 568 Filter Set</td><td>Carl Zeiss Microscopy</td><td>N/A</td><td>Ex/Em 576/603 nm</td></tr><tr><td>AxioVision LE64 v.4.9.1.0 Software</td><td>Carl Zeiss Microscopy</td><td>N/A</td><td>Image Processing Software</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog Number&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Other&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Tips</td><td>VWR</td><td>10034-132</td><td>200 uL pipette tips; Thin and smooth tip for applying the protein solution into the microfluidic channel</td></tr><tr><td>Tips</td><td>VWR</td><td>53509-070</td><td>10 uL pipette tips; Thin and smooth tip for applying the vesicle solution into the microfluidic channel</td></tr><tr><td>Orion Star A321 pH meter</td><td>Thermo Scientific</td><td>STARA3210</td><td>pH meter</td></tr><tr><td>Orion micro pH probe</td><td>Thermo Scientific</td><td>8220BNWP</td><td>micro pH probe</td></tr><tr><td>N-(2-Hydroxyethyl)-Piperazine-N&#039;-(2-Ethanesulfonic Acid)</td><td>VWR</td><td>VWRB30487</td><td>HEPES, Free Acid</td></tr><tr><td>Sodium Chloride</td><td>VWR</td><td>BDH8014-2.5KGR</td><td>NaCl</td></tr><tr><td>Tubing</td><td>Allied Wire &amp;amp; Cable</td><td>TFT-200-24 N</td><td>Internal Diameter: 0.020-0.026 inches (0.051-0.066 cm); Wall Thickness: 0.010 inches (0.025 cm); Flexible Polytetrafluoroethylene Thin-Wall Tubing; Natural Color</td></tr><tr><td>Nitrogen Gas - Industrial</td><td>Praxair</td><td>N/A</td><td>Local Provider</td></tr><tr><td>Oxygen Gas - Industrial</td><td>Praxair</td><td>N/A</td><td>Local Provider</td></tr><tr><td>Liquid Nitrogen</td><td>Praxair</td><td>N/A</td><td>Local Provider</td></tr></tbody></table>

pip-on-a-chip: a label-free study of protein-phosphoinositide interactions

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions

Numerous cellular proteins interact with membrane surfaces to affect essential cellular processes. These interactions can be directed towards a specific lipid component within a membrane, as in the case of phosphoinositides (PIPs), to ensure specific subcellular localization and/or activation. PIPs and cellular PIP-binding domains have been studied extensively to better understand their role in cellular physiology. We applied a pH modulation assay on supported lipid bilayers (SLBs) as a tool to study protein-PIP interactions. In these studies, pH sensitive ortho-Sulforhodamine B conjugated phosphatidylethanolamine is used to detect protein-PIP interactions. Upon binding of a protein to a PIP-containing membrane surface, the interfacial potential is modulated (i.e. change in local pH), shifting the protonation state of the probe. A case study of the successful usage of the pH modulation assay is presented by using phospholipase C delta1 Pleckstrin Homology (PLC-&#948;1 PH) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) interaction as an example. The apparent dissociation constant (Kd,app) for this interaction was 0.39 &#177; 0.05 &#181;M, similar to Kd,app values obtained by others. As previously observed, the PLC-&#948;1 PH domain is PI(4,5)P2 specific, shows weaker binding towards phosphatidylinositol 4-phosphate, and no binding to pure phosphatidylcholine SLBs. The PIP-on-a-chip assay is advantageous over traditional PIP-binding assays, including but not limited to low sample volume and no ligand/receptor labeling requirements, the ability to test high- and low-affinity membrane interactions with both small and large molecules, and improved signal to noise ratio. Accordingly, the usage of the PIP-on-a-chip approach will facilitate the elucidation of mechanisms of a wide range of membrane interactions. Furthermore, this method could potentially be used in identifying therapeutics that modulate protein&#39;s capacity to interact with membranes.

We used the pH modulation assay to study the PLC-δ1 PH domain-PI(4,5)P2 interaction within a PIP-on-a-chip microdevice (Figure 1). Through a detailed protocol, we demonstrated how to prepare and assemble microfluidic device components, make small unilamellar vesicles (SUVs) (Figure 2), form SLBs within a device (Figure 3), and tested protein binding to PIP-containing SLBs. A flowchart of a...

Here we present a supported lipid bilayer in the context of a microfluidic platform to study protein-phosphoinositide interactions using a label-free method based on pH modulation.

Numerous cellular proteins interact with membrane surfaces to affect essential cellular processes. These interactions can be directed towards a specific ...

The overall goal of the PIP-on-a-chip assay is to assess protein membrane interactions in a quantitative label-free manner. Protein membrane interactions are the heart of so many processes of the cell and its pathogens, but techniques to study these interactions are few. The advantages of this technique are low simple volume, no ligand or receptor labeling requirements combined with the ability to test membrane interactions in a physiologically relevant manner.Many therapeutic targets of viruses are membrane proteins, studies of these target proteins are often performed in solution using detergents. Our technique provides a more biologically relevant alternative. While you will see that this assay is capable of monitoring the interactions of proteins with membranes, it's actually quite a versatile assay and can be used to monitor iron membrane, small molecule membrane and even peptide membrane interactions.To begin, mix polydimethylsiloxane or PDMS prepolymer and the curing agent at a 10:1 ratio, in a large plastic weigh boat. Degas the mixture in a vacuum for one hour with the vacuum strength at 500 tor or less. Place the silicon master which contains multiple replicates of the same SU8 micropattern in a large plastic weigh boat and pour in the degas PDMS, then, cure it in a dry oven at 60 degrees celsius overnight.The next day, gently peel off the PDMS from the silicon master using one's hands. Mark the boundaries of each micro pattern in rectangles using a surgical scalpel and a ruler. Then, cut the PDMS into blocks, punch 16 holes at both ends of each micro channel with a biopsy punch, to make holes with 1.0 millimeter diameter.Pipette calculated volumes of phosphatidylcholine, Phosphatidylinositol 4, 5-bisphosphate and pH sensitive fluorescent probe into a single 20 milliliter glass ventilation vial. Dry the mixture in a stream of nitrogen gas inside the chemical fume hood for 10 minutes or until the solvent evaporates and the thin lipid film forms at the bottom of the vial. Then, desiccate the mixture under vacuum for at least three hours at a vacuum strength of 10 millitor to remove any residual organic solvent.Rehydrate the dried lipid film with five milliliters of running buffer, place the rehydrated lipid in an ultrasonic bath at an operating frequency of 35 kilohertz for 30 minutes at room temperature. Freeze thaw the vesicle suspension with liquid nitrogen and the 40 degree celsius water bath to get unilaminar vesicles. Repeat the freeze thaw 10 times, extrude the vesicle suspension to a 0.1 micron track edge polycarbonate membrane, using a lipid extruder to enrich for small unilaminar vesicles.Repeat the extrusion 10 times. Test the inlets and outlets of the PDMS block for blockage by squirting de-ionized water through the holes using a water wash bottle, then, dry the PDMS block with nitrogen gas. Next, place the PDMS block and the pre-cleaned cover slip inside the oxygen plasma system sample chamber.Expose the PDMS block and the cover slip with oxygen plasma for 45 seconds with the power settings at 75 watts, oxygen flow speed at 10 cubic centimeters per minute and the vacuum strength of 200 millitor. Next, place the pattern surface of the PDMS block in the contact with the cover slip immediately after the oxygen plasma treatment. Press gently to remove any air bubbles at contact sites.Place the device on a level hot plate at 100 degree celsius for three minutes to enhance the bonding. Use a wet lint-free wipe with 100%ethanol to remove any dust particles from the top and the bottom of the device. Then, tape the device on top of a glass microscope slide.Transfer 100 microliters of the Phosphatidylinositol 4, 5-bisphosphate containing small unilaminar vesicles into a 0.65 milliliter microcentrifuge tube. Adjust the pH of the solution to approximately 3/2 by adding 6.4 microliters of 0.2 normal hydrochloric acid. Pipette 10 microliters of the pH adjusted small unilaminar vesicle solution into each channels through the inlet and apply pressure through the pipette until the solution reaches the outlet.Detach the tip from the pipette and leave it attached to the device. After repeating this step for each channel, incubate the device for 10 minutes at room temperature, injection of vesicles into micro channels should be performed immediately after the device assembly. Meanwhile, cut sets of inlet and outlet tubing, using tweezers, connect the outlet tubing set to the device and then tape the device onto a microscope stage.Submerge one end of the inlet tubing set in 25 milliliters of running buffer contained in a conical tube and tape it to make sure that the tubing is secured. Using a lab jack, place the conical tube on a higher ground than the device in order to push the solution through the micro channels via gravity flow. For each inlet tube, use a syringe to draw one milliliter of running buffer from the free end of the tubing.Remove the pipette tip from the inlet and insert the free end of the inlet tubing into the device. Repeat this process to connect all the inlet tubing pieces to the device. Flowing running buffer through the channels helps to remove excess unruptured vesicles and equilibrate the bilayer to experimental conditions.Next, open the microscope control software. On the left panel, click on the microscope tab and choose the 10x objective. Click on live and then the Alexa 568 image icons on the toolbar, using the fine and coarse adjustment knobs, focus on the micro channels.Scan through the device to check through the quality of the SLBs and the channels. Then, click the FL shutter closed image icon on the toolbar, click on the acquisition tab and under basic adjustments, select exposure time. Set the exposure time to 200 milliseconds.On the left panel, click on multi-dimensional acquisition. Under the filters menu, select the red channel. Then, click on the timelapse menu, set the time interval to five minutes, duration to 30 minutes and lapse menu.Select the circle tool under the measure tab and draw a circle in any channel. Right click while the circle is selected and choose properties. Under the profile tab, check all T to view the fluorescence intensity as a function of time.Make sure this curve reaches a plateau which indicates equilibrium before proceeding to the next step, lower the buffer solution to an equal ground as the device, to stop the flow. One at a time, detach each outlet tubing and apply 200 microliters of each protein dilution into the outlet channel using a pipette. Do not apply any pressure, let gravity do the work.Detach the tip from the pipette and leave it attached to the micro fluidic device. Repeat this process for each channel and make sure that air bubbles are not introduced into the channels during this process. Next, lower the inlet tubing to a ground below the microfluidic device to start flowing the protein through the micro channels.Tape the free end of the tubing to a waste container. Flow the dilutions of the pleckstrin homology domain for 30 minutes. On the left panel of the software, under the timelapse tab, click on start, to begin imaging again.Shown here, is a representative view of the Phosphatidylinositol 4, 5-bisphosphate containing SLBs within micro channels. Before, and after, adding the pleckstrin homology domain at the indicated concentrations. Fluorescence intensities from the line scanned across micro channels are plotted as a function of distance and pixels for phosphatidylcholine, Phosphatidylinositol 4 phosphate, and Phosphatidylinositol 4, 5-bisphosphate binding experiments.Then, normalize binding data from individual experiments, is plotted as a function of phospholipase C delta 1 pleckstrin homology domain concentration and fit to a binding isoterm to extract apparent association constants. Comparison of the apparent association constants, shows that phospholipase C Delta 1 pleckstrin homology domain interacts with Phosphatidylinositol 4, 5-bisphosphate specifically, as expected. After watching this video, you should have a good understanding of how to make small unilaminar vesicles, make microfluidic devices, form supported lipid bilayers inside these microfluidic devices, as your protein membrane binding interactions, using this assay with our PIP-on-a-chip approach.Once mastered, this technique can be done in three hours if it is performed properly. Following this procedure, other methods like fluorescence recovery after photo bleaching can be performed in order to assess the effect of protein membrane binding on the lateral diffusion of the lipids. This technique paves the way to study protein membrane interactions with the assemble of lipids found in cells instead of one at a time, this approach will therefore broadly impact biochemistry and cell biology of protein membrane interactions.

pip-on-chip-label-free-study-protein-phosphoinositide

Research

JoVE Journal

Bioengineering

In this video, we demonstrate protein-phosphoinositide interactions in a microfluidic pattern using the pH modulation assay, using pH-sensitive fluorescent dye tagged to phosphatidylethanolamine lipid of a supported lipid bilayer, called a microfluidic platform. The modulations in pH after protein binding to phospholipid cause fluorescence quenching.

pH Modulation Assay on Supported Lipid Bilayers to Detect Protein-Phosphoinositide Interactions

Phosphoinositides are signaling lipids whose relative abundance rapidly changes in response to various stimuli. This article describes a method to measure the abundance of phosphoinositides by metabolically labeling cells with 3H-myo-inositol, followed by extraction and deacylation. Extracted glycero-inositides are then separated by high-performance liquid chromatography and quantified by flow scintillation.

Radiolabeling and Quantification of Cellular Levels of Phosphoinositides by High Performance Liquid Chromatography-coupled Flow Scintillation

PI(4,5)P2 regulates various cellular functions, but its nanoscale organization in the cell plasma membrane is poorly understood. By labeling PI(4,5)P2 with a dual-color fluorescent probe fused to the Pleckstrin Homology domain, we describe a novel approach to study the PI(4,5)P2 spatial distribution in the plasma membrane at the nanometer scale.

Single-molecule Super-resolution Imaging of Phosphatidylinositol 4,5-bisphosphate in the Plasma Membrane with Novel Fluorescent Probes

The protocol here describes the interactions of purified hEAG1 ion channel protein with the small molecule lipid ligand phosphatidylinositol 4, 5-bisphosphate (PIP2). The measurement demonstrates that BLI could be a potential method for novel small-molecule ion channel ligand screening.

Capturing the Interaction Kinetics of an Ion Channel Protein with Small Molecules by the Bio-layer Interferometry Assay

This protocol focuses on the identification of proteins that bind to inositol phosphates or phosphoinositides. It uses affinity chromatography with biotinylated inositol phosphates or phosphoinositides that are immobilized via streptavidin to agarose or magnetic beads. Inositol phosphate or phosphoinositide binding proteins are identified by Western blotting or mass spectrometry.

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Here, we describe protocols using fluorescent lipid sensors and liposomes to determine whether a protein extracts and transports phosphatidylserine or phosphatidylinositol 4-phosphate in vitro.

Fluorescence-Based Measurements of Phosphatidylserine/Phosphatidylinositol 4-Phosphate Exchange Between Membranes

Here, we present a protocol for the enrichment of endogenous phosphoprotein phosphatases and their interacting proteins from cells and tissues and their identification and quantification by mass spectrometry-based proteomics.

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

We present a cost-effective method for assessing liposomal membrane permeability with superior sensitivity and resolution over conventional techniques. Using a novel encapsulated ligand substitution reaction, this technique detects phospholipase A2-induced changes in model membranes. Easily integrated with standard analyses, this accessible approach enhances resolution for studying membrane biophysics and toxin interactions.

A Liposome Membrane Permeability Assay for Investigating the Effects of Phosphatidylinositol Phosphate Groups on Membranotropic Action of Venom PLA2

A novel approach that allows the high-resolution analysis of cancer cell interactions with exogenous hyaluronic acid (HA) is described.  Patterned surfaces are fabricated by combining carbodiimide chemistry and microcontact printing.

Micropatterned Surfaces to Study Hyaluronic Acid Interactions with Cancer Cells

Raman spectroscopy is a suitable technique for the non-contact, label-free analysis of living cells, tissue-engineered constructs and native tissues. Source-specific spectral fingerprints can be generated and analyzed using multivariate analysis.

Non-contact, Label-free Monitoring of Cells and Extracellular Matrix using Raman Spectroscopy

Learn label-free protein-phosphoinositide interaction analysis using the PIP-on-a-chip microfluidic assay. This method enables quantitative assessment of membrane binding in physiologically relevant conditions without detergents.

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions

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