Name: cell-free production of proteoliposomes for functional analysis and antibody development targeting membrane proteins
Uploaded: 2020-09-22T15:00:00
Description: Watch this Scientific Journal Video about Cell-Free Production of Proteoliposomes for Functional Analysis and Antibody Development Targeting Membrane Proteins at JoVE.com

This research was supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP20am0101077. This work was also partially supported by JSPS KAKENHI Grant Number 20K05709.

1. Preparation of pEU expression plasmid
NOTE: pEU expression plasmid should include start codon, open reading frame of target membrane protein, and stop codon in the fragment (see Figure 1). Add detection/purification tag sequence(s) at the appropriate position when required. Either restriction enzyme digestion or seamless cloning is applicable for subcloning. Here we describe a protocol using a seamless cloning method.
<ol>
	<li>Prepare insert DNA fragment.
	<...

The presented protocol provides a method of producing membrane proteins at a high success rate. This protocol is simple, highly reproducible, and easy to scale up. It also has the potential to reduce the time and cost of experiments that consume a large amount of membrane proteins. The bilayer-dialysis method improves the productivity by 4&#8211;10 times compared with bilayer method or dialysis method (Figure 2B)45. In an extreme case, the yield of an ion channel and ...

Membrane proteins are one of the most important drug targets in diagnosis and therapeutics. Indeed, half of small compound drugs target are membrane proteins, such as G-protein-coupled receptors (GPCRs) and ion channels1. Over the years, researchers have been working on biochemical, biophysical, and structural studies of membrane proteins to elucidate their structure and function2,3. Development of monoclonal antibodies against membrane proteins is also performed actively in order to accelerate functional and structural studies and to develop therapeutic and diagnostic applications4,5,6,7,8,9. All these studies require a large amount of high quality membrane proteins10. For example, several milligrams of purified membrane proteins with natural conformation are needed for antibody development. A much larger quantity of highly purified membrane proteins are required for X-ray crystallography. However, mass production of membrane proteins remains a bottleneck in membrane protein research11. Membrane proteins have complicated structures with one or more transmembrane helices and play important roles in cell homeostasis. Heterologous overexpression of membrane proteins leads to multiple obstacles such as aggregation of membrane proteins that accumulate at high local concentrations or disturbance of cellular signal pathways. Even if the expression is successful, subsequent steps of sample preparation also face difficulty. For instance, preparation of proteoliposome, requires high-level skills and professional experiences in solubilization, purification, and stabilization of membrane proteins, and costs much effort and time as well12,13.
On the other hand, some advanced technologies have emerged in recent decades to produce proteins without the use of living cells14,15,16,17,18. Cell-free protein synthesis technology reconstitutes translation reaction in a test tube. Since there are no limitations that the cellular expression system has, cell-free systems have potential to synthesize a variety of proteins that are difficult to express or show toxicity in cells. Purified cell extract or reconstituted translational machinery is mixed with template mRNAs, amino acids, and energy sources, and recombinant proteins are synthesized in a short time. Regarding the membrane protein synthesis, some kinds of scaffolds composed of lipids or amphiphiles, such as liposomes, bicelles, nanodiscs, or copolymers are added to the cell-free reaction19,20,21,22,23,24. Synthesized membrane proteins interact with the scaffolds and can be stabilized in water. Cell-free synthesized membrane proteins are used widely in functional studies and antibody production25,26,27,28,29,30,31.
In this protocol, we describe an efficient cell-free method of proteoliposome production using wheat cell-free system and liposomes. Wheat cell-free protein synthesis system is a powerful in vitro translation system using extract from wheat germ15,32,33. Wheat germ contains a large amount of translational machinery and few translation inhibitors. The translational machinery in wheat, a member of eukaryotes, is suitable for translating eukaryotic proteins, and its translation efficiency is hardly affected by codon usage of the template mRNA. Using wheat cell-free system, we have synthesized a variety of proteins including protein kinases34,35, ubiquitin ligases36, transcription factors37, and membrane proteins with high success rates. For membrane protein production, we add lipid vesicle liposome into the translation mixture as scaffold19,38. Hydrophobic domains of membrane protein interact with lipid bilayer and are spontaneously integrated with liposome. Density gradient centrifugation is used to strictly separate proteoliposome from endogenous wheat proteins, even though a common centrifugation of the translation reaction mixture is sufficient for a simple purification of proteoliposome20. Many kinds of integral membrane proteins have been synthesized using wheat cell-free system and applied for various researches and developments25,38,39,40,41,42,43,44. Moreover, we developed the &#8220;bilayer-dialysis method&#8221; for large scale production45,46. In this method, cup-type dialysis device is immersed in the substrate feeding buffer, and two layers of translation reaction mixture and substrate feeding buffer are formed in the cup as shown in Figure 1. Continuous supply of substrates and removal of the byproduct can be efficiently conducted at both the top and the bottom of the reaction mixture for a long time, which leads to excellent translation efficacy (Figure 2A and Figure 2B)45.

<table>
	<tbody>
		<tr>
			<td>&#215;3 SDS-PAGE sample buffer</td>
			<td></td>
			<td></td>
			<td>Containing 10% 2-mercaptoethanol</td>
		</tr>
		<tr>
			<td>5-20% gradient SDS-PAGE gel</td>
			<td>ATTO</td>
			<td>E-D520L</td>
			<td></td>
		</tr>
		<tr>
			<td>70% ethanol</td>
			<td></td>
			<td></td>
			<td>Diluted ethanol by ultrapure water.</td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Takara Bio</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium acetate</td>
			<td>Nakalai tesque</td>
			<td>02406-95</td>
			<td>As this reagent is deliquescent, dissolve all of it in water once opened and store it at -30&#176;C.</td>
		</tr>
		<tr>
			<td>Ampicillin Sodium</td>
			<td>Nakalai tesque</td>
			<td>02739-74</td>
			<td></td>
		</tr>
		<tr>
			<td>Asolectin Liposome, lyophilized</td>
			<td>CellFree Sciences</td>
			<td>CFS-PLE-ASL</td>
			<td>A vial contains 10 mg of lyophilized liposomes.</td>
		</tr>
		<tr>
			<td>BSA standard</td>
			<td></td>
			<td></td>
			<td>1000 ng, 500 ng, 250 ng, 125 ng BSA / 10 &#181;L &#215;1 SDS-PAGE sample buffer</td>
		</tr>
		<tr>
			<td>CBB gel stain</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>cDNA clone of interest</td>
			<td></td>
			<td></td>
			<td>Plasmid harboring cDNA clone or synthetic DNA fragment</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Nakalai tesque</td>
			<td>08402-84</td>
			<td></td>
		</tr>
		<tr>
			<td>Cooled incubator</td>
			<td></td>
			<td></td>
			<td>Temperature ranging from 0 to 40 &#176;C or wider.</td>
		</tr>
		<tr>
			<td>Creatine kinase</td>
			<td>Roche Diagnostics</td>
			<td>04524977190</td>
			<td></td>
		</tr>
		<tr>
			<td>Dialysis cup (0.1 mL)</td>
			<td>Thermo Fisher Scientific</td>
			<td>69570</td>
			<td>Slide-A-Lyzer MINI Dialysis Device, 10K MWCO, 0.1 mL</td>
		</tr>
		<tr>
			<td>Dialysis cup (2 mL)</td>
			<td>Thermo Fisher Scientific</td>
			<td>88404</td>
			<td>Slide-A-Lyzer MINI Dialysis Device, 10K MWCO, 2 mL</td>
		</tr>
		<tr>
			<td>DNA ladder marker</td>
			<td>Thermo Fisher Scientific</td>
			<td>SM0311</td>
			<td>GeneRuler 1 kb DNA Ladder</td>
		</tr>
		<tr>
			<td>DpnI</td>
			<td>Thermo Fisher Scientific</td>
			<td>FD1703</td>
			<td>FastDigest DpnI</td>
		</tr>
		<tr>
			<td>E. coli strain JM109</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Electrophoresis chamber</td>
			<td>ATTO</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol (99.5%)</td>
			<td>Nakalai tesque</td>
			<td>14713-95</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethidium bromide</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Evaporation flask, 100 mL</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Gel imager</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Gel scanner</td>
			<td></td>
			<td></td>
			<td>We use document scanner and LED immuninator as a substitute.</td>
		</tr>
		<tr>
			<td>LB broth</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Lipids of interest</td>
			<td>Avanti Polar Lipids</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Micro centrifuge</td>
			<td>TOMY</td>
			<td>MX-307</td>
			<td></td>
		</tr>
		<tr>
			<td>NTP mix</td>
			<td>CellFree Sciences</td>
			<td>CFS-TSC-NTP</td>
			<td>Mixture of ATP, GTP, CTP, UTP, at 25 mM each</td>
		</tr>
		<tr>
			<td>Nuclease-free 25 mL tube</td>
			<td>IWAKI</td>
			<td>362-025-MYP</td>
			<td></td>
		</tr>
		<tr>
			<td>Nucrease-free plastic tubes</td>
			<td>Watson bio labs</td>
			<td></td>
			<td>Do not autoclave. Use them separately from other experiments.</td>
		</tr>
		<tr>
			<td>Nucrease-free tips</td>
			<td>Watson bio labs</td>
			<td></td>
			<td>Do not autoclave. Use them separately from other experiments.</td>
		</tr>
		<tr>
			<td>PBS buffer</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PCR purification kit</td>
			<td>MACHEREY-NAGEL</td>
			<td>740609</td>
			<td>NucleoSpin Gel and PCR Clean-up</td>
		</tr>
		<tr>
			<td>pEU-E01-MCS vector</td>
			<td>CellFree Sciences</td>
			<td>CFS-11</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenol/chloroform/isoamyl alcohol (25:24:1)</td>
			<td>Nippon Gene</td>
			<td>311-90151</td>
			<td></td>
		</tr>
		<tr>
			<td>Plasmid prep Midi kit</td>
			<td>MACHEREY-NAGEL</td>
			<td>740410</td>
			<td>NucleoBond Xtra Midi</td>
		</tr>
		<tr>
			<td>Primer 1</td>
			<td>Thermo Fisher Scientific</td>
			<td>Custom oligo synthesis</td>
			<td>5&#8217;-CCAAGATATCACTAGnnnnnnnnnnnnnnnnnnnnnnnn-3&#8217; 
			Gene specific primer, forward. Upper case shows overlap sequence to be added for seamless cloning. Lower case nnnn&#8230;. (20-30 bp) shows gene specific sequence.</td>
		</tr>
		<tr>
			<td>Primer 2</td>
			<td>Thermo Fisher Scientific</td>
			<td>Custom oligo synthesis</td>
			<td>5&#39;-CCATGGGACGTCGACnnnnnnnnnnnnnnnnnnnnnnnn-3&#8217; 
			Gene specific primer, reverse. Upper case shows overlap sequence to be added for seamless cloning. Lower case nnnn&#8230;. (20-30 bp) shows gene specific sequence.</td>
		</tr>
		<tr>
			<td>Primer 3</td>
			<td>Thermo Fisher Scientific</td>
			<td>Custom oligo synthesis</td>
			<td>5&#39;-GTCGACGTCCCATGGTTTTGTATAGAAT-3&#39; 
			Forward primer for vector linearization. Underline works as overlap in seamless cloning.</td>
		</tr>
		<tr>
			<td>Primer 4</td>
			<td>Thermo Fisher Scientific</td>
			<td>Custom oligo synthesis</td>
			<td>5&#39;-CTAGTGATATCTTGGTGATGTAGATAGGTG-3&#39; 
			Reverse primer for vector linearization. Underline works as overlap in seamless cloning.</td>
		</tr>
		<tr>
			<td>Primer 5</td>
			<td>Thermo Fisher Scientific</td>
			<td>Custom oligo synthesis</td>
			<td>5&#8217;-CAGTAAGCCAGATGCTACAC-3&#8217; 
			Sequencing primer, forward</td>
		</tr>
		<tr>
			<td>Primer 6</td>
			<td>Thermo Fisher Scientific</td>
			<td>Custom oligo synthesis</td>
			<td>5&#8217;- CCTGCGCTGGGAAGATAAAC-3&#8217; 
			Sequencing primer, reverse</td>
		</tr>
		<tr>
			<td>Protein size marker</td>
			<td>Bio-Rad</td>
			<td>1610394</td>
			<td>Precision Plus Protein Standard</td>
		</tr>
		<tr>
			<td>Rotary evaporator</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>seamless cloning enzyme mixture</td>
			<td>New England BioLabs</td>
			<td>E2611L</td>
			<td>Gibson Assembly Master Mix 
			Other seamless cloning reagents are also avairable.</td>
		</tr>
		<tr>
			<td>SP6 RNA Polymerase &#38; RNase Inhibitor</td>
			<td>CellFree Sciences</td>
			<td>CFS-TSC-ENZ</td>
			<td></td>
		</tr>
		<tr>
			<td>Submarine Electrophoresis system</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>TAE buffer</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Transcription Buffer LM</td>
			<td>CellFree Sciences</td>
			<td>CFS-TSC-5TB-LM</td>
			<td></td>
		</tr>
		<tr>
			<td>Translation buffer</td>
			<td>CellFree Sciences</td>
			<td>CFS-SUB-SGC</td>
			<td>SUB-AMIX SGC (&#215;40) stock solution (S1, S2, S3, S4). 
			Prepare &#215;1 translation buffer before use by mixing stock S1, S2, S3, S4 stock and ultrapure water.</td>
		</tr>
		<tr>
			<td>Ultrapure water</td>
			<td></td>
			<td></td>
			<td>We recommend to prepare ultrapure water by using ultrapure water production system every time you do experiment. Do not autoclave. 
			We preparaed ultrapure water by using Milli-Q Reference and Elix10 system. 
			Commercially available nuclease-free water (not DEPC-treated water) can be used as a substitute. Take care of contamination after open the bottle.</td>
		</tr>
		<tr>
			<td>Ultrasonic homogenizer</td>
			<td>Branson</td>
			<td>SONIFIER model 450D-Advanced</td>
			<td>Ultrasonic cleaner can be used as a substitute.</td>
		</tr>
		<tr>
			<td>UV transilluminator</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Vacuum desiccator</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Wheat germ extract</td>
			<td>CellFree Sciences</td>
			<td>CFS-WGE-7240</td>
			<td>WEPRO7240</td>
		</tr>
	</tbody>
</table>

cell-free production of proteoliposomes for functional analysis and antibody development targeting membrane proteins

Membrane proteins play essential roles in a variety of cellular processes and perform vital functions. Membrane proteins are medically important in drug discovery because they are the targets of more than half of all drugs. An obstacle to conducting biochemical, biophysical, and structural studies of membrane proteins as well as antibody development has been the difficulty in producing large amounts of high-quality membrane protein with correct conformation and activity. Here we describe a &#8220;bilayer-dialysis method&#8221; using a wheat germ cell-free system, liposomes, and dialysis cups to efficiently synthesize membrane proteins and prepare purified proteoliposomes in a short time with a high success rate. Membrane proteins can be produced as much as in several milligrams, such as GPCRs, ion channels, transporters, and tetraspanins. This cell-free method contributes to reducing the time, cost and effort for preparing high-quality proteoliposomes, and provides suitable means for functional analysis of membrane proteins, drug targets screening, and antibody development.

Using this protocol, partially purified proteoliposomes can be obtained in a short time. Representative results are shown in Figure 2A. Twenty five GPCRs of Class A, B, and C were successfully synthesized using the bilayer-dialysis method (small scale) and partially purified by centrifugation and buffer wash. Although the amount of synthesized proteins varies according to the type of protein, 50 to 400 &#181;g of membrane proteins usually can be synthesized per reaction when large dialysis c...

Watch this Scientific Journal Video about Cell-Free Production of Proteoliposomes for Functional Analysis and Antibody Development Targeting Membrane Proteins at JoVE.com

Cell-Free Production of Proteoliposomes for Functional Analysis and Antibody Development Targeting Membrane Proteins

This protocol describes an efficient cell-free method for production of high-quality proteoliposome by bilayer-dialysis method using wheat cell-free system and liposomes. This method provides suitable means for functional analysis of membrane proteins, drug targets screening, and antibody development.

Membrane proteins play essential roles in a variety of cellular processes and perform vital functions. Membrane proteins are medically important in drug ...

All the membrane proteins are important targets in drug discovery. The largest scale production of membrane proteins remains a bottleneck to conducting biochemical, biophysical, and structural membrane protein studies. This method can be used to efficiently synthesize membrane proteins in-vitro and to prepare purified proteoliposomes in a short time with a high success rate.After adding the appropriate reagents, including the cell-free expression plasmid to generate a transcription reaction mixture, mix the tube contents by gentle inversion or tapping and perform a quick spin in a microcentrifuge. After the spin, incubate the transcription reaction mixture for six hours at 37 degrees Celsius followed by mixing and a spin down step. To prepare the translation buffer, dilute the stock solution by fresh ultrapure water.For small scale translation, use 100 microliter dialysis cups washed with ultrapure water to remove the glycerol from the dialysis membrane. Add one milliliter of ultrapure water to a new 1.5 milliliter tube and insert a small scale dialysis cup into the tube. Then add 500 microliters of ultrapure water to the cup for a 30-minute incubation at room temperature.To prepare liposomes, transfer a lipid solution containing 50 milligrams of lipids to an evaporation flask. Place the flask in a rotary evaporator to evaporate the solvent. When a thin, evenly spread layer of lipid has been generated on the surface of the flask bottom, transfer the flask to a vacuum desiccator under negative pressure overnight to remove the solvent completely.The next morning, remove the flasks from the desiccator and check the thin film of lipids. Add one milliliter of translation buffer to the flask and rotate the flask to spread the buffer over the thin lipid film. After five minutes, sonicate the flask changing the angle occasionally to allow the solution to contact the entire lipid film surface.Stop sonication when the lipid is completely stripped from the flask and the liposome suspension becomes uniform. Then transfer the liposome suspension to a new 1.5 milliliter tube. Before performing an in-vitro protein translation, float a tube of wheat germ extract from minus 80 degrees storage on water at room temperature for a few minutes to quickly thaw the material.Upon thawing the extract, immediately mix the tube contents by gentle inversion. Then spin down and place the tube on ice. Add the wheat germ extract mRNA and liposomes to generate a translation reaction mixture.Mix the tube contents by gentle inversion or tapping and perform a quick spin in a microcentrifuge. To conduct a small scale in-vitro protein translation, remove the water from the small scale dialysis cup and tube and add one milliliter of translation buffer to the tube and 300 microliters to the cup. Take 60 microliters of translation reaction mixture.Insert the pipette tip into the translation buffer in the dialysis cup. Then inject the mixture slowly and gently. The reaction mixture with higher density spontaneously sinks to the bottom of the cup and forms a layer.Cover the cup with a lid to prevent evaporation. To conduct a large scale translation, add 22 milliliters of translation buffer to a 25 milliliter tube and place a two milliliter dialysis cup into the tube. Add two milliliters of translation buffer to the dialysis cup.Take 500 microliters of the translation reaction mixture, slowly and gently inject the mixture into the translation buffer in the cup. Incubate the reactions for 24 hours at 15 degrees Celsius. The next day thoroughly mix the reaction in the dialysis cup by pipetting and transfer the crude proteoliposome suspensions to new tubes.To purify the proteoliposomes, sediment the proteoliposome in the crude suspensions by centrification. Then wash the proteoliposome by resuspending in the appropriate volume of ice cold PBS buffer three times. After washing, thoroughly resuspend the proteoliposome pellets in a small volume of PBS and measure the suspension volume by using a micropipette.Then add PBS to adjust the volume of suspension. Transfer each suspension into a new micro tube. To set up an SDS page analysis, add 70 microliters of water and 40 microliters of three time concentrated SDS page sample buffer to 10 microliters of each proteoliposome suspension.Set up a five to 20%gradient SDS page gel in an electrophoresis chamber. Load the gel with two microliters of the protein size marker three, six, and 12 microliters of each proteoliposome sample and 10 microliters of bovine serum albumin standards. After loading samples, run the electrophoresis followed by staining the gel with Coomassie Brilliant Blue dye.Finally, decolorize the gel in hot water with gentle shaking and scan the gel image. Using this protocol as demonstrated, a variety of membrane proteins with three or more transmembrane helices can be easily produced as proteoliposomes in a short time. In this bilayer dialysis method, a continuous supply of substrates and the removal of the byproduct can be efficiently conducted at both the top and bottom of the reaction mixture over a long period of time, leading to an excellent translation efficacy.The bilayer dialysis method results in a four to 10 times increase in the productivity compared to using the bilayer or dialysis methods alone. Collection of the synthesized proteoliposomes by centrification and their partially purification with a washing buffer greatly shortens the purification process of the membrane proteins. This cell-free system is easy to manipulate and highly scalable.It can also be used to produce memory proteins that are difficult to express using other methods. This method is extremely helpful for investigations and experiments that use or target membrane proteins such as antimembrane protein, antibody production, SPR, Elisa, and AlphaScreen.

Research

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Detergent-free Ultrafast Reconstitution of Membrane Proteins into Lipid Bilayers Using Fusogenic Complementary-charged Proteoliposomes.

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Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture (CARIC) Strategy

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A Fluorescence Fluctuation Spectroscopy Assay of Protein-Protein Interactions at Cell-Cell Contacts

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Fluorescent Silver Staining of Proteins in Polyacrylamide Gels

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Identification of Functional Protein Regions Through Chimeric Protein Construction

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