#PromegaWorks

Descriptions of Promega products in action from examples of Promega products in the peer-reviewed literature to technical tips on how to address common laboratory and experimental questions

Cell-Free Applications:Protein Arrays (Nucleic Acid Programmable)

Posted on by Gary Kobs

The traditional methods of generating protein arrays require the separate expression of hundreds of proteins, followed by purification and immobilization of the proteins on a solid surface. Cell-Free protein array technology produces protein microarrays by performing in vitro synthesis of the target protein from their DNA templates.
One approach for the generation of cell- free based microarrays is the nucleic acid programmable protein array (NAPPA).

NAPPA uses DNA template that is biotinylated and is bound to avidin that is pre-coated onto the protein capture surface. Newly synthesized proteins which are tagged with GST are then immobilized next to the template DNA by binding to an adjacent polyclonal anti-GST capture antibody. The following references illustrate the use of NAPPA to screen hundreds of proteins. Continue reading “Cell-Free Applications:Protein Arrays (Nucleic Acid Programmable)”

Purification of biotinylated proteins

Posted on by Gary Kobs

Biotinylation is an attractive approach for protein complex purification due to the very high affinity (Kd = 10–15 M) of avidin/streptavidin for biotinylated templates. With typical avidin or streptavidin, the biotin-binding affinity is so great that purification with these traditional media require denaturing conditions for elution,such as 8 M Guanidine•HCl at pH 1.5 or boiling in reducing SDS-PAGE sample loading buffer. To avoid these harsh conditions SoftLink™ Soft Release Avidin resin can be used. These particles consist of monomeric avidin coupled to a methylacrylate resin.

This resin provides the same specificity of binding to biotin afforded by tetrameric biotin, but enables the release of biotinlylated molecules under mild nondenaturing conditions (5mM biotin).

The following are recent references that used the SoftLink™ Resin for the noted application:

Kashwayama, Y. et al. (2010) Identification of a substrate-binding site in a peroxisomal beta-oxidation enzyme by photoaffinity labeling with a novel palmitoyl derivative. J. Biol. Chem. 285, 26315–25. (Purification of photoaffinity labeled proteins for subquenant binding/activity experiments)

Takahashi, M. et al. (2010) Tailor-made RNAi knockdown against triplet repeat disease-causing alleles. Proc. Natl. Acad. Sci. 107, 21731-36 (Innovated procedure using biotin labeled cDNAs for the identification of nucleotide variations)

Kress, D. et al. (2009) An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases. J. Biol.Chem. 284, 28401–9 (Purification of Clostridium biotin carrier proteins that play a role in decarboxylation)

Akahori, Y. et al. (2009) Characterization of neutralizing epitopes of varicella-zoster virus glycoprotein H. J. Virol. 83, 2020–4. (purification of double stranded cDNA fragments amplified by PCR with a biotin-tagged PCR primer)

Shonsey, E.M. et al. (2008) Inactivation of human liver bile acid CoA:amino acid N-acyltransferase by the electrophilic lipid, 4-hydroxynonenal. J. Lipid Res. 49, 282–94 (purification of recombinant protein expressed in E.coli containing C-terminal avidin tag)

Andachi, Y. et al. (2008) A novel biochemical method to identify target genes of individual microRNAs: identification of a new Caenorhabditis elegans let-7 target. RNA 14, 2440–51 (purification of double stranded cDNA fragments amplified by PCR with a biotin-tagged PCR primer)

For more information about SoftLink™ Soft Release Avidin Resin, please visit our website.

Cell Free Expression Application: Production of Soluble Protein for Structural Analysis

Posted on by Gary Kobs

The TNT® SP6 High-Yield Protein Expression System uses a high-yield wheat germ extract supplemented with SP6 RNA polymerase and other components. Coupling transcriptional and translational activities eliminates the inconvenience of separate in vitro transcription and purification steps for the mRNA, while maintaining the high levels of protein expression. All that is required is the addition of DNA templates containing the SP6 promoter and the protein coding region for the protein of interest. Furthermore no specialized equipment is required for protein screening and production. The system enables the expression of approximately 100µg/ml of protein in batch reaction and 200–440µg/ml in dialysis reaction in 10–20 hours .

In a recent publication (Zhao, L. et.al. (2010) J. Struct. Genomics 11, 201–9), the Northeast Structural Genomics Consortium (www.nesg.org) in their quest to express 5,000 eukaryotic proteins, report that even with different cloning strategies they could only produce 26% of the proteins in a soluble form. To improve the efficiency of expressing soluble protein, they investigated the use of wheat germ cell free system as a alternative to E.coli.

In this publication 59 human constructs were expressed in both E.coli and the wheat germ cell free system. Only 30% of human proteins could be produced in a soluble form using E.coli -based expression. Some 70% could be produced using the TNT® SP6 High Yield Wheat Germ system.
To further demonstrate the utility of expressing proteins that were suitable for structural studies from a wheat germ-based system, two of the proteins were isotope enriched and analyzed successfully by 2D NMR.

Alternative Applications for Cell-Free Expression #3

Posted on by Gary Kobs

Protein location: outer mitochondrial membrane (Yeast in vitro import assay)

Curado, S. et.al. (2010) Dis.Mod. Mech. 3, 486-95. PubMed ID 20483998.
Chemically mutagenized zebra fish were assayed for liver defects in their F3 progeny.This screen led to the identification of mutant called oliver. Oliver mutants have an o-shaped liver of a much deprived size due to the depletion of most of the hepatocytes. This mutation maps to the Tomm22gene which encodes a translocase of the outer membrane and thought to play an important role in protein import into mitochondria. Various Tomm22 mutants were expressed and used in a yeast in vitro import systemto determine if correct inserted into the yeast outer mitochondrial membrane.

Protein modification: hydroxylation

Serchov, T. et.al. (2010) J. Biol. Chem. 285, 21223-232. PubMed ID 20418372 .

Proline hydroxylation is also a vital component of hypoxia via hyposxia inducible factors. The cellular response to hypoxia involves the induction of the hypoxia-inducible factor considered to be the major transcription factor involved in gene regulation of hypoxia. This factor is hydroxylated by prolyl-hydroxase dolman proteins (PHDs). To investigate if a newly identified component of the hypoxia pathway (Elk3) is also hydroxylated, proteins were expressed +/- PHDs cofactors and protein mobility was measured via gel analysis.

Gene Experession: Programmed Ribosomal Frameshift

Kobayashi, Y. et.al. (2010) J. Biol. Chem. 285, 19776-784. PubMed ID 20427288.

Programmed -1 ribosomal frameshifting (PRF) is a distinctive mode of gene expression utilized by some viruses (HIV-1 for example). Recently a genome-wide screen demonstrated that down regulation of eukaryotic release factor (eRF1) inhibited HIV-1 replication. In order to characterize the dose dependent effect of eRF1, increasing amounts were expressed in the presence of dual luciferase reporter vectors harboring a HIV-1 PRF signal

Screening for Protein Activity Using Cell-Free Expression

Posted on by Gary Kobs

The analysis of functional protein typically requires lengthy laborious cell based protein expression that can be complicated by the lack of stability or solubility of the purified protein. Cell free protein expression eliminates the requirement for cell culture thus providing quick access to the protein of interest (1).

The HaloTag® Technology provides efficient, covalent and oriented protein immobilization of the fusion protein to solid surfaces (2).

A recent publication demonstrated the feasibility of using cell free expression and the HaloTag technology to express and capture a fusion protein for the rapid screening of protein kinase activity (3). The catalytic subunit of human cAMP dependent protein kinase was expressed in a variety of cell free expression formats as a HaloTag fusion protein. The immobilized cPKA fusion protein was assayed directly on magnetic beads in the active form and was shown to be inhibited by known PKA inhibitory compounds.

Therefore this unique combination of protein expression and capture technologies can greatly facilitate the process of activity screening and characterization of potential inhibitors

References
ResearchBlogging.org

  1. Zhao, K.Q. et al. (2007) Functional protein expression from a DNA based wheat germ cell-free system. J. Struc. Funct. Genomics. 8, 199-208.
  2. Los, G.V. and Wood, K. (2007) The HaloTag: A novel technology for cell imaging and protein analysis. Meth. Mol. Biol. 356, 195-208
  3. Leippe DM, Zhao KQ, Hsiao K, & Slater MR (2010). Cell-free expression of protein kinase a for rapid activity assays. Analytical chemistry insights, 5, 25-36 PMID: 20520741

6X His Protein Pulldowns: An Alternative to GST

Posted on by Gary Kobs

ResearchBlogging.orgPull-down assays probe interactions between a protein of interest that is expressed as fusion protein (e.g.,
(e.g., bait) and the potential interacting partners (prey).

In a pull-down assay one protein partner is expressed as a fusion protein (e.g., bait protein) in E. coli and then immobilized using an affinity ligand specific for the fusion tag. The immobilized
bait protein can then be incubated with the prey protein. The source of the prey protein depends on whether the experiment is designed to confirm an interaction or to identify new interactions. After a series of wash steps, the entire complex can be eluted from the affinity support using SDS-PAGE loading buffer or by competitive analyte elution, then evaluated by SDS-PAGE.

Successful interactions can be detected by Western blotting with specific antibodies to both the prey and bait proteins, or measurement of radioactivity from a [35S] prey protein. bait) and potential interacting partners (prey).

The most commonly used method to generate a bait protein is expression as a fusion protein contain a GST (glutathione-S transferase) tag in E. coli. This is followed by immobilization on particles that contain reduced glutathione, which binds to the GST tag of the fusion protein. The primary advantage of a GST tag is that it can increase the solubility of insoluble or semi-soluble proteins expressed in E. coli.

Among fusion tags, His-tag is the most widely used and has several advantages including: 1) It’s small in size, which renders it less immunogenically active, and often it does not need to be removed from the purified protein for downstream applications; 2) There are a large number of commercial vectors available for expressing His-tagged proteins; 3) The tag may be placed at either the N or C terminus; 4) The interaction of the His-tag does not depend on the tag structure, making it possible to purify otherwise insoluble proteins using denaturing conditions. Continue reading “6X His Protein Pulldowns: An Alternative to GST”

Trypsin: Innovative Applications

Posted on by Gary Kobs
3D model of protein and protease cleavage

Tryptic digestion of samples and subsequent analysis by mass spectrometry is a popular technique for the identification of proteins typically those related to interaction partners or biomarkers characterization. This powerful tool can also be used for less traditional experimental designs. Three examples are:

Continue reading “Trypsin: Innovative Applications”

Running A Victory Lap For Promega’s Bioluminescence Technologies

Posted on by Robert Deyes

Helping scientists design experiments and interpret data is what we do best at Promega Technical Services. This may mean spending time at the bench attempting to reproduce anomalous results or forming a team, perhaps with members of other departments, to brainstorm seemingly intractable experimental road blocks.  Still, for many of us nothing surpasses the experience of meeting these same scientists face to face whether it be on their home turf or at a booth during a tradeshow. PCArticle Continue reading “Running A Victory Lap For Promega’s Bioluminescence Technologies”

Optimized Wheat Germ Extract for High-Yield Protein Expression of Functional, Soluble Protein

Posted on by Gary Kobs
Wheat Germ Extract for high-yield protein expression

Cell-free protein synthesis has emerged as powerful alternative to cell based protein expression for functional and structural proteomics. The TNT® SP6 High-Yield Protein Expression System uses a high-yield wheat germ extract supplemented with SP6 RNA polymerase and other components. Coupling transcriptionaland translational activities eliminates the inconvenience of separate in vitro transcription and purification steps for the mRNA, while maintaining the high levels of protein expression (1).

Continue reading “Optimized Wheat Germ Extract for High-Yield Protein Expression of Functional, Soluble Protein”

Variations on the Two-Hybrid Assay

Posted on by Isobel Maciver
two-hybrid assays help fit molecules together like puzzle pieces image shows a puzzle

The use of reporter genes for simple analysis of promoter activity (promoter bashing) is a well known practice. However, there are many other elegant applications of reporter technologies. One such application is illustrated in the paper by Zheng et al., published in the Sept. 2008 issue of Cancer Research. These researchers from the Hormel Institute at the University of Minnesota showed that the cyclin-dependent kinase cdk3 phosphorylates the transcription factor ATF1 and enhances its transcriptional and transactivation activity. The observed cdk/ATF1 signaling was shown to have an important role in cell proliferation and transformation. To do this they used several variations of a reporter-based two-hybrid assay.

Continue reading “Variations on the Two-Hybrid Assay”