Name: laboratory scale production and purification of a therapeutic antibody
Uploaded: 2017-01-24T13:00:00
Description: Watch this Scientific Journal Video about Laboratory Scale Production and Purification of a Therapeutic Antibody at JoVE.com

The research was supported by the University of Sydney. pVITRO1-Trastuzumab-IgG1/&#954; was a gift from Andrew Beavil (Addgene plasmid # 61883). We thank Tihomir S. Dodev for useful discussions regarding pVITRO1-Trastuzumab-IgG1/&#954;.

NOTE: A suitable mammalian expression vector must be used for this protocol. Here, a single construct containing two expression cassettes is used (i.e. heavy and light chain expression is driven by separate promoters). Trastuzumab heavy and light chains were previously cloned into the vector. This vector was a gift from Andrew Beavil, obtained through a not-for-profit plasmid repository 13.
1. Recovery and Scale-up of Vector DNA
NOTE: Vector DNA was received as a soft agar sta...

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This protocol details the transfection, stable expression and purification of a therapeutic antibody in HEK-293 cells. Stable expression of antibody genes is the first step in generating an antibody-producing cell line for the development and manufacture of a therapeutic antibody. While Chinese hamster ovary (CHO) cells remain the expression platform of choice for therapeutic proteins, the HEK-293 cell line is gaining prominence with the realization that proteins produced in these cells are a closer match to naturally oc...

The success of therapeutic antibodies continues to drive substantial investment into antibody development as a wave of next generation therapeutics begins. The antibody market is expected to be reshaped by antibody fragments 1, antibody-drug conjugates 2, bispecific antibodies 3 and engineered antibodies with favorable properties 4. Another class gaining pharmaceutical interest are biosimilars. Biosimilar antibodies are &#39;highly similar&#39; replicate products of a therapeutic antibody that has already received regulatory approval. A proposed biosimilar must be comparable with the originator antibody with respect to its structure, function, animal toxicity, clinical safety and effectiveness, human pharmacokinetics (PK), pharmacodynamics (PD) and immunogenicity 5,6.
The approval rates of biosimilar antibodies have been slow due to the strict constraints on the final quality of the product. The exact manufacturing processes such as specific cell lines and culturing conditions through to the final processing steps can remain proprietary. What is more, the manufacturing of antibodies inherently involves a degree of variability which can add to the challenge of producing a highly similar product. A comprehensive physiochemical and biophysical characterization and comparison is quite difficult, yet a number of studies demonstrating the characteristics of biosimilar antibodies are emerging in the literature 7,8,9.
Generating a therapeutic antibody begins with transfection of mammalian host cells with a vector carrying the genes for the respective antibody. Vector design, cell line and culture conditions are key considerations for setting up the expression system.
The DNA sequences of antibodies can be sourced from Drug Bank (www.drugbank.ca), IMGT (www.igmt.org) or research publications including patents. For example, the sequence of trastuzumab is available through Drug Bank (DB ID: DB00072). The amino acid sequence of the variable regions can undergo gene design and optimization for synthesis in the desired host species. It is important for a biosimilar antibody that no modification is made to the amino acid sequence. Once synthesized, antibody genes can be subcloned into the appropriate vector of choice.
Human IgG antibodies consist of two identical heavy chains and two identical light chains. Tightly regulated expression of both chains is essential for optimal production of heterologous IgG protein in mammalian cells 10. Intra- as well as inter-chain disulfide bonds have to be formed and a number of post-translational modifications have to be introduced during protein biosynthesis. A number of vectors are available that have been designed specifically to express antibody genes (refer to Table of Materials). These antibody-specific vectors usually express the constant regions for both heavy and light chains so only the variable regions of each chain require cloning.
Transfection of cells with two independent constructs (co-transfection) is the most common approach for delivering heavy and light chain-encoding genes. That is, each gene is driven by its own promoter and transcribed as separate antibody chains before being assembled in the endoplasmic reticulum. On the other hand, multi-cistronic vectors have internal ribosome entry site (IRES) elements incorporated that allow expression of multiple genes as a single mRNA transcript with translation permitted from internal regions of the mRNA 11. In this instance, the heavy and light chain-encoding genes are coupled in an arrangement to achieve co-expression of both antibody chains 10,12.
While transiently transfected cells yield sufficient protein to perform a limited number of experiments, stably transfected cell lines that have undergone selection for genome integration can deliver higher yields. Higher protein amounts allow for assay development relating to in vitro characterization and can provide an indication of antibody quality in consideration for downstream applications such as clonal cell line and lead candidate selection.
The goal of this article is to describe the stable expression and purification of a therapeutic antibody produced in a mammalian expression system. Indeed, this method can be applied to the expression of a biosimilar antibody. The method can be used for the initial characterization of antibodies before proceeding on to the critical, albeit time-consuming steps of identifying a desirable clone for larger scale manufacturing. Moreover, this method can be used to express other proteins and not just antibodies.
The following detailed protocol describes the expression of therapeutic antibody trastuzumab. This consists of preparation of vector DNA followed by stable transfection in HEK-293 cell line and purification of antibody protein by an automated chromatographic method.

<table border="0" cellpadding="0" cellspacing="0" width="1730">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:348px;">pFUSE vector series</td>
			<td style="width:189px;">N/A</td>
			<td style="width:191px;">InvivoGen</td>
			<td style="width:1003px;">Heavy and light antibody genes expressed in separate vectors that require co-transfection.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">mAbXpress vector series</td>
			<td>N/A</td>
			<td>ACYTE Biotech Pty Ltd.</td>
			<td>Heavy and light antibody genes expressed in separate vectors that require co-transfection. Refer to: Jones, M. L. et al. A method for rapid, ligation-independent reformatting of recombinant monoclonal antibodies. J Immunol Methods. 354 (1-2), 85-90, doi:10.1016/j.jim.2010.02.001, (2010).</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pVITRO1 vector</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Heavy and light antibody genes are each driven by a separate promoter in a single vector.&#160; Refer to: Dodev, T. S. et al. A tool kit for rapid cloning and expression of recombinant antibodies. Sci Rep. 4 5885, doi:10.1038/srep05885, (2014).</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">GS vector series</td>
			<td>N/A</td>
			<td>Lonza</td>
			<td>Multi-cistronic vector with heavy and light antibody genes co-expressed and translated as single transcript.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Multi-cistronic vector series 1</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Multi-cistronic vector with heavy and light antibody genes co-expressed and translated as single transcript. Refer to: Li, J. et al. A comparative study of different vector designs for the mammalian expression of recombinant IgG antibodies. J Immunol Methods. 318 (1-2), 113-124, doi:10.1016/j.jim.2006.10.010, (2007).</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Multi-cistronic vector series 2</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Multi-cistronic vector with heavy and light antibody genes co-expressed and translated as single transcript. Refer to: Ho, S. C. et al. IRES-mediated Tricistronic vectors for enhancing generation of high monoclonal antibody expressing CHO cell lines. J Biotechnol. 157 (1), 130-139, doi:10.1016/j.jbiotec.2011.09.023, (2012).</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pVITRO1-Trastuzumab-IgG1/&#954;</td>
			<td>61883</td>
			<td>Addgene</td>
			<td>Mammalian expression vector containing trastuzumab antibody genes with hygromycin resistance gene; pVITRO1-Trastuzumab-IgG1/&#954; was a gift from Andrew Beavil.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Fast-Media Hygro Agar</td>
			<td>fas-hg-s</td>
			<td>Jomar Life Research</td>
			<td>Used to prepare low salt LB agar containing 75 &#181;g/ml hygromycin.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Fast-Media Hygro TB</td>
			<td>fas-hg-l</td>
			<td>Jomar Life Research</td>
			<td>Used to prepare low salt TB broth containing 75 &#181;g/ml hygromycin.&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Glycerol, BioXtra, &#8805;99%</td>
			<td>G6279</td>
			<td>Sigma-Aldrich</td>
			<td>Prepare to 80% with water and autoclave. Store at room temperature.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Jestar 2.0/LFU Plasmid Maxi Kit</td>
			<td>G221020</td>
			<td>Astral Scientific</td>
			<td>Plasmid Maxi Prep Kit; elute or resuspend DNA in water (pH 7.0-8.5).</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">FreeStyle 293-F Cells</td>
			<td>R790-07</td>
			<td>Life Technologies</td>
			<td>HEK-293 cell line adapted to suspension culture in serum-free media.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">FreeStyle 293 Expression Medium</td>
			<td>12338-018</td>
			<td>Life Technologies</td>
			<td>Serum-free media specially formulated for maintaing 293-F cell line and high protein expression.</td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Kolliphor P188</td>
			<td>K4894</td>
			<td>Sigma-Aldrich</td>
			<td>Non-ionic surfactant; pluronic F-68; prepare to 10% in water and filter-sterilize using 0.22 &#956;m filter. Store at 4oC.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">DMEM, high glucose&#160;</td>
			<td>11995-065</td>
			<td>Life Technologies</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Heat-Inactivated Foetal Bovine Serum</td>
			<td>10082-147</td>
			<td>Life Technologies</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:348px;">Polyethylenimine, Linear, MW 25,000&#160;</td>
			<td>23966</td>
			<td>Polysciences, Inc.</td>
			<td>Prepare to 1 mg/ml in water. Adjust to pH 7.0 with 1 M HCl (solution becomes clear) and filter-sterilize using 0.22 &#956;m filter. Store at -80oC until use.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">OptiPro SFM</td>
			<td>12309-050</td>
			<td>Life Technologies</td>
			<td>Transfection formulated serum-free media</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Hygromycin B Solution</td>
			<td>ant-hg-1</td>
			<td>Jomar Life Research</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Dimethylsulphoxide (DMSO)</td>
			<td>AJA2225</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Tryptone (casein peptone)</td>
			<td>LP0042B</td>
			<td>Thermo Fisher Scientific</td>
			<td>Prepare to 20% in PBS and filter-sterilize using 0.22 &#956;m filter. Store at 4oC.&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Phosphate Buffered Saline (PBS) Tablets, pH 7.4, 100 ml</td>
			<td>09-2051-100</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">HiTrap Protein A High Performance, 1 x 5 ml column</td>
			<td>GE17-0403-01</td>
			<td>Sigma-Aldrich</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">AKTApurifier 100</td>
			<td>28406266</td>
			<td>GE Healthcare</td>
			<td>Automated FPLC system, which can include a P-960 sample pump and Frac-920 fraction collector.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Glycine-HCl</td>
			<td>G2879</td>
			<td>Sigma-Aldrich</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Citric Acid, monohydrate</td>
			<td>BIOC2123</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Sodium Citrate, trisodium salt dihydrate&#160;</td>
			<td>BIOCB0035</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">1 M Tris-HCl solution pH 9.0</td>
			<td>BIOSD8146</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Amicon Ultra Centrifugal Filters (30 MWCO)</td>
			<td>UFC803008/UFC903008</td>
			<td>Merck Millipore</td>
			<td>Used to buffer exchange and concentrate purified protein.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Pierce Bicinchoninic Acid (BCA) Assay Kit</td>
			<td>23227</td>
			<td>Thermo Fisher Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">BLItz System</td>
			<td>45-5000</td>
			<td>fort&#233;BIO</td>
			<td>Instrument used for bio-layer interferometry (BLI) measurements.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Protein A biosensors</td>
			<td>18-5010</td>
			<td>fort&#233;BIO</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Acrylamide/Bisacrylamide (37.5:1), 40% solution</td>
			<td>786-502</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Ammonium Persulfate (APS)</td>
			<td>AM0486</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">TEMED</td>
			<td>AM0761</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Coomassie Brilliant Blue R-250</td>
			<td>786-498</td>
			<td>Astral Scientific</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Precision Plus Dual-Color Protein Standard</td>
			<td>1610374</td>
			<td>Bio-Rad</td>
			<td></td>
		</tr>
	</tbody>
</table>

laboratory scale production and purification of a therapeutic antibody

Ensuring the successful production of a therapeutic antibody begins early on in the development process. The first stage is vector expression of the antibody genes followed by stable transfection into a suitable cell line. The stable clones are subjected to screening in order to select those clones with desired production and growth characteristics. This is a critical albeit time-consuming step in the process. This protocol considers vector selection and sourcing of antibody sequences for the expression of a therapeutic antibody. The methods describe preparation of vector DNA for stable transfection of a suspension variant of human embryonic kidney 293 (HEK-293) cell line, using polyethylenimine (PEI). The cells are transfected as adherent cells in serum-containing media to maximize transfection efficiency, and afterwards adapted to serum-free conditions. Large scale production, setup as batch overgrow cultures is used to yield antibody protein that is purified by affinity chromatography using an automated fast protein liquid chromatography (FPLC) instrument. The antibody yields produced by this method can provide sufficient protein to begin initial characterization of the antibody. This may include in vitro assay development or physicochemical characterization to aid in the time-consuming task of clonal screening for lead candidates. This method can be transferable to the development of an expression system for the production of biosimilar antibodies.

Stable production of trastuzumab by transfected HEK-293 cells was confirmed using bio-layer interferometry (BLI) as presented in Figure 1. An IgG standard curve was generated by measuring the binding rate between an IgG antibody standard and Protein A biosensor (Figure 1A). The crude supernatant sample was similarly measured, then its concentration interpolated from the standard curve (Figure 1B). The supernatant concentration was measure...

Watch this Scientific Journal Video about Laboratory Scale Production and Purification of a Therapeutic Antibody at JoVE.com

Laboratory Scale Production and Purification of a Therapeutic Antibody

This protocol describes the production of a therapeutic antibody in a mammalian expression system. The methods described include preparation of vector DNA, stable transfection and serum-free adaptation of a human embryonic kidney 293 cell line, set up of large scale cultures and purification using affinity chromatography.

Ensuring the successful production of a therapeutic antibody begins early on in the development process. The first stage is vector expression of the ...

The overall goal of this method is to develop a high-yielding serum free expression system for the lab scale production of a therapeutic antibody. This method can address key considerations in the design of an antibody expression system such as producing a stable cell line, the addition of supplements, and optimizing purification strategies. The main advantage of this technique is that producing a stable cell line adapted to serum media will yield robust and reproducible quantities of therapeutic antibody.To begin, culture HEK-293 cells according to standard protocols in serum-free medium supplemented with 0.1%nonionic surfactant, in Erlenmeyer flasks. Incubate the cells at 37 degrees Celsius and 5%carbon dioxide at 120 rotations per minute. Maintain the culture at two times 10 to the fifth cells per milliliter and subculture every fourth day.On the day prior to transpection, seed HEK-293 cells at three times 10 to the fifth cells per milliliter in the wells of a 12 vial plate in two milliliters of DMEM with 10%heat inactivated FBS. On the day of transpection, check that the cells have reached 80 to 90%confluency. Dilute 1.25 micrograms of vector DNA per well, in 300 microliters of transpection medium.Then use 300 microliters of transpection medium to dilute 2.5 microliters of one milligram per milliliter of polyethylenimine, or PEI solution, per well. Incubate both solutions at room temperature for 5 minutes. Next, add the diluted DNA to the diluted PEI.Gently mix, and incubate the solution at room temperature for fifteen minutes. Then add 50 microliters of the DNA PEI mixture drop wise to each well of the plate. Gently rock the plate to distribute the transpection mixture then incubate the plate at 37 degrees Celsius and 5%carbon dioxide for 24 hours.The following day, add 50 micrograms per milliliter of hygromycin B per well and return the plate to the incubator for 10 days. Following transpection, successful stable transfectants will remain viable and adherent. To carry out serum-free adaptation, replace the medium in the wells with 1/4 the volume of serum-free medium and 3/4 the volume of DMEM with 10%FBS.Incubate the cultures for four days. Then replace the medium with half the volume of serum-free medium and half the volume of DMEM with 10%FBS. And incubate for an additional four days.Now, replace the medium with 3/4 the volume of serum-free medium and 1/4 the volume DMEM supplemented with 10%FBS. And incubate for an additional four days. Finally, replace the medium with serum-free medium supplemented with 0.1%of a nonionic surfactant and incubate for four more days.Following the successful adaptation of stable cells, use a pipette to gently mix the suspension cultures in a 12 well plate and pool the cells in a separate tube. With the hemocytometer, enumerate the pooled cells and seed the cells in 30 milliliters of serum-free medium in a flask at two times 10 to the fifth cells per milliliter. Culture the cells at 37 degrees Celsius and 5%carbon dioxide at 120 rotations per minute.Subculture the cells and expand every fourth day. To compare antibody yields from unsupplemented and nutrient-supplemented cultures, seed cells at two times 10 to fifth cells per milliliter in 100 milliliters of serum-free medium in two flasks. Incubate the cells at 37 degrees Celsius and 5%carbon dioxide at 120 rotations per minute for 24 hours.To the nutrient-supplemented culture, add tryptone to a final concentration of 0.5%then use serum-free medium to equalize the volume of the unsupplemented culture. Incubate the cells for an additional seven days. From the eighth day of culturing forward, count the cells daily using a hemocytometer to monitor cell viability.Once the cell viability reaches less than 80%harvest the culture by centrifugation at 3000 times G for 15 minutes. Then filter sterilized a supernatant through a 0.22 micrometer filter. Store the supernatants at four degrees Celsius in the short term or freeze at negative 20 degrees Celsius long term.After preparing buffers and initializing the FPLC system according to the text protocol, use the method editor to set up the run steps as follows. Equilibrate the system with five column volumes, or CV of binding buffer. Load the sample onto the column and collect the sample flow through.And then use five CV of binding buffer to wash the system. Use five CV of elution buffer to elute the column via isocratic fractionation. And collect the purified antibody samples as fractions using the fraction collector.Finally, equilibrate the system with five CV of binding buffer and collect the flow through into a waste container. Once the method set up is complete, specify the volume of conditioned medium to be a applied to the column and save the method. Next, submerge the sample pump tubing into the vessel containing the conditioned medium.Then prepare a separate container to collect sample flow through via the specified outlet tubing. Insert collection tubes in the fraction collector and add neutralization buffer to each collection tube. In the system control module of the software, open the method to be used.Then click start to initiate the run. When the purification is complete, in the evaluation module, check the resulting chromatogram. Combine all the protein containing fractions into a tube and then use PBS and a centrifugal filter device with a 30 kilodalton cut-off to concentrate the sample and carry out buffer exchange.Finally, use the BCA assay to measure the antibody concentration according to the manufacturer's instructions. Stable production of trastuzumab bar transfected HEK-293 cells was confirmed using biolayer interferometry as presented in this figure. An IGG standard curve was generated by measuring the binding rate between an IGG antibody standard and a protein A biosensor.The crude supernatant sample was similarly measured and its concentration interpolated at 25 micrograms per milliliter from the standard curve. As shown in this chromatogram, measurement of PH conductivity and system pressure are monitored during sample loading, column washing, and finally, elution of the bound protein. Three buffers were tested for optimal binding of trastuzumab to the column and washing to maximize elution yield.Scouting the optimal elution PH and buffer revealed that the antibody eluded more efficiently at a lower PH using 0.1 molar glycine HCL or citric acid. In addition, elution peaks with 0.1 molar glycine HCL appeared less broadened when compared with 0.1 molar citric acid at a similar PH.The purification chromatograms of batch overgrow cultures are shown here. The tryptone supplemented culture yielded 3.8 milligrams and the unsupplemented culture 1.7 milligrams of trastuzumab as measured following buffer exchange and concentration.Finally, this STS page shows that trastuzumab grown in unsupplemented and tryptone supplemented conditions results in similar antibody profiles under non-reducing and reducing conditions. Once optimized, this process of producing a stable cell line that is adapted to serum-free culture and harvesting practical quantities of antibody can be done in under six weeks if it is performed without mishap. While attempting this procedure, it's important to critically monitor the cells during the adaption process.The four day turnover is a recommendation and if cells are struggling at a particular adaption step, then subculture at the previous adaption step before proceeding. Following this procedure, other methods such as size exclusion HPLC, ELISA, and western blotting can be performed in order to further characterize and confirm the antibody product. After watching this video, you should have a good understanding of how to produce a stable cell line and adapt it to serum-free conditions in pursuit of developing a high-yielding expression system for the lab scale production of antibody protein.

laboratory-scale-production-and-purification-of-a-therapeutic-antibody

Research

JoVE Journal

Biochemistry

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

An increasing interest in applying synthetic biology techniques to program outer membrane vesicles (OMV) are leading to some very interesting and unique applications for OMV where traditional nanoparticles are proving too difficult to synthesize. To date, all Gram-negative bacteria have been shown to produce OMV demonstrating packaging of a variety of cargo that includes small molecules, peptides, proteins and genetic material. Based on their diverse cargo, OMV are implicated in many biological processes ranging from cell-cell communication to gene transfer and delivery of virulence factors depending upon which bacteria are producing the OMV. Only recently have bacterial OMV become accessible for use across a wide range of applications through the development of techniques to control and direct packaging of recombinant proteins into OMV. This protocol describes a method for the production, purification, and use of enzyme packaged OMV providing for improved overall production of recombinant enzyme, increased vesiculation, and enhanced enzyme stability. Successful utilization of this protocol will result in the creation of a bacterial strain that simultaneously produces a recombinant protein and directs it for OMV encapsulation through creating a synthetic linkage between the recombinant protein and an outer membrane anchor protein. This protocol also details methods for isolating OMV from bacterial cultures as well as proper handling techniques and things to consider when adapting this protocol for use for other unique applications such as: pharmaceutical drug delivery, medical diagnostics, and environmental remediation.

Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

A protocol for the production, purification, and use of enzyme packaged outer membrane vesicles (OMV) providing for enhanced enzyme stability for implementation across diverse applications is presented.

An increasing interest in applying synthetic biology techniques to program outer membrane vesicles (OMV) are leading to some very interesting and unique ...

Bacterial Inner-membrane Display for Screening a Library of Antibody Fragments

Antibodies engineered for intracellular function must not only have affinity for their target antigen, but must also be soluble and correctly folded in the cytoplasm. Commonly used methods for the display and screening of recombinant antibody libraries do not incorporate intracellular protein folding quality control, and, thus, the antigen-binding capability and cytoplasmic folding and solubility of antibodies engineered using these methods often must be engineered separately. Here, we describe a protocol to screen a recombinant library of single-chain variable fragment (scFv) antibodies for antigen-binding and proper cytoplasmic folding simultaneously. The method harnesses the intrinsic intracellular folding quality control mechanism of the Escherichia coli twin-arginine translocation (Tat) pathway to display an scFv library on the E. coli inner membrane. The Tat pathway ensures that only soluble, well-folded proteins are transported out of the cytoplasm and displayed on the inner membrane, thereby eliminating poorly folded scFvs prior to interrogation for antigen-binding. Following removal of the outer membrane, the scFvs displayed on the inner membrane are panned against a target antigen immobilized on magnetic beads to isolate scFvs that bind to the target antigen. An enzyme-linked immunosorbent assay (ELISA)-based secondary screen is used to identify the most promising scFvs for additional characterization. Antigen-binding and cytoplasmic solubility can be improved with subsequent rounds of mutagenesis and screening to engineer antibodies with high affinity and high cytoplasmic solubility for intracellular applications.

We provide a method to simultaneously screen a library of antibody fragments for binding affinity and cytoplasmic solubility by using the Escherichia coli twin-arginine translocation pathway, which has an inherent quality control mechanism for intracellular protein folding, to display the antibody fragments on the inner membrane.

Antibodies engineered for intracellular function must not only have affinity for their target antigen, but must also be soluble and correctly folded in ...

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

New therapies are needed to treat Clostridium difficile infections that are a major threat to human health. The C. difficile metalloprotease PPEP-1 is a target for future development of inhibitors to decrease the virulence of the pathogen. To perform biophysical and structural characterization as well as inhibitor screening, large amounts of pure and active protein will be needed. We have developed a protocol for efficient production and purification of PPEP-1 by the use of E. coli as the expression host yielding sufficient amounts and purity of protein for crystallization and structure determination. Additionally, using microseeding, highly intergrown crystals of PPEP-1 can be grown to well-ordered crystals suitable for X-ray diffraction analysis. The methods could also be used to produce other recombinant proteins and to study the structures of other proteins producing intergrown crystals.

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Proline-proline endopeptidase-1 (PPEP-1) is a secreted metalloprotease and promising drug-target from the human pathogen Clostridium difficile. Here we describe all methods necessary for the production and structure determination of this protein.

New therapies are needed to treat Clostridium difficile infections that are a major threat to human health. The C. difficile metalloprotease PPEP-1 is a ...

Expression, Purification, and Antimicrobial Activity of S100A12

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some S100 proteins have the capacity to bind transition metals with high affinity and effectively sequester them away from invading microbial pathogens in a process that is termed "nutritional immunity". S100A12 (EN-RAGE) binds both zinc and copper and is highly abundant in innate immune cells such as macrophages and neutrophils. We report a refined method for the expression, enrichment and purification of S100A12 in its active, metal-binding configuration. Utilization of this protein in bacterial growth and viability analyses reveals that S100A12 has antimicrobial activity against the bacterial pathogen, Helicobacter pylori. The antimicrobial activity is predicated on the zinc-binding activity of S100A12, which chelates nutrient zinc, thereby starving H. pylori which requires zinc for growth and proliferation.

Here, we present a method to express and purify S100A12 (calgranulin C). We describe a protocol to measure its antimicrobial activity against the human pathogen H. pylori.

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some ...

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be greatly facilitated by the production of milligram amounts of pure, folded ligand binding domains. Attempts to heterologously express periplasmic ligand binding domains of bacterial chemoreceptors in Escherichia coli (E. coli) often result in their targeting into inclusion bodies. Here, a method is presented for protein recovery from inclusion bodies, its refolding and purification, using the periplasmic dCACHE ligand binding domain of Campylobacter jejuni (C. jejuni) chemoreceptor Tlp3 as an example. The approach involves expression of the protein of interest with a cleavable His6-tag, isolation and urea-mediated solubilisation of inclusion bodies, protein refolding by urea depletion, and purification by means of affinity chromatography, followed by tag removal and size-exclusion chromatography. The circular dichroism spectroscopy is used to confirm the folded state of the pure protein. It has been demonstrated that this protocol is generally useful for production of milligram amounts of dCACHE periplasmic ligand binding domains of other bacterial chemoreceptors in a soluble and crystallisable form.

A procedure is presented for the refolding of the dCACHE periplasmic ligand binding domain of Campylobacter jejuni chemoreceptor Tlp3 from inclusion bodies and the purification to yield milligram quantities of protein.

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be ...

Purification and Reconstitution of TRPV1 for Spectroscopic Analysis

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine and remain largely unknown. With recent advances in single-particle cryo-electron microscopy (cryo-EM) shedding light on the structural features of agonist binding sites and the activation mechanism of several ion channels, the stage is set for an in-depth dynamic analysis of their gating mechanisms using spectroscopic approaches. Spectroscopic techniques such as electron paramagnetic resonance (EPR) and double electron-electron resonance (DEER) have been mainly restricted to the study of prokaryotic ion channels that can be purified in large quantities. The requirement for large amounts of functional and stable membrane proteins has hampered the study of mammalian ion channels using these approaches. EPR and DEER offer many advantages, including determination of the structure and dynamic changes of mobile protein regions, albeit at low resolution, that might be difficult to obtain by X-ray crystallography or cryo-EM, and monitoring reversible gating transition (i.e., closed, open, sensitized, and desensitized). Here, we provide protocols for obtaining milligrams of functional detergent-solubilized transient receptor potential cation channel subfamily V member 1 (TRPV1) that can be labeled for EPR and DEER spectroscopy.

This article describes specific methods to obtain biochemical quantities of detergent-solubilized TRPV1 for spectroscopic analysis. The combined protocols provide biochemical and biophysical tools that can be adapted to facilitate structural and functional studies for mammalian ion channels in a membrane-controlled environment.

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine ...

Transient Expression in Nicotiana Benthamiana Leaves for Triterpene Production at a Preparative Scale

The triterpenes are one of the largest and most structurally diverse families of plant natural products. Many triterpene derivatives have been shown to possess medicinally relevant biological activity. However, thus far this potential has not translated into a plethora of triterpene-derived drugs in the clinic. This is arguably (at least partially) a consequence of limited practical synthetic access to this class of compound, a problem that can stifle the exploration of structure-activity relationships and development of lead candidates by traditional medicinal chemistry workflows. Despite their immense diversity, triterpenes are all derived from a single linear precursor, 2,3-oxidosqualene. Transient heterologous expression of biosynthetic enzymes in N. benthamiana can divert endogenous supplies of 2,3-oxidosqualene towards the production of new high-value triterpene products that are not naturally produced by this host. Agro-infiltration is an efficient and simple means of achieving transient expression in N. benthamiana. The process involves infiltration of plant leaves with a suspension of Agrobacterium tumefaciens carrying the expression construct(s) of interest. Co-infiltration of an additional A. tumefaciens strain carrying an expression construct encoding an enzyme that boosts precursor supply significantly increases yields. After a period of five days, the infiltrated leaf material can be harvested and processed to extract and isolate the resulting triterpene product(s). This is a process that is linearly and reliably scalable, simply by increasing the number of plants used in the experiment. Herein is described a protocol for rapid preparative-scale production of triterpenes utilizing this plant-based platform. The protocol utilizes an easily replicable vacuum infiltration apparatus, which allows the simultaneous infiltration of up to four plants, enabling batch-wise infiltration of hundreds of plants in a short period of time.

Transient Expression in Nicotiana Benthamiana Leaves for Triterpene Production at a Preparative Scale

Transient heterologous expression of biosynthetic enzymes in Nicotiana benthamiana leaves can divert endogenous supplies of 2,3-oxidosqualene towards the production of new high-value triterpene products. Herein is described a detailed protocol for rapid (5 days) preparative-scale production of triterpenes and analogs utilizing this powerful plant-based platform.

The triterpenes are one of the largest and most structurally diverse families of plant natural products. Many triterpene derivatives have been shown to ...

Large-scale Production of Recombinant RNAs on a Circular Scaffold Using a Viroid-derived System in Escherichia coli

With increasing interest in RNA biology and the use of RNA molecules in sophisticated biotechnological applications, the methods to produce large amounts of recombinant RNAs are limited. Here, we describe a protocol to produce large amounts of recombinant RNA in Escherichia coli based on co-expression of a chimeric molecule that contains the RNA of interest in a viroid scaffold and a plant tRNA ligase. Viroids are relatively small, non-coding, highly base-paired circular RNAs that are infectious to higher plants. The host plant tRNA ligase is an enzyme recruited by viroids that belong to the family Avsunviroidae, such as Eggplant latent viroid (ELVd), to mediate RNA circularization during viroid replication. Although ELVd does not replicate in E. coli, an ELVd precursor is efficiently transcribed by the E. coli RNA polymerase and processed by the embedded hammerhead ribozymes in bacterial cells, and the resulting monomers are circularized by the co-expressed tRNA ligase reaching a remarkable concentration. The insertion of an RNA of interest into the ELVd scaffold enables the production of tens of milligrams of the recombinant RNA per liter of bacterial culture in regular laboratory conditions. A main fraction of the RNA product is circular, a feature that facilitates the purification of the recombinant RNA to virtual homogeneity. In this protocol, a complementary DNA (cDNA) corresponding to the RNA of interest is inserted in a particular position of the ELVd cDNA in an expression plasmid that is used, along the plasmid to co-express eggplant tRNA ligase, to transform E. coli. Co-expression of both molecules under the control of strong constitutive promoters leads to production of large amounts of the recombinant RNA. The recombinant RNA can be extracted from the bacterial cells and separated from the bulk of bacterial RNAs taking advantage of its circularity.

Large-scale Production of Recombinant RNAs on a Circular Scaffold Using a Viroid-derived System in Escherichia coli

Here, we present a protocol to produce large amounts of recombinant RNA in Escherichia coli by co-expressing a chimeric RNA that contains the RNA of interest in a viroid scaffold and a plant tRNA ligase. The main product is a circular molecule that facilitates purification to homogeneity.

With increasing interest in RNA biology and the use of RNA molecules in sophisticated biotechnological applications, the methods to produce large amounts ...

Expression and Purification of Nuclease-Free Oxygen Scavenger Protocatechuate 3,4-Dioxygenase

Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, fluorophores are prone to loss of signal via photobleaching by dissolved oxygen (O2). To prevent photobleaching and extend the fluorophore lifetime, oxygen scavenging systems (OSS) are employed to reduce O2. Commercially available OSS may be contaminated by nucleases that damage or degrade nucleic acids, confounding interpretation of experimental results. Here we detail a protocol for the expression and purification of highly active Pseudomonas putida protocatechuate-3,4-dioxygenase (PCD) with no detectable nuclease contamination. PCD can efficiently remove reactive O2 species by conversion of the substrate protocatechuic acid (PCA) to 3-carboxy-cis,cis-muconic acid. This method can be used in any aqueous system where O2 plays a detrimental role in data acquisition. This method is effective in producing highly active, nuclease free PCD in comparison with commercially available PCD.

Protocatechuate 3,4-dioxygenase (PCD) can enzymatically remove free diatomic oxygen from an aqueous system using its substrate protocatechuic acid (PCA). This protocol describes the expression, purification, and activity analysis of this oxygen scavenging enzyme.

Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, ...

A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products

Diterpenoids form a diverse class of small molecule natural products that are widely distributed across the kingdoms of life and have critical biological functions in developmental processes, interorganismal interactions, and environmental adaptation. Due to these various bioactivities, many diterpenoids are also of economic importance as pharmaceuticals, food additives, biofuels, and other bioproducts. Advanced genomics and biochemical approaches have enabled a rapid increase in the knowledge of diterpenoid-metabolic genes, enzymes, and pathways. However, the structural complexity of diterpenoids and the narrow taxonomic distribution of individual compounds in often only a single species remain constraining factors for their efficient production. Availability of a broader range of metabolic enzymes now provide resources for producing diterpenoids in sufficient titers and purity to facilitate a deeper investigation of this important metabolite group. Drawing on established tools for microbial and plant-based enzyme co-expression, we present an easily operated and customizable protocol for the enzymatic production of diterpenoids in either Escherichia coli or Nicotiana benthamiana, and the purification of desired products via silica chromatography and semi-preparative HPLC. Using the group of maize (Zea mays) dolabralexin diterpenoids as an example, we highlight how modular combinations of diterpene synthase (diTPS) and cytochrome P450 monooxygenase (P450) enzymes can be used to generate different diterpenoid scaffolds. Purified compounds can be used in various downstream applications, such as metabolite structural analyses, enzyme structure-function studies, and in vitro and in planta bioactivity experiments.

Here we present easy to use protocols for producing and purifying diterpenoid metabolites through the combinatorial expression of biosynthetic enzymes in Escherichia coli or Nicotiana benthamiana, followed by chromatographic product purification. The resulting metabolites are suitable for various studies including molecular structure characterization, enzyme functional studies, and bioactivity assays.

Diterpenoids form a diverse class of small molecule natural products that are widely distributed across the kingdoms of life and have critical biological ...