Protein Purification Core

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

The staff of the Protein Purification Core (PPC) use a number of techniques for successful protein production. The PPC has access to a wide variety of tools for the expression of recombinant protein in bacteria (our primary expression system), including many types of plasmid expression vectors and specialized bacterial strains. There is a rather large collection of strains to choose from, with genetic defects that influence proteolytic activity, mRNA stability, membrane permeability, and intracellular redox potential. In addition, there are strains that overproduce protein disulfide isomerase, molecular chaperones, transfer RNAs, and redox enzymes for co-expression with target proteins. There is an equally large and diverse collection of bacterial plasmid vectors for recombinant protein expression. Many of these use Gateway cloning technology (Thermo Fisher Scientific), making them quick and easy to use. The PPC staff has experience with all of the major regulatory systems (e.g., T7, tac, pBAD, trc, lambda PL, etc.) and various formats for the production of recombinant proteins (untagged or fused to MBP, GST, NusA, thioredoxin, Sumo, His-tag, Arg-tag, FLAG-tag, biotin acceptor peptide, Strep Tag II, etc.) to make full use of these reagents. The PPC has also established an insect cell protein production facility to compliment its bacterial production capability, using both the Bac-to-Bac baculovirus expression system (Invitrogen) and the Drosophila expression system (Thermo Fisher Scientific). Like most bacterial production, the insect cell facility utilize Gateway cloning technology to maximize productivity. The PPC plans to evaluate other expression systems as time permits. One of these, the flashBAC baculovirus expression system of Oxford Expression Technologies, is on the list. Indications are that this system may be valuable for secretory and membrane-bound protein production, and may be a good complement to our current insect cell expression systems. Similarly, in collaboration with the Protein Engineering Core of the Center for Structural Biology (formally the Protein Engineering Section), the PPC has evaluated a new series of baculovirus expression cassettes designed to enhanced secretion of recombinant proteins from baculovirus-infected insect cells. This study is ongoing and demonstrates that the new expression cassettes work remarkably well. The PPC will incorporated this new technology into our insect cell protein production tool kit. Finally, and most important, the PPC is currently developing mammalian cell expression for the production of proteins unsuitable for bacterial or insect cell systems. We will use both Gateway and Lentivirus cloning and expression strategies to accomplish this goal. The PPC personnel are experienced with all standard chromatography techniques required for protein purification. The core maintains a full array of supplies necessary for ion exchange, hydrophobic interaction, lectin, hydroxyapatite, dye, size exclusion, and affinity chromatography. Materials for IMAC and chromatofocusing are also on hand. In addition to purification technology, the staff is very knowledgeable of methods required to characterize recombinant protein products. Among those used are gel electrophoresis and isoelectric focusing, mass spectroscopy, western analysis, N-terminal sequencing, dynamic light scattering and analytical ultracentrifugation, and circular dichroism spectroscopy. For structural studies, the PPC has in place standard operating procedures for the production of isotopically enriched proteins for heteronuclear nuclear magnetic resonance experiments and selenomethionine-substituted proteins for crystallography. Methods have been established for bacteria that eliminate the need to change strain by manipulating the medium formulation and induction parameters, and produce recombinant protein at levels equivalent to wild-type expression. For those proteins that fail to crystallize, the core can perform limited proteolysis as a way to identify potential structural domains, providing the Center for Structural Biology investigator additional avenues for structural studies. This method has been extensively used both analytically, and on a preparative scale to produce structural domains that can be purified using conventional chromatography. The core produces and maintains five different types of tobacco etch virus (TEV) protease (catalytic domain) that are used by the Center for Structural Biology (and others in the CCR) for in vitro cleavage of fusion proteins that contain an intervening protease recognition sequence. Available are an N-terminal heptahistidine-tagged TEV protease, an untagged TEV protease, an N-terminal heptahistidine-tagged TEV protease with a mutation that relaxes the amino acid requirement at the P1' position in the protease recognition sequence, an N-terminal and C-terminal polyhistidine-tagged TEV protease, and a maltose binding protein-TEV protease fusion protein. All contain a mutation that minimizes autoinactivation. Each has its advantage depending on the design of the protein purification scheme. Similarly, the core produces and maintains two types of tobacco vein mottling virus (TVMV) protease (catalytic domain) also used for in vitro cleavage of fusion proteins. These are available as an N-terminal hexahistidine-tagged TVMV protease and an untagged TVMV protease. The protease recognition site is different from the TEV protease site and allows the use of both recognition sequences in a single fusion protein. As an alternative to these potyvirus proteases, the PPC has purified the human rhinovirus 3C protease (i.e., PreScission protease) using bacterial expression plasmids obtained from Arie Geerlof (Helmholtz Center Munich, Institute of Structural Biology, Neuherberg, Germany). Both the N-terminal hexahistidine tagged protease and the GST-3C protease fusion protein have good activity even at 4C and will be quite useful in cleaving fusion proteins produced in several commercial vectors such as the pGEX-P series, pTriEx-9 and pET-47b(+). The core has also purified untagged 3C protease by cleavage of the GST fusion with thrombin. This version is currently being characterized. In addition, the PPC has also purified the amidase Peptide-N-Glycosidase F and the hydrolases endo-beta-N-acetylglucosaminidase H and endo-beta-N-acetylglucosaminidase F1 using bacterial expression plasmids obtained from Daniel Leahy (Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland). These enzymes will be invaluable at removing asparagine-linked oligosaccharide side chains from glycoproteins produced by our insect cell and mammalian cell production facility, which often impede the crystallization process. Plans to expand our repertoire to include other glycosylhydrolases is underway as time permits. Recently the PPC has obtained from the Protein Engineering Core a series of expression plasmids producing a number of DARPins in various formats. These particular DARPins are specific for MBP and have been shown to enhance crystallization of MBP fusion proteins. In addition, an expression plasmid producing an MBP-specific monobody has been obtained (also from Protein Engineering Core) which similarly enhances crystallization of MBP fusion proteins. We have completed the purification of three MBP-specific DARPins and the MBP-specific monobody. Once tested, the proteins will be available to all members of the Center for Structural Biology. For FY2021, as part of our research support to the Center for Structural Biology, the PPC has completed 28 cloning projects and performed 59 protein purifications. In addition 18 insect cell protein productions and 12 mammalian protein productions at the pilot and preparative levels were completed.