Refolding and single-step purification of porcine interferon-gamma from Escherichia coli inclusion bodies. Conditions for reconstitution of dimeric IFN-gamma

Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.

Expression of bioactive porcine interferon-gamma by recombinant Lactococcus lactis

Lactococcus lactis is an immunomodulator and candidate live mucosal delivery vehicle for vaccine antigens and for biologically active molecules, including immunoregulatory cytokines such as interferon-gamma (IFN-gamma). To provide a tool for investigating downregulation of allergic predisposition of pigs to experimental food allergy, porcine IFN-gamma was cloned and expressed as a fusion protein with the usp45 secretion signal. Immunoblot analysis with polyclonal anti-pIFN-gamma-antibody demonstrated that the recombinant porcine IFN-gamma (rpIFN-gamma) protein was expressed in the L. lactis transformants as a secreted product. Activity of rpIFN-gamma was confirmed by ability to upregulate class II major histocompatibility complex (MHC) on cells of the porcine monocytic cell line 3D4/31. The L. lactis producing biologically active rpIFN-gamma will be used to investigate its possible ability to modulate the allergic immune response phenotype of pigs.

Increased yield of high purity recombinant human interferon-gamma utilizing reversed phase column chromatography

Increasing therapeutic applications for recombinant human interferon-gamma (rhIFN-gamma), an antiviral proinflammatory cytokine, has broadened interest in optimizing methods for its production and purification. We describe a reversed phase chromatography (RPC) procedure using Source-30 matrix in the purification of rhIFN-gamma from Escherichia coli that results in a higher yield than previously reported. The purified rhIFN-gamma monomer from the RPC column is refolded in Tris buffer. Optimal refolding occurs at protein concentrations between 50 and 100 microg/ml. This method yields greater than 90% of the dimer form with a yield of 40 mg/g cell mass. Greater than 99% purity is achieved with further purification over a Superdex G-75 column to obtain specific activities of from 2 x 10(7) to 4 x 10(7)IU/mg protein as determined via cytopathic antiviral assay. The improved yield of rhIFN-gamma in a simple chromatographic purification procedure promises to enhance the development and therapeutic application of this biologically potent molecule.

Preparation of a monolithic column for weak cation exchange chromatography and its application in the separation of biopolymers

A procedure for the preparation of a monolithic column for weak cation exchange chromatography was presented. The structure of the monolithic column was evaluated by mercury intrusion. The hydrodynamic and chromatographic properties of the monolithic column--such as back pressures at different flow rates, effects of pH on protein retention, dynamic loading capacity, recovery, and stability--were determined under conditions typical for ion-exchange chromatography. The prepared monolithic column might be used in a relatively broad pH range from 4.0 to 12.0 and exhibited an excellent separation to five proteins at the flow rates of both 1.0 and 8.0 mL/min, respectively. In addition, the prepared column was first used in the purification and simultaneous renaturation of recombinant human interferon gamma (rhIFN-gamma) in the extract solution with 7.0 mol/L guanidine hydrochloride. The purity and specific bioactivity of the purified rhIFN-gamma in only one chromatographic step were obtained to be 93% and 7.8 x 10(7) IU/mg, respectively.

Cloning and expression of interferon-alpha/gamma from a domestic porcine breed and its effect on classical swine fever virus

To further evaluate the clinical impact of recombinant PoIFN-alpha/gamma, PoIFN-alpha/gamma genes from a Chinese domestic big-white porcine breed were cloned using PCR, and expressed in a high-level prokaryotic system. The antiviral activities of rPoIFN-alpha/gamma on vesicular stomatitis virus (VSV), porcine reproductive and respiratory syndrome virus (PRRSV), and classical swine fever virus (CSFV) were investigated in different cell lines. The cloned PoIFN-alpha gene encodes a protein of 166 amino acids and has been named PoIFN-alphac. In a comparison of PoIFN-alphac with reported PoIFN-alphaI genes, eight amino acid substitutions at positions 43 (F to L), 78 (N to D), 86 (Y to C), 104 (A to V), 118 (R to L), 128 (T to P), 151 (S to V), and 156 (R to T) were observed, and resulted in no potential N-glycosylation site in the deduced PoIFN-alpha amino acid sequences. In contrast to PoIFN-alphac, one nucleotide substitution was found at position 462 (A to G), hence 0.1% synonymity is specific for the PoIFN-gamma gene. Both PoIFN-alphac and PoIFN-gamma genes were inserted into a prokaryotic vector pQE30, and expressed in E. coli M15 (pREP4) or SC11103 (pREP4) with the N-terminal six consecutive histidine residues, respectively. rPoIFN-alphac and rPoIFN-gamma proteins were detected by SDS-PAGE and Western blotting analysis at 20.7 and 18.0 kDa, respectively. In addition, the rPoIFN-alphac and rPoIFN-gamma protein were purified using Ni-NTA metal-affinity chromatography, and their anti-VSV, anti-PRRSV, and anti-CSFV activities were surveyed in homologous and heterologous cell lines. The results suggested that rPoIFN-alpha and rPoIFN-gamma could inhibit classical swine fever virus and other important viral pathogens in different cell lines.

Link between protein-solvent and weak protein-protein interactions gives insight into halophilic adaptation

Malate dehydrogenase (Hm MalDH) from the extreme halophile Haloarcula marismortui is a very acidic protein with extensive ion binding properties. It is a good model for the study of solvation-solubility relationships. We measured the small-angle neutron or X-ray scattering profiles of folded and stable Hm MalDH at various protein concentrations and derived the second virial coefficients A(2). In NaCl, CsCl, KF, KCl, and NaCH(3)CO(2), A(2) values are positive, indicating globally repulsive protein-protein interactions. Below 1 M MgCl(2) and MgSO(4) or above 2 M (NH(4))(2)SO(4), A(2) rapidly decreases. From structure factor modeling with DLVO (Derjaguin, Landau, Verwey, and Overbeek)-like potentials, an effective diameter of 80-82 A is found for the protein particle in solution, compatible with its structural dimensions; the effective charge of the particle is undefined because of the high salt concentration. The strong variations of the protein-protein interaction are correlated to an attractive potential whose depth evolves with the salinity but in an opposite way in Mg salts and (NH(4))(2)SO(4). A repulsive Donnan term, corresponding to counterion dissociation, and an attractive term related to previously measured preferential salt binding parameters are discussed from well-established thermodynamics considerations and qualitatively account for the behavior of the protein-protein interactions in the various solutions. Because a solvation shell with a composition different from bulk induces protein-protein attraction, molecular adaptation to high salt would be directed to allow protein-salt interactions in order to avoid water or salt enrichment at the surface of the protein and thus preserve its solubility.

The conserved helix C region in the superfamily of interferon-gamma /interleukin-10-related cytokines corresponds to a high-affinity binding site for the HSP70 chaperone DnaK

HSP70 chaperones mediate protein folding by ATP-dependent interaction with short linear peptide segments that are exposed on unfolded proteins. The mode of action of the Escherichia coli homolog DnaK is representative of all HSP70 chaperones, including the endoplasmic reticulum variant BiP/GRP78. DnaK has been shown to be effective in assisting refolding of a wide variety of prokaryotic and eukaryotic proteins, including the alpha-helical homodimeric secretory cytokine interferon-gamma (IFN-gamma). We screened solid-phase peptide libraries from human and mouse IFN-gamma to identify DnaK-binding sites. Conserved DnaK-binding sites were identified in the N-terminal half of helix B and in the C-terminal half of helix C, both of which are located at the IFN-gamma dimer interface. Soluble peptides derived from helices B and C bound DnaK with high affinity in competition assays. No DnaK-binding sites were found in the loops connecting the alpha-helices. The helix C DnaK-binding site appears to be conserved in most members of the superfamily of interleukin (IL)-10-related cytokines that comprises, apart from IL-10 and IFN-gamma, a series of recently discovered small secretory proteins, including IL-19, IL-20, IL-22/IL-TIF, IL-24/MDA-7 (melanoma differentiation-associated gene), IL-26/AK155, and a number of viral IL-10 homologs. These cytokines belong to a relatively small group of homodimeric proteins with highly interdigitated interfaces that exhibit the strongly hydrophobic character of the interior core of a single-chain folded domain. We propose that binding of DnaK to helix C in the superfamily of IL-10-related cytokines may constitute the hallmark of a novel conserved regulatory mechanism in which HSP70-like chaperones assist in the formation of a hydrophobic dimeric "folding" interface.

Construction and deconstruction of bacterial inclusion bodies

Bacterial inclusion bodies (IBs) are refractile aggregates of protease-resistant misfolded protein that often occur in recombinant bacteria upon gratuitous overexpression of cloned genes. In biotechnology, the formation of IBs represents a main obstacle for protein production since even favouring high protein yields, the in vitro recovery of functional protein from insoluble deposits depends on technically diverse and often complex re-folding procedures. On the other hand, IBs represent an exciting model to approach the in vivo analysis of protein folding and to explore aggregation dynamics. Recent findings on the molecular organisation of embodied polypeptides and on the kinetics of inclusion body formation have revealed an unexpected dynamism of these protein aggregates, from which polypeptides are steadily released in living cells to be further refolded or degraded. The close connection between in vivo protein folding, aggregation, solubilisation and proteolytic digestion offers an integrated view of the bacterial protein quality control system of which IBs might be an important component especially in recombinant bacteria.

Protein disulfide isomerase-mediated cell-free assembly of recombinant interleukin-12 p40 homodimers

Interleukin-12 (IL-12) is a heterodimeric cytokine composed of two subunits, p35 and p40. The disulfide-linked homodimer (p40)2 has been shown to be a potent IL-12 antagonist. In the present study, the p40 subunit was refolded from Escherichia coli inclusion bodies. Formation of (p40)2 was greatly increased in a redox buffer containing reduced and oxidized glutathione, but was not significantly affected by the cosolvents urea, GdnHCl or Chaps. While protein disulfide isomerase (PDI), GroEL/ES or DnaK/J/GrpE suppressed aggregation during refolding of p40, only DnaK/J/GrpE and PDI enhanced p40 dimerization. Oxidative assembly of p40 into (p40)2 by PDI, but not suppression of aggregation, was strongly dependent on inclusion of BSA in the refolding buffer. It is concluded that both chaperone-like and disulfide isomerase effects are essential for correct folding of p40 into dimers.

Refolding and characterization of rat liver methionine adenosyltransferase from Escherichia coli inclusion bodies

Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine, the major methyl donor for transmethylation reactions. Attempts to perform structural studies using rat liver MAT have met with problems because the protein purified from cellular extracts is heterogeneous. Overexpression of the enzyme in Escherichia coli rendered most of the protein as inclusion bodies. These aggregates were purified by specific washes using urea and Triton X-100 and used for refolding. Maximal activity was obtained when chaotropic solubilization included the structural cation Mg(2+), the protein concentration was kept below 0.1 mg/ml, and denaturant removal was carried out in a two-step process, namely, a fast dilution followed by dialysis in the presence of 10 mM DTT or GSH/GSSG redox buffers. Refolding by this procedure generated the oligomeric forms, MAT I and III, which were basically indistinguishable from the purified rat liver forms in secondary structure and catalytic properties.

A step toward the prediction of the fluorescence lifetimes of tryptophan residues in proteins based on structural and spectral data

A method is presented that allows the calculation of the lifetimes of tryptophan residues on the basis of spectral and structural data. It is applied to two different proteins. The calcium binding protein from the sarcoplasm of the muscles of the sand worm Nereis diversicolor (NSCP) changes its conformation upon binding of Ca2+ or Mg2+. NSCP contains three tryptophan residues at position 4, 57, and 170, respectively. The fluorescence lifetimes of W57 are investigated in a mutant in which W4 and W170 have been replaced. The time resolved fluorescence properties of W57 are linked to its different microconformations, which were determined by a molecular dynamics simulation map. Together with the determination of the radiative rate constant from the wavelength of maximum intensity of the decay associated spectra, it was possible to determine an exponential relation between the nonradiative rate constant and the distance between the indole CE3 atom and the carbonyl carbon of the peptide bond reflecting a mechanism of electron transfer as the main determinant of the value for the nonradiative rate constant. This result allows the calculation of the fluorescence lifetimes from the protein structure and the spectra. This method was further tested for the tryptophan of Ha-ras p21 (W32) and for W43 of the Tet repressor, which resulted in acceptable values for the predicted lifetimes.

High pressure fosters protein refolding from aggregates at high concentrations

High hydrostatic pressures (1-2 kbar), combined with low, nondenaturing concentrations of guanidine hydrochloride (GdmHCl) foster disaggregation and refolding of denatured and aggregated human growth hormone and lysozyme, and beta-lactamase inclusion bodies. One hundred percent recovery of properly folded protein can be obtained by applying pressures of 2 kbar to suspensions containing aggregates of recombinant human growth hormone (up to 8.7 mg/ml) and 0.75 M GdmHCl. Covalently crosslinked, insoluble aggregates of lysozyme could be refolded to native, functional protein at a 70% yield, independent of protein concentration up to 2 mg/ml. Inclusion bodies containing beta-lactamase could be refolded at high yields of active protein, even without added GdmHCl.

Recombinant porcine IFN-gamma potentiates the secondary IgG and IgA responses to an inactivated suid herpesvirus-1 vaccine and reduces postchallenge weight loss and fever in pigs

The effect of recombinant porcine interferon-gamma (IFN-gamma) on the immunogenicity in vivo of inactivated suid herpesvirus-1 (SHV-1, Phylaxia strain) was studied applying two successive i.m. immunizations. The animals were injected with inactivated virus alone or inactivated virus supplemented with 10(4) or 10(6) U IFN-gamma. After the first immunization, none of the animals responded with measurable virus-neutralizing antibody (VNAb), virus-specific IgG or IgA. Following a second immunization 4 weeks later, a significantly increased VNAb response was noted in animals that had received vaccine doses containing 10(4) U IFN-gamma (p < 0.05). These animals also had significantly augmented serum levels of IgG (p < 0.01) and IgA (p < 0.05). Inclusion of 10(6) U IFN-gamma in the vaccine preparation did not affect the antibody response. In one experiment, the pigs were challenged oronasally with 10(5) TCID50 of the 75V19 strain of SHV-1, 7 weeks after administration of the second vaccine dose. Those that had received 10(4) U IFN-gamma in the vaccination developed less fever during the postchallenge period (p < 0.004). In all challenged pigs, growth performance was compromised during the first week after challenge. However, the only animals retaining an average net increase in body mass were those covaccinated with 10(4) U IFN-gamma (p < 0.05). Nasal excretion of virus was not significantly different between groups that had been vaccinated with or without IFN-gamma. Multiple linear regression analysis of variables from individual vaccinated animals revealed the VNAb response to be correlated with serum IgG levels (p < 0.025) and with postchallenge growth performance (p < 0.0001) but not with serum IgA levels (p > 0.5). On the other hand, serum IgA appeared to be inversely correlated with early nasal virus excretion after challenge (p < 0.006). Taken together, our data suggest that addition of IFN-gamma to inactivated SHV-1 vaccine may be a useful tool for enhancement of both mucosal and systemic immune responses in pigs.

Interferon-gamma is a target for binding and folding by both Escherichia coli chaperone model systems GroEL/GroES and DnaK/DnaJ/GrpE

IFN-gamma can be physicochemically distinguished from interferons-alpha, -beta or -omega through the loss of its tertiary structure and biological activity upon exposure to acid or heat. This loss is due to the irreversible aggregation of an unfolded or partially folded state. The conformational instability of IFN-gamma is reflected by its impairment to fold properly when overexpressed in Escherichia coli, resulting in its accumulation in cytoplasmic inclusion bodies. Chaperones were originally identified as a heterogeneous group of proteins that mediate the folding and correct assembly of various polypeptide substrates, and protect thermolabile proteins against inactivation. In either of both cases, chaperones prevent irreversible misfolding by assisting the substrate protein along its pathway to a stable tertiary conformation. Among the best characterized chaperones are the Escherichia coli Hsp60 and Hsp70 heat shock protein complexes, i.e., GroEL/GroES and DnaK/DnaJ/GrpE. They exhibit entirely different reaction mechanisms, which, however, both depend on hydrolysis of ATP. The unfolding of recombinant IFN-gamma by acid or heat can be used as a tool to assess its in vitro interaction with each of both chaperone systems at physiological temperature (35 degrees C). Using such an experimental set-up, both the DnaK and GroEL chaperone systems appeared to form complexes with IFN-gamma from which correctly folded protein was released in an ATP-dependent manner. In addition to the biotechnological implication of these observations, the relevance to de novo folding of IFN-gamma is discussed.

Actinobacillus pleuropneumonia serotype 2--effects on the interferon-alpha production of porcine leukocytes in vivo and in vitro

Effects of a bacterial infection on the IFN-alpha production in vivo and in vitro were studied in eight specific pathogen free pigs experimentally infected with Actinobacillus pleuropneumoniae. Clinically, the experimental infection was manifested as a febrile stage which lasted approximately one week and by signs of respiratory disease. The Aujeszky's disease virus (ADV) induced IFN-alpha production, assessed in whole blood cultures, was increased for the infected pigs during the febrile stage. Potentiating effects on the IFN-alpha production could be transferred to cultures of purified peripheral blood mononuclear cells with sera collected from the infected pigs during this period of time. Although the experimental infection with A. pleuropneumoniae did not induce any detectable amounts of IFN-alpha in serum or nasal secretion, both a phenol-extract and a heat-inactivated preparation of the bacteria induced low levels of IFN-alpha in cultures of purified PBMC. The interferogenic structures of the bacteria were not identified but there were indications that the bacteria induced IFN-alpha production in the same cell type as ADV.

Tissue chambers--a useful model for in vivo studies of cytokine production in the pig

An in vivo tissue chamber model was developed to enable studies of local cytokine production and cellular events during inflammatory and immune reactions in the pig. Tissue chambers made of sialistic rubber tubing were surgically implanted in the subcutaneous tissue- and samples of tissue chamber fluid (TCF) and inflammatory cells were collected by aspiration with a syringe. To evaluate the model for local cytokine production, two cytokine inducers, polyribinosinic-polyribocytidylic acid (poly I:C) and fixed Aujeszky's disease virus infected PK15 cells (ADV-PK15), were injected into the tissue chambers and samples of TCF were collected 0, 4, 8, 12, 24 and 48 h post injection. Poly I:C injections induced local production of interferon-alpha (IFN-alpha) as well as tumor necrosis factor (TNF) in the TCF but kinetic differences in the production of the cytokines were noted. Poly I:C also induced an increase in cell numbers in the TCF, mainly due to increased neutrophil numbers. Injections of ADV-PK15 induced local IFN-alpha production in the TCF as long as the pigs were serologically negative to ADV. Immunofluorescence and in situ hybridization techniques could be applied for characterization of TCF cells. Moreover, cells recovered from the tissue chambers were viable and could be used in functional in vitro tests. Taken together, this tissue chamber model could prove very useful in in vivo studies of inflammatory/immune responses and cytokine production in the pig.

Examination of the Tn5 transposase overproduction phenotype in Escherichia coli and localization of a suppressor of transposase overproduction killing that is an allele of rpoH

Tn5 transposase (Tnp) overproduction is lethal to Escherichia coli. Tnp overproduction causes cell filamentation, abnormal chromosome segregation, and an increase in anucleated cell formation. There are two simple explanations for the observed phenotype: induction of the SOS response or of the heat shock response. The data presented here show that overproduction of Tnp neither induces an SOS response nor a strong heat shock response. However, our experiments do indicate that induction of some sigma32-programmed function(s) (either due to an rpoH mutation, a deletion of dnaK, or overproduction of sigma32) suppresses Tnp overproduction killing. This effect is not due to overproduction of DnaK, DnaJ, or GroELS. In addition, Tnp but not deltall Tnp (whose overproduction does not kill the host cells) associates with the inner cell membrane, suggesting a possible correlation between cell killing and Tnp membrane association. These observations will be discussed in the context of a model proposing that Tnp overproduction titrates an essential host factor(s) involved in an early cell division step and/or chromosome segregation.

Purification and characterization of the carboxyl-domain of human hexokinase type III expressed as fusion protein

In mammalian tissues hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) exists as four isoenzymes encoded by distinct genes. These proteins are homologous and are organized in two homologous domains, with the exception of hexokinase type IV which has only one. This organization is believed to be the result of a duplication and tandem fusion event involving the gene encoding for the ancestral hexokinase. In this study, we cloned the carboxyl-domain of human hexokinase type III and expressed it in Escherichia coli as a glutathione S-transferase fusion protein, using the pGEX-2T expression vector. The recombinant protein showed catalytic activity. A comparative study of the kinetic properties of the expressed carboxyl-domain and the enzyme partially purified from human lymphocytes is also shown. The results now allow a better understanding of the role of the carboxyl-domain in determining the catalytic properties of the enzyme.

Controlling the speed of hirudin folding

The folding of hirudin undergoes an initial stage of non-specific packing, followed by consolidation (re-organization) of partially packed intermediates to attain the native structure [Chatrenet and Chang (1993) J. Biol. Chem. 268, 20988-20996]. Non-specific packing leads to the formation of scrambled hirudins as folding intermediates. A systematic study was carried out to search for conditions which would selectively control and enhance the processes of packing and consolidation. It is demonstrated here that under optimized conditions, including the use of cystine/cysteine and protein disulphide isomerase, the folding of hirudin in vitro can be achieved quantitatively within 30 s.