Chromatofocusing of N-terminally processed forms of proteins. Isolation and characterization of two forms of interleukin-1 beta and of bovine growth hormone

N-Terminal Methionine Processing

Protein synthesis is initiated by methionine in eukaryotes and by formylmethionine in prokaryotes. N-terminal methionine can be co-translationally cleaved by the enzyme methionine aminopeptidase (MAP). When recombinant proteins are expressed in bacterial and mammalian expression systems, there is a simple universal rule that predicts whether the initiating methionine will be processed by MAP based on the size of the residue adjacent (penultimate) to the N-methionine. In general, if the side chains of the penultimate residues have a radius of gyration of 1.29 Å or less, methionine is cleaved. © 2017 by John Wiley & Sons, Inc.

Overview of the purification of recombinant proteins

When the first version of this unit was written in 1995, protein purification of recombinant proteins was based on a variety of standard chromatographic methods and approaches, many of which were described and mentioned throughout Current Protocols in Protein Science. In the interim, there has been a shift toward an almost universal usage of the affinity or fusion tag. This may not be the case for biotechnology manufacture where affinity tags can complicate producing proteins under regulatory conditions. Regardless of the protein expression system, questions are asked as to which and how many affinity tags to use, where to attach them in the protein, and whether to engineer a self-cleavage system or simply leave them on. We will briefly address some of these issues. Also, although this overview focuses on E.coli, protein expression and purification, other commonly used expression systems are mentioned and, apart from cell-breakage methods, protein purification methods and strategies are essentially the same.

Preparation of Soluble Proteins from Escherichia coli

Purification of human IL-1β is used in this unit as an example of the preparation of a soluble protein from E. coli. Bacteria containing IL-1β are lysed, and IL-1 β in the resulting supernatant is purified by anion-exchange chromatography, salt precipitation, and cation-exchange chromatography, and then concentrated. Finally, the IL-1 β protein is applied to a gel-filtration column to separate it from remaining higher- and lower-molecular-weight contaminants, the purified protein is stored frozen or is lyophilized. The purification protocol described is typical for a protein that is expressed in fairly high abundance (i.e., >5% total protein) and accumulates in a soluble state. In addition, the purification procedure serves as an example of how to use classical protein purifications methods, which may also be used in conjunction with the affinity-based methods now more commonly used.

Folding and Purification of Insoluble (Inclusion Body) Proteins from Escherichia coli

Heterologous expression of recombinant proteins in E. coli often results in the formation of insoluble and inactive protein aggregates, commonly referred to as inclusion bodies. To obtain the native (i.e., correctly folded) and hence active form of the protein from such aggregates, four steps are usually followed: (1) the cells are lysed, (2) the cell wall and outer membrane components are removed, (3) the aggregates are solubilized (or extracted) with strong protein denaturants, and (4) the solubilized, denatured proteins are folded with concomitant oxidation of reduced cysteine residues into the correct disulfide bonds to obtain the native protein. This unit features three different approaches to the final step of protein folding and purification. In the first, guanidine·HCl is used as the denaturant, after which the solubilized protein is folded (before purification) in an "oxido-shuffling" buffer system to increase the rate of protein oxidation. In the second, acetic acid is used to solubilize the protein, which is then partially purified by gel filtration before folding; the protein is then folded and oxidized by simple dialysis against water. Thirdly, folding and purification of a fusion protein using metal-chelate affinity chromatography are described.

Overview of the purification of recombinant proteins produced in Escherichia coli

The updated version of this unit presents an overview of recombinant protein purification with special emphasis on proteins expressed in E. coli. The first section deals with information pertinent to protein purification that can be derived from translation of the cDNA sequence. This is followed by a discussion of common problems associated with bacterial protein expression. A flow chart summarizes approaches for establishing solubility and localization of bacterially produced proteins. Purification strategies for both soluble and insoluble proteins are also reviewed. A section on glycoproteins produced in bacteria in the nonglycosylated state is included to emphasize that, although they may not be useful for in vivo studies, such proteins are well suited for structural studies. Finally, protein handling, scale and aims of purification, and specialized equipment needed for recombinant protein purification and characterization are discussed. The methodologies and approaches described here are essentially suitable for laboratory-scale operations.

Preparation of soluble proteins from Escherichia coli

Purification of human IL-1beta is used in this unit as an example of the preparation of soluble proteins from E. coli. Bacteria containing IL-1beta are lysed, and IL-1 beta in the resulting supernatant is purified by anion-exchange chromatography, salt precipitation and cation-exchange chromatography, and then concentrated. Finally, the IL-1 beta protein is applied to a gel-filtration column to separate it from remaining higher- and lower-molecular-weight contaminants, the purified protein is stored frozen or is lyophilized. The purification protocol described is typical for a protein that is expressed in fairly high abundance (i.e., >5% total protein) and accumulates in a soluble state.

The additional methionine residue at the N-terminus of bacterially expressed human interleukin-2 affects the interaction between the N- and C-termini

To gain insight into the origin of the difference in isoelectric point (pI) values for wild-type human interleukin-2 (IL-2) and IL-2 with an additional methionine residue at the N-terminus (Met-IL-2), conformational properties of the two molecular forms of IL-2 were compared by utilizing 1H NMR spectroscopy. Although overall conformations were conserved in the two forms, the presence of the additional methionine residue at the N-terminus induced chemical shift changes for residues Ala1 to Lys8 as well as for Thr133, which is located at the C-terminus. These observations indicate that the effect of the additional methionine residue is confined to the N- and C-terminal regions and unveil the existence of an interaction between the N- and C-terminal regions. The chemical shift change observed for Thr133 can be interpreted in terms of a change in pKa of the C-terminal carboxyl group, which interacts differently with the N-terminal amino group in the two forms of IL-2. It seems to be reasonable to conclude that the difference in pI values for the two forms of IL-2 is the consequence of the different interactions between the C- and N-terminal residues.

Somatotropin delivery to farmed animals

Bovine somatotropin (bST) is marketed worldwide for increased milk production in cows while porcine somatotropin (pST) is approved in one country for increasing growth in swine. Somatotropin physicochemical properties, animal production method limitations and the need for cost effectiveness each contribute to the type of formulation developed. Various somatotropin physicochemical properties made formulation design difficult: heat and enzyme lability, tendency to aggregate, pH dependent solubility and stability, complicated degradation pathways and rapid in vivo clearance. The main problem of improving chemical and physical stability has been partially solved using certain excipients and vehicles. Formulations design to prolong somatotropin release include implants (matrix, osmotic), oleaginous suspensions and microparticles. This article presents the current status of somatotropin delivery in farmed animals, reviews the challenges encountered with formulation development, summarizes formulation approaches and discusses future somatotropin uses.

Separation of interleukins by a preparative chromatofocusing-like method

A chromatofocusing-like method used in the large-scale separation of deamidated from amidated recombinant human interleukin-1 alpha (amino acids 117-271), derived from Escherichia coli, is described. Two major protein species having isoelectric points (pI) of approximately 5.3 and 5.1 were separated by high-performance liquid chromatography using a sulfopropyl strong cation-exchange column. Unlike standard chromatofocusing technique, this method does not use carrier ampholytes during gradient separation of proteins, nor does it employ increased ionic strength for protein elution, the usual method for performing standard ion-exchange chromatography. N-Terminal sequence analysis of the protein with a pI of 5.3 revealed an Asn residue at position 32 as predicted by the cDNA sequence. The pI 5.1 species showed an Asp residue at the same position as a result of deamidation of Asn. This method was also used in the large-scale separation of N-Met from des-Met recombinant human interleukin-1 beta.

Purification, partial characterization, and heterologous radioimmunoassay of growth hormone (cGH) in red deer

Red deer growth hormone (cGH; 3.3 mg) was purified from an aqueous extract of seven pituitary glands (4.01 g wet weight) by preparative gel filtration on Sephadex G-100, gel filtration on Sephadex G-100 SF, and anion exchange chromatography on DEAE-Sepharose CL-6B. Purified cGH gave a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a molecular weight under reducing conditions of 20,000 Da and gave a single peak on reverse-phase high-performance liquid chromatography. N-Terminal amino acid determination of 42 residues gave a sequence identical with those published for bovine and ovine GH. In a radioreceptor assay based on binding of iodinated recombinant bovine GH (rbGH) to liver microsomes prepared from a pregnant ewe, cGH was equipotent with an ovine GH (oGH) standard. In an oGH radioimmunoassay, cGH diluted in parallel with oGH and rbGH. Using this assay plasma GH concentrations were determined in adult nonpregnant red deer hinds over a 12-month period. There was a significant seasonality in plasma GH concentrations with concentrations consistently low between mid-May and mid-September. This is the period when voluntary food intake and liveweight gain are greatest. It is suggested that in the presence of low plasma GH concentrations nutrients may be diverted toward lipogenesis and hence promote fat deposition.

Isolation and characterization of recombinant eel growth hormone expressed in Escherichia coli

To obtain information about the microheterogeneity of recombinant protein, recombinant eel growth hormone II (EGH) analogues expressed in Escherichia coli were isolated and characterized. The modification was classified into three types: monodeamidation of Asn, oxidation of Met and N-terminal formylation. Monodeamidated EGH was isolated by ion-exchange chromatography. The major deamidation site (Asn 147) was determined by peptide mapping using the substrate specificity of trypsin. Oxidized EGH and N-terminal-formylated EGH were isolated by reversed-phase high-performance liquid chromatography. Oxidized EGH was identified by amino acid composition analysis and N-terminal-formylated peptide by mass spectrometry.

Preparation, characterization and application of interleukin-1 beta mutant proteins with surface-accessible cysteine residues

Two mutants of interleukin-1 beta (K27C and K138C) were produced using site-specific mutagenesis in which lysine residues at positions 27 and 138 of the mature protein sequence were substituted by cysteine residues. The conformations of the mutant proteins were studied by 1H-NMR spectroscopy and shown to be similar to the wild-type protein. The receptor-binding affinity and biological activity of K27C and K138C were also similar to wild-type protein. The substituted cysteines in both mutant proteins were shown to be solvent-accessible as judged by their reactivity towards sulfhydryl reagents. As the wild-type protein contains two cysteines, which are both solvent-inaccessible in the native state, the mutants offer the opportunity to introduce probes in a sequence-specific manner via reaction with sulfhydryl groups. Examples of this are described in which the K138C was disulfide-linked to phycobiliproteins. The highly fluorescent conjugates had similar receptor-binding affinities to that of the wild-type unconjugated protein and were found suitable for flow-cytometric analysis.

N-terminal-methionylated interleukin-1 beta has reduced receptor-binding affinity

The receptor-binding affinity of recombinant-derived interleukin-1 beta containing unprocessed N-terminal methionine (MAPV-) was 10-fold lower than protein containing the authentic N-terminal sequence (APV-). Structural analysis of the methionylated and non-methionylated proteins by NMR spectroscopy detected no (or minor) conformational differences. The differences in binding affinity, therefore, suggest that the additional N-terminal methionine causes a small, direct or indirect, perturbation of the receptor-binding region.

N-terminal methionine-specific peptidase in Salmonella typhimurium

Crude extracts of a multiply peptidase-deficient strain of Salmonella typhimurium contain an aminopeptidase that specifically removes N-terminal methionine from peptides. This activity shows pronounced specificity for the peptide's second amino acid. Methionine is removed from peptides with alanine, threonine, or glycine in this position but not when the second amino acid is leucine or methionine. The activity is stimulated by Co2+ and is inhibited by EDTA. Mutations that lead to overproduction (up to 30-fold) of the activity have been obtained by selecting for growth on Met-Gly-Gly as a methionine source. These mutations map at approximately 3 map units, phage P22 cotransducible with leu. The overproducer mutations are dominant to wild type, and duplication of the wild-type allele of the locus leads to a gene dosage effect on peptidase levels. This suggests that the locus of the overproducer mutations may be the structural gene for the peptidase. NaDodSO4/PAGE shows an increased level of a single protein (34 kDa) in the overproducer mutant. This protein is highly enriched in a purified preparation of the peptidase. The specificity of this enzyme suggests that it is involved in the cleavage of methionine from newly synthesized peptide chains. This activity can specifically remove methionine from the N terminus of a completed protein. Treatment of purified, unprocessed (N-terminal methionine) interleukin 1 beta with the purified peptidase results in removal of N-terminal methionine with no additional alterations. N-terminal processing of at least this protein can occur after translation is complete. We propose to call this enzyme peptidase M (methionine-specific aminopeptidase).

Preparation and characterization of bovine growth hormones produced in recombinant Escherichia coli

Two analogues of bovine growth hormone (BGH) have been produced in Escherichia coli by recombinant DNA techniques. In analogue Delta-1, the N-terminal alanine residue of the full-length bovine sequence is replaced by methionine. In analogue Delta-9, which is expressed at much higher levels than is Delta-1, the full-length bovine sequence is truncated at the N-terminus by eight residues and there is a serine-for-glycine substitution in the first position of the truncated protein. Both analogues, which were characterized by isoelectric focusing (i.e.f.), polyacrylamide-gel electrophoresis in the presence of SDS (SDS/PAGE), amino acid analysis and N-terminal amino acid sequence determination using combined g.l.c.-m.s., are compared with BGH isolated from pituitaries. In contrast with pituitary-derived BGH, the recombinant-derived proteins are homogeneous on SDS/PAGE and on i.e.f. In a radioimmunoassay, a radioreceptor assay and a bioassay in vivo (rat tibia), Delta-9 BGH showed very similar characteristics to the pituitary-derived hormone. Similar results have also been obtained with the Delta-1 analogue.