Purification of a viral coat protein by an engineered polyionic sequence

Affinity Tags in Protein Purification and Peptide Enrichment: An Overview

The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific toward particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications in proteins and peptides widen the application of affinity ligand-tag receptors pairs toward universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely the affinity tags and receptors employed on the production of recombinant fusion proteins, and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.

Isolation of secreted proteins from Drosophila ovaries and embryos through in vivo BirA-mediated biotinylation

The extraordinarily strong non-covalent interaction between biotin and avidin (kD = 10-14-10-16) has permitted this interaction to be used in a wide variety of experimental contexts. The Biotin Acceptor Peptide (BAP), a 15 amino acid motif that can be biotinylated by the E. coli BirA protein, has been fused to proteins-of-interest, making them substrates for in vivo biotinylation. Here we report on the construction and characterization of a modified BirA bearing signals for secretion and endoplasmic reticulum (ER) retention, for use in experimental contexts requiring biotinylation of secreted proteins. When expressed in the Drosophila female germline or ovarian follicle cells under Gal4-mediated transcriptional control, the modified BirA protein could be detected and shown to be enzymatically active in ovaries and progeny embryos. Surprisingly, however, it was not efficiently retained in the ER, and instead appeared to be secreted. To determine whether this secreted protein, now designated secBirA, could biotinylate secreted proteins, we generated BAP-tagged versions of two secreted Drosophila proteins, Torsolike (Tsl) and Gastrulation Defective (GD), which are normally expressed maternally and participate in embryonic pattern formation. Both Tsl-BAP and GD-BAP were shown to exhibit normal patterning activity. Co-expression of Tsl-BAP together with secBirA in ovarian follicle cells resulted in its biotinylation, which permitted its isolation from both ovaries and progeny embryos using Avidin-coupled affinity matrix. In contrast, co-expression with secBirA in the female germline did not result in detectable biotinylation of GD-BAP, possibly because the C-terminal location of the BAP tag made it inaccessible to BirA in vivo. Our results indicate that secBirA directs biotinylation of proteins bound for secretion in vivo, providing access to powerful experimental approaches for secreted proteins-of-interest. However, efficient biotinylation of target proteins may vary depending upon the location of the BAP tag or other structural features of the protein.

Polyionic Tags as Enhancers of Protein Solubility in Recombinant Protein Expression

Since the introduction of recombinant protein expression in the second half of the 1970s, the growth of the biopharmaceutical field has been rapid and protein therapeutics has come to the foreground. Biophysical and structural characterisation of recombinant proteins is the essential prerequisite for their successful development and commercialisation as therapeutics. Despite the challenges, including low protein solubility and inclusion body formation, prokaryotic host systems and particularly Escherichia coli, remain the system of choice for the initial attempt of production of previously unexpressed proteins. Several different approaches have been adopted, including optimisation of growth conditions, expression in the periplasmic space of the bacterial host or co-expression of molecular chaperones, to assist correct protein folding. A very commonly employed approach is also the use of protein fusion tags that enhance protein solubility. Here, a range of experimentally tested peptide tags, which present specific advantages compared to protein fusion tags and the concluding remarks of these experiments are reviewed. Finally, a concept to design solubility-enhancing peptide tags based on a protein’s pI is suggested.

Viruses and Virus-Like Particles in Biotechnology: Fundamentals and Applications

Although viruses are simple biological systems, they are capable of evolving highly efficient techniques for infecting cells, expressing their genomes, and generating new copies of themselves. It is possible to genetically manipulate most of the different classes of known viruses in order to produce recombinant viruses that express foreign proteins. Recombinant viruses have been used in gene therapy to deliver selected genes into higher organisms, in vaccinology and immunotherapy, and as important research tools to study the structure and function of these proteins.

Virus-like particles (VLPs) are multiprotein structures that mimic the organization and conformation of authentic native viruses but lack the viral genome. They have been applied not only as prophylactic and therapeutic vaccines but also as vehicles in drug and gene delivery and, more recently, as tools in nanobiotechnology.

In this chapter, basic and advanced features of viruses and VLPs are presented and their major applications are discussed. The different production platforms based on animal cell technology are explained, and their main challenges and future perspectives are explored. The implications of large-scale production of viruses and VLPs are discussed in the context of process control, monitoring, and optimization. The main upstream and downstream technical challenges are identified and discussed accordingly.

Salt-Dependent Aggregation and Assembly of E coli-Expressed Ferritin

Ferritin, with the primary function of iron storage, is a nearly ubiquitous protein found in most living organisms. Our recent investigations suggest that ferritin can assemble nanoparticles. So we use ferritin as a novel type of delivery vehicle for recombinant epitope vaccines. And, we found that ferritin form nonnative aggregates depended sensitively on NaCl concentrations. Here, we report that ferritin is an ion-sensitive protein and has the attribute of salt-dependent aggregation. Our results indicate that recombinant ferritin can be released as a soluble form from Escherichia coli at low NaCl concentrations (≤50 mmol/L). Moreover, this result affords us to confirm a proper self-assembling solution for soluble ferritin or other ferritin-based fusion proteins to assemble nanoparticles.

Challenges and opportunities in the purification of recombinant tagged proteins

The purification of recombinant proteins by affinity chromatography is one of the most efficient strategies due to the high recovery yields and purity achieved. However, this is dependent on the availability of specific affinity adsorbents for each particular target protein. The diversity of proteins to be purified augments the complexity and number of specific affinity adsorbents needed, and therefore generic platforms for the purification of recombinant proteins are appealing strategies. This justifies why genetically encoded affinity tags became so popular for recombinant protein purification, as these systems only require specific ligands for the capture of the fusion protein through a pre-defined affinity tag tail. There is a wide range of available affinity pairs "tag-ligand" combining biological or structural affinity ligands with the respective binding tags. This review gives a general overview of the well-established "tag-ligand" systems available for fusion protein purification and also explores current unconventional strategies under development.

Affinity tags in protein purification and peptide enrichment: an overview

The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific towards particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications on proteins and peptides widen the application of affinity ligand-tag receptor pairs towards universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely, the affinity tags and receptors employed on the production of recombinant fusion proteins and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.

Preparative purification of recombinant proteins: current status and future trends

Advances in fermentation technologies have resulted in the production of increased yields of proteins of economic, biopharmaceutical, and medicinal importance. Consequently, there is an absolute requirement for the development of rapid, cost-effective methodologies which facilitate the purification of such products in the absence of contaminants, such as superfluous proteins and endotoxins. Here, we provide a comprehensive overview of a selection of key purification methodologies currently being applied in both academic and industrial settings and discuss how innovative and effective protocols such as aqueous two-phase partitioning, membrane chromatography, and high-performance tangential flow filtration may be applied independently of or in conjunction with more traditional protocols for downstream processing applications.

Viruses and Virus-Like Particles in Biotechnology

Although viruses are simple biological systems, they are capable of evolving highly efficient techniques for infecting cells, expressing their genomes, and generating new copies of themselves. It is possible to genetically manipulate most of the different classes of known viruses in order to produce recombinant viruses that express foreign proteins. Recombinant viruses have been used in gene therapy to deliver selected genes into higher organisms, in vaccinology and immunotherapy, and as important research tools to study the structure and function of these proteins.

Virus-like particles (VLPs) are multiprotein structures that mimic the organization and conformation of authentic native viruses but lack the viral genome. They have been applied not only as prophylactic and therapeutic vaccines but also as vehicles in drug and gene delivery and, more recently, as tools in nanobiotechnology.

In this article, basic and advanced features of viruses and VLPs are presented and their major applications are discussed. The different production platforms based on animal cell technology are explained, and their main challenges and future perspectives are explored. The implications of large-scale production of viruses and VLPs are discussed in the context of process control, monitorization, and optimization. The main upstream and downstream technical challenges are identified and discussed accordingly.

Purification of Bionanoparticles

The recent demand for nanoparticulate products such as viruses, plasmids, protein nanoparticles, and drug delivery systems have resulted in the requirement for predictable and controllable production processes. Protein nanoparticles are an attractive candidate for gene and molecular therapy due to their relatively easy production and manipulation. These particles combine the advantages of both viral and non-viral vectors while minimizing the disadvantages. However, their successful application depends on the availability of selective and scalable methodologies for product recovery and purification. Downstream processing of nanoparticles depends on the production process, producer system, culture media and on the structural nature of the assembled nanoparticle, i.e., mainly size, shape and architecture. In this paper, the most common processes currently used for the purification of nanoparticles, are reviewed.

Zbasic—A novel purification tag for efficient protein recovery

A positively charged protein domain, Z(basic), can be used as a general purification tag to achieve efficient recovery of recombinantly produced target proteins using cation-exchange chromatography. To construct a protein domain usable for ion-exchange chromatography, the surface of protein Z was engineered to be highly charged, which allowed for selective capture of target proteins on a cation-exchanger at physiological pH values. Interestingly, the novel domain, denoted Z(basic), was shown to be selective also under denaturing conditions and could preferably be used for purification of proteins solubilised from inclusion bodies. Moreover, a flexible process for solid-phase refolding was developed, using Z(basic) as a reversible linker to the cation-exchanger resin. This procedure has the inherited advantage of combining purification and refolding into a single step and still enabling elution of a concentrated product in a suitable buffer. This article summarizes development and use of the Z(basic) tag in small and pilot-plant-scale downstream processing.

Towards the preparative and large-scale precision manufacture of virus-like particles

Virus-like particles (VLPs) are of interest in vaccination, gene therapy and drug delivery, but their potential has yet to be fully realized. This is because existing laboratory processes, when scaled, do not easily give a compositionally and architecturally consistent product. Research suggests that new process routes might ultimately be based on chemical processing by self-assembly, involving the precision manufacture of precursor capsomeres followed by in vitro VLP self-assembly and scale-up to required levels. A synergistic interaction of biomolecular design and bioprocess engineering (i.e. biomolecular engineering) is required if these alternative process routes and, thus, the promise of new VLP products, are to be realized.

Engineering of Escherichia coli to improve the purification of periplasmic Fab′ fragments: changing the pI of the chromosomally encoded PhoS/PstS protein

Escherichia coli is a widely used host for the heterologous expression of proteins of therapeutic and commercial interest. The scale and speed at which it can be cultured can result in the rapid generation of large quantities of product. However, to achieve low costs of production a simple and robust purification process is also required. The general factors that impact on the cost of a purification process are the scale at which a process can be performed, the cost of the purification matrix, and the number and complexity of the chromatographic steps employed. Purification of Fab' fragments of antibodies from the periplasm of E. coli using ion exchange chromatography can result in the co-purification of E. coli host proteins having similar functional pI: such as the periplasmic phosphate binding protein, PhoS/PstS. In such circumstances, an additional chromatographic step is required to separate Fab' from PhoS. Here, we change the functional pI of the chromosomally encoded PhoS/PstS to effect its non-purification with Fab' fragments, enabling the removal of an entire chromatographic step. This exemplifies the strategy of the modification of host proteins with the aim of simplifying the production of heterologous proteins.

Cell-type specific targeting and gene expression using a variant of polyoma VP1 virus-like particles

The variant VP1-Z of the polyomavirus coat protein VP1 has been recently described as an engineered fusion protein of VP1 and the antibody binding domain protein Z. This construct is able to specifically bind and functionally present antibodies on the surface of virus-like particles of VP1-Z. Here we demonstrate that with the binding of Herceptin, an antibody directed against the receptor tyrosine kinase ErbB2, a cell type-specific targeting was established. ErbB2-positive cell lines were transduced with different plasmids encoding eGFP or beta-galactosidase. With both reporter systems functional gene expression in transduced cells could be observed. The transduction was strictly dependent on the use of a ternary complex formed of VLPs of VP1-Z, Herceptin, and the reporter plasmid DNA. The use of single components or ErbB2-negative cell lines did not result in functional gene transfer. The transduction was also completely dependent on the use of chloroquine, a lysosomotropic reagent. This indicates that the complex is internalized by ErbB2-mediated endocytosis.

Assessment of cell type specific gene transfer of polyoma virus like particles presenting a tumor specific antibody Fv fragment

Application of delivery systems in cancer therapy is restricted as a result of the lack of cell specificity of the respective vectors. Recently, a vector system based on virus-like particles (VLPs) of modified polyoma-VP1 was described which were able to bind specifically a tumor-specific antibody fragment, thus directing the vector system towards tumor cells. The functional gene transfer using the VP1 variant VP1-E8C, coupled with the antibody fragment of the tumor-specific antibody B3 is described in this paper. The specific targeting of the antigen expressing cells was highly efficient as determined by fluorescence microscopy. However, only a low percentage of these cells showed a functional gene transfer. This discrepancy could be accounted for by a rather low capacity of the virus like particles to transport DNA and the mechanism of their internalization by the target cells, which led to a lysosomal degradation of the particles. These limitations could be surmounted partially in cell culture experiments, and the principles suitable for applying this vector system in vivo are discussed.

Applications of novel affinity cassette methods: use of peptide fusion handles for the purification of recombinant proteins

In this article, recent progress related to the use of different types of polypeptide fusion handles or 'tags' for the purification of recombinant proteins are critically discussed. In addition, novel aspects of the molecular cassette concept are elaborated, together with areas of potential application of these fundamental principles in molecular recognition. As evident from this review, the use of these concepts provides a powerful strategy for the high throughput isolation and purification of recombinant proteins and their derived domains, generated from functional genomic or zeomic studies, as part of the bioprocess technology leading to their commercial development, and in the study of molecular recognition phenomena per se. In addition, similar concepts can be exploited for high sensitivity analysis and detection, for the characterisation of protein bait/prey interactions at the molecular level, and for the immobilisation and directed orientation of proteins for use as biocatalysts/biosensors.

Polyionic fusion peptides function as specific dimerization motifs

The de novo design of a molecular adapter for directed association and covalent linkage of two polypeptides is presented. Using peptides containing charged amino acid residues and an additional cysteine residue (AlaCysLys(8) and AlaCysGlu(8)) we demonstrate that the electrostatic interaction promotes the association of two synthetic peptides and, subsequently, disulfide bond formation. The reaction depends on both the redox potential and on the ionic strength of the buffer. Varying the redox potential, the interaction of the peptides was quantified by a Delta G(0') of 6.6 +/- 0.2 kcal/mol. Heterodimerization of the peptides is highly specific, a competition of association by other cysteine containing compounds could not be observed. Two proteins comprising cysteine-containing polyionic fusion peptides, a modified Fab fragment and an alpha-glucosidase fusion, could be specifically conjugated by directed association and subsequent disulfide bond formation. Both proteins retain their functional characteristics within the bifunctional conjugate: enzymatic activity of the alpha-glucosidase and antigen-binding capacity of the Fab fragment are equivalent to the non-conjugated components.

Binding of external ligands onto an engineered virus capsid

The development of novel delivery systems for therapeutic substances includes targeting of the carriers to a specific site or tissue within the body of the recipient. This can be accomplished by appropriate receptor-binding domains and requires linking of these domains to the carrier. We have used recombinantly expressed polyomavirus-like particles as a model system and inserted the sequence of a WW domain into different surface loops of the viral capsid protein VP1. In one variant, the WW domain maintained its highly selective binding properties of proline-rich ligands and showed an increased affinity but also an accelerated association/dissociation equilibrium compared to the isolated WW domain, thus allowing a short-term coupling of external ligands onto the surface of the virus-like particles.

Conjugation of an antibody Fv fragment to a virus coat protein: cell-specific targeting of recombinant polyoma-virus-like particles

The development of cell-type-specific delivery systems is highly desirable for gene-therapeutic applications. Current virus-based vector systems show broad cell specificity, which results in the need to restrict the natural tropism of these viral systems. Here we demonstrate that tumour-cell-specific virus-like particles can be functionally assembled in vitro from recombinant viral coat protein expressed in Escherichia coli. The insertion of a negatively charged peptide in the HI loop of polyoma VP1 interferes with the binding of VP1 to the natural recognition site on mammalian cells and also serves as an adapter for the coupling of antibody fragments that contain complementary charged fusion peptides. A recombinant antibody fragment of the tumour-specific anti-(Lewis Y) antibody B3 could be coupled to the mutant VP1 by engineered polyionic peptides and an additional disulphide bond. With this system an entirely recombinant cell-specific delivery system assembled in vitro could be generated that transfers genes preferentially to cells presenting the tumour-specific antigen on the cell surface.

Coupling of antibodies via protein Z on modified polyoma virus-like particles

Therapeutic application of virus-based delivery systems often implies a change of the tropism of these vectors. This can be achieved by insertion of polypeptides (e.g., antibody fragments) in viral coat proteins. Such fusion proteins have only been used in viral vectors so far and, as part of a virus, they have not been available for a detailed biophysical characterization. We analyzed a fusion protein called VP1-Z, which is based on the polyoma virus coat protein VP1 and protein Z. Protein Z is an engineered antibody-binding domain derived from protein A from Staphylococcus aureus. The fusion VP1-Z was constructed by insertion of protein Z in the HI-loop of VP1. As wild-type VP1, VP1-Z formed pentameric capsomers and assembled to VLPs in vitro. The stability of these particles was very similar compared to that of VLPs of wild-type VP1. Protein Z was fully structured in the fusion protein and was still capable of binding antibodies on the surface of VLPs of VP1-Z. Using this fusion protein, we could change the tropism of polyoma VLPs toward cells presenting on their surface the antigen of the coupled antibody.