Protein Folding Intermediates and Inclusion Body Formation

Gram-scale synthesis of recombinant chitooligosaccharides in Escherichia coli

Cultivation of Escherichia coli harbouring heterologous genes of oligosaccharide synthesis is presented as a new method for preparing large quantities of high-value oligosaccharides. To test the feasibility of this method, we successfully produced in high yield (up to 2.5 g/L) penta-N-acetyl-chitopentaose (1) and its deacetylated derivative tetra-N-acetyl-chitopentaose (2) by cultivating at high density cells of E. coli expressing nodC or nodBC genes (nodC and nodB encode for chitooligosaccharide synthase and chitooligosaccharide N-deacetylase, respectively). These two products were easily purified by charcoal adsorption and ion-exchange chromatography. One important application of compound 2 could be its utilisation as a precursor for the preparation of synthetic nodulation factors by chemical acylation.

Purification and characterization of human and mouse recombinant alpha-fetoproteins expressed in Escherichia coli

Alpha-fetoprotein (AFP) is a tumor-associated embryonic molecule whose precise biological function(s) remains unclear. A more complete analysis of the physiological activities of this oncofetal protein has, until now, been severely limited by the lack of an appropriate source from which to obtain pure AFP in any sizeable quantity. In the present investigation, we obviate this problem by cloning and efficiently overexpressing mature mouse and human AFP cDNA's in Escherichia coli. For recombinant mouse AFP (rMoAFP), large segments of the coding region were excised from the preexisting plasmids pAFP1 and pAFP2, which together encompass 90% of the AFP sequence. The mouse cDNA was made complete by the addition of N- and C-terminal encoding oligonucleotides. Mouse AFP cDNA was expressed directly as a full-length molecule in vector pTrp4 or as fusion proteins in plasmids pMALc and pRX1 under the transcriptional control of trp or tac promoters. Accumulation of rMoAFP was significantly increased in protease-deficient E. coli strains over nonprotease-deficient strains, > or = 10% of total cell protein. Of the gene fusion proteins examined, none offered significant advantage over the direct expression product in terms of recombinant protein stability, overall levels of synthesis, or facilitated purification. Recombinant AFP polypeptides expressed by pTrp4 were as expected, deposited in bacterial inclusion bodies. Subsequent to resolubilization/refolding, rMoAFP was first enriched by passage over Q-Sepharose resin followed by final purification using immobilized copper-chelate affinity chromatography. Protein sequencing of the N-terminus revealed that purified rMoAFP had a deletion of the first nine amino acids coded for by the full-length mouse AFP cDNA. Similar N-terminal deletions are observed with AFP isolates originating from natural sources. A complete human AFP cDNA was generated from a fetal liver cDNA library and was cloned into vector pTrp4. Recombinant human AFP (rHuAFP) was expressed under the identical conditions employed for rMoAFP but purification had to be modified to include preparative Mono Q anion exchange chromatography. N-terminal sequencing, amino acid compositional analysis, and electrospray mass spectrometry revealed that purified rHuAFP was intact and unaltered and that the initiator methionine was completely removed. The biological activity of recombinant AFP, as judged by its inhibitory effects on in vitro lymphocyte proliferation, was equivalent to that of the native protein. The availability of large quantities of mouse and human recombinant AFP molecules should now permit detailed structure-function analyses of this important oncofetal protein to proceed in a manner unimpeded by previous limitations in both quantity and quality of the native proteins.

Cell display library for gene cloning of variable regions of human antibodies to hepatitis B surface antigen

A novel cell display system was developed for cloning the variable region (V) genes of antigen-specific human antibodies. The system is based on an antibody library displayed on the surface of COS cells, using a plasmid vector designed to direct expression of membrane-bound antibodies. COS cells expressing antigen-specific antibodies were separated using a flow cytometer for their binding to a fluorescent dye-labeled antigen. To test the performance of this system. We cloned V genes of 4 antibodies directed against hepatitis B surface antigen (HBsAg) from a library prepared from peripheral blood lymphocytes of a vaccinated donor. These membrane-bound anti-HBsAg antibodies were easily converted to soluble forms, all of which showed a size similar to human serum IgG in SDS-PAGE and the same specific binding to HBsAg as membrane-bound forms in ELISA. All VH and VK gene segments of the 4 clones isolated in this study belonged to VHIII and VKI subgroups, respectively. These findings demonstrate the potential and selection capabilities of our cell display system for cloning the V genes of antigen-specific human antibodies.

Prevalence of temperature sensitive folding mutations in the parallel beta coil domain of the phage P22 tailspike endorhamnosidase

Temperature sensitive mutations fall into two general classes: tl mutations, which render the mature protein thermolabile, and tsf (temperature sensitive folding) mutations, which destabilize an intermediate in the folding pathway without altering the functions of the folded state. The molecular defects caused by tsf mutations have been intensively studied for the elongated tailspike endorhamnosidase of Salmonella phage P22. The tailspike, responsible for host cell recognition and attachment, contains a 13 strand parallel beta coil domain. A set of tsf mutants located in the beta coil domain have been shown to cause folding defects in the in vivo folding pathway for the tailspike. We report here additional data on 17 other temperature sensitive mutants which are in the beta coil domain. Using mutant proteins formed at low temperature, the essential functions of assembling on the phage head, and binding to the O-antigen lipopolysaccharide (LPS) receptor of Salmonella were examined at high temperatures. All of the mutant proteins once folded at permissive temperature, were functional at restrictive temperatures. When synthesized at restrictive temperature the mutant chains formed an early folding intermediate, but failed to reach the mature conformation, accumulating instead in the aggregated inclusion body state. Thus this set of mutants all have the temperature sensitive folding phenotype. The prevalence of tsf mutants in the parallel beta coil domain presumably reflects properties of its folding intermediates. The key property may be the tendency of the intermediate to associate off pathway to the kinetically trapped inclusion body state.

Expression of aggregation-prone recombinant proteins at low temperatures: a comparative study of the Escherichia coli cspA and tac promoter systems

The aggregation-prone fusion protein preS2-S'-beta-galactosidase was used as a model system to compare the efficiencies of the IPTG-inducible tac promoter and the low-temperature-inducible cspA promoter in directing the expression of soluble recombinant polypeptides at reduced growth temperatures in Escherichia coli. At 37 degrees C, the fusion protein was produced at high levels from the tac promoter, but aggregated quantitatively in a biologically inactive form. In contrast, little preS2-S'-beta-galactosidase was synthesized from the cspA promoter at this temperature, presumably due to transcript instability. The highest yields of active enzyme were obtained following temperature downshift from 37 to 30 degrees C for the tac promoter and 25 degrees C for the cspA promoter. At 25 degrees C, the kinetics of accumulation of beta-galactosidase activity, ratios of soluble to insoluble fusion protein, and synthesis rates of preS2-S'-beta-galactosidase were virtually identical for both promoters for a period of 2 h postinduction. Thereafter, the cspA promoter became repressed, whereas synthesis of the fusion protein continued with the tac system. Following transfer to 10 degrees C, the tac promoter was almost completely inhibited while the cspA promoter was able to direct the synthesis of soluble preS2-S'-beta-galactosidase for up to 2 h. However, the levels of active enzyme produced were approximately threefold lower than those measured at 25 degrees C. Overexpression of native CspA had no effect on the accumulation of active preS2-S'-beta-galactosidase from the cspA promoter. It is therefore unlikely that CspA acts as it own positive inducer. Our results indicate that the cspA promoter can efficiently substitute for the tac system at 25 degrees C and may be particularly valuable for the expression of highly aggregation-prone or unstable gene products at 10 degrees C.

Inclusion bodies and purification of proteins in biologically active forms

Even though recombinant DNA technology has made possible the production of valuable therapeutic proteins, its accumulation in the host cell as inclusion body poses serious problems in the recovery of functionally active proteins. In the last twenty years, alternative techniques have been evolved to purify biologically active proteins from inclusion bodies. Most of these remain only as inventions and very few are commercially exploited. This review summarizes the developments in isolation, refolding and purification of proteins from inclusion bodies that could be used for vaccine and non-vaccine applications. The second section involves a discussion on inclusion bodies, how they are formed, and their physicochemical properties. In vivo protein folding in Escherichia coli and kinetics of in vitro protein folding are the subjects of the third and fourth sections respectively. The next section covers the recovery of bioactive protein from inclusion bodies: it includes isolation of inclusion body from host cell debris, purification in denatured state alternate refolding techniques, and final purification of active molecules. Since purity and safety are two important issues in therapeutic grade proteins, the following three sections are devoted to immunological and biological characterization of biomolecules, nature, and type of impurities normally encountered, and their detection. Lastly, two case studies are discussed to demonstrate the sequence of process steps involved.

Expression in bacteria other than Escherichia coli

Although many bacteria are used for the expression of foreign genes, there is still a need to develop better expression systems. Advances have been made in the stabilization of gene maintenance and in the control of expression, therefore increasing the potential usefulness of some of these bacteria.

Versatile E. coli thioredoxin specific monoclonal antibodies afford convenient analysis and purification of prokaryote expressed soluble fusion protein

A recently developed E. coli thioredoxin (Trx) gene fusion expression system has circumvented the difficulties associated with inclusion body formation. Although ample quantities of soluble recombinant protein can be expressed using this system, no universal means of quantifying or purifying the fusion product exists. To facilitate the study of Trx fusion proteins, anti-E. coli Trx monoclonal antibodies (mAb) were generated. Two distinct Trx epitopes were defined by competitive ELISA. Both mAb were capable of detecting Trx fusion proteins by sandwich ELISA, and by immunoblot analysis under reducing and non-reducing conditions. In addition, these mAb enabled purification of Trx fusion proteins by immunoprecipitation, as well as affinity chromatography. This report provides the first description of anti-Trx antibodies. These reagents represent a major advance in the isolation and analysis of prokaryote expressed recombinant Trx fusion proteins.

Optimized bacterial production of nonglycosylated human transferrin and its half-molecules

Transferrin is a glycoprotein functioning in iron transport in higher eukaryotes, and consists of two highly homologous domains. To study the function of the glycan residues attached exclusively to the C-terminal domain, we have constructed a plasmid allowing production of nonglycosylated human transferrin in Escherichia coli. By molecular biological and genetic techniques, production was stepped up to 60 mg/l. Similar plasmids were constructed for production of the two half-transferrins. The recombinant proteins accumulate in inclusion-body-like aggregates, where they appear to bind iron without causing bacteriostasis. Proteins active in iron binding have been purified from these inclusion bodies.

Refolding of alpha 1-antitrypsin expressed as inclusion bodies in Escherichia coli: characterization of aggregation

Recombinant alpha 1-antitrypsin (alpha 1AT) produced as inclusion bodies in Escherichia coli was purified via several steps including solubilization of the inclusion bodies in 8 M urea and refolding by direct dilution of denaturant, followed by ion-exchange chromatography. The purified recombinant alpha 1AT has an activity comparable to human plasma alpha 1AT. During refolding, prolonged incubation of the alpha 1AT polypeptides at intermediate urea concentration favored production of inactive but soluble aggregates, which could regain activity after denaturation and renaturation. Nondenaturing polyacrylamide gel electrophoresis of the aggregates revealed the existence of dimers and higher oligomers. Immunological approach to characterize conformation showed that the oligomers were distinct from the native, the cleaved, or the denatured form, but was similar to the polymers induced from the native structure in mild denaturing condition. These results suggest that the oligomers are formed through specific interactions between aggregation-competent species which are stabilized at intermediate denaturant concentration.

Production of a biologically active recombinant teleostean growth hormone in E. coli cells

We have isolated and characterized several recombinant lambda phage clones carrying growth hormone (GH) cDNA of striped bass (Morone saxatilis). Nucleotide sequence and the predicted amino acid sequence of sbGH was determined from a recombinant clone carrying the longest cDNA insert. The sbGH cDNA encodes a pre-hormone of 204 amino acid residues. Comparison of the predicted amino acid sequence of sbGH with those of other vertebrates revealed different degrees of sequence identity: approximately 98% with European sea bass; 90% with bluefin tuna; bonito and red seabream; 71% with winter flounder; 64% with salmonids; 55% with carp; and 38% with human. Expression of the mature sbGH cDNA (without the signal peptide sequence) in E. coli cells under regulation of the lambda phage PL promoter produced a polypeptide of 20 kDa. Following renaturation, this recombinant hormone was shown to be biologically active in a radioreceptor competition binding assay and in the induction of hepatic insulin-like growth factor I (IGF-I) mRNA synthesis in vivo.

Strategies to suppress aggregation of recombinant keratinocyte growth factor during liquid formulation development

Recombinant human keratinocyte growth factor (rhKGF) is a fairly unstable protein, posing a challenging problem for long-term storage. During storage, the protein unfolds at relatively low temperatures and the unfolded proteins aggregate rapidly, leading to the formation of large visible precipitates. Thermal unfolding of rhKGF displays a similar pattern, i.e., unfolding is followed immediately by aggregation as the temperature is increased. As the unfolding and aggregation (precipitation) of rhKGF limit the storage life of the protein, a search for stabilizers to suppress rhKGF unfolding and aggregation has been done by examining the effects of excipients on thermal melting temperature and on the rate of protein aggregation during storage. Sulfated polysaccharides and citrate are found to be effective in increasing the melting temperature of rhKGF or preventing its aggregation. In particular, 0.5% (w/v) heparin and high molecular weight dextran sulfate, and 0.5 M citrate are highly effective, decreasing the rates of rhKGF aggregation by about 50-fold. Other negatively charged small ions, such as phosphate, also have moderate stabilizing effects on rhKGF. A mechanistic study of the aggregation pathway of rhKGF has led to a better understanding of the stabilizing effects of these molecules. Molecules which enhance rhKGF conformational stability are capable of effectively suppressing rhKGF aggregation.

Refolding of RNAse A at high concentrations: identification of non-native species

In this paper, we present an analysis of the soluble species formed on refolding of RNase A at various concentrations, in order to characterize these species with respect to structure and activities. Studies were carried out using reverse-phase high-performance liquid chromatography, circular dichroism, chromatography and ultracentrifugation. At all concentrations of protein used, RNase A refolded to the native form, together with formation of non-native species. These non-native species are either misfolded monomers or aggregates; the percentage of such species increases with increasing concentration of enzyme. Such aggregation appears to be a non-random process governed by intermolecular disulfide crosslinking between monomers. These results reaffirm the principle that the information for folding of the protein is encoded in the amino acid sequence itself.

Mutations and off-pathway aggregation of proteins

The off-pathway aggregation of proteins is a ubiquitous, yet poorly understood, phenomenon. In vitro, aggregation places limits on both protein stability and refolding yields. In vivo, it is responsible for inclusion-body formation in the bacterial production of proteins, as well as amyloid disease and related phenomena in animals. An important common feature of these processes is their sensitivity to point mutations, a feature that offers important clues for understanding controversial aspects of off-pathway aggregation such as its molecular specificity and the nature of the aggregating species. Results of a number of studies illustrate that the sensitivity of aggregation can derive from the ability of a mutation to either (1) facilitate the accumulation of a non-native state that is prone to aggregation, or (2) increase the intrinsic tendency of such a state to aggregate.

Expression of alpha 1-proteinase inhibitor in Escherichia coli: effects of single amino acid substitutions in the active site loop on aggregate formation

Overproduction of eukaryotic proteins in microorganisms often leads to the formation of insoluble protein aggregates which accumulate as intracellular inclusion bodies. alpha 1-Proteinase inhibitor (alpha 1-PI) when produced as a cytoplasmic protein in Escherichia coli (E. coli) forms inclusion bodies containing the majority of the inhibitor in an inactive form. Several variants of alpha 1-PI with single amino acid substitutions within their active site loop (amino acids 345-358) were produced in a bioreactor showing that substitution of Met351 with Glu resulted in significantly reduced aggregate formation compared to the other variants and to wild-type protein. In addition, this variant proved to be fully functional as a proteinase inhibitor. Based on these findings and on results of previous structural studies a mechanism for aggregate formation during expression of alpha 1-PI is suggested.

Renaturation of recombinant proteins produced as inclusion bodies

Expression of recombinant proteins in Escherichia coli often results in the formation of insoluble inclusion bodies. Within the last few years specific methods and strategies have been developed to prepare active proteins from these inclusion bodies. These methods include (i) isolation of inclusion bodies after disintegration of cells by mechanical forces and purification by washing with detergent solutions or low concentrations of denaturant, (ii) solubilization of inclusion bodies with high concentrations of urea or guanidine-hydrochloride in combination with reducing reagents, and (iii) renaturation of the proteins including formation of native disulphide bonds. Renatured and native disulphide bond formation are accomplished by (a) either air oxidation, (b) glutathione reoxidation starting from reduced material, or (c) disulphide interchange starting from mixed disulphides containing peptides. The final yield of renatured proteins can be increased by adding low concentrations of denaturant during renaturation.

Genetically engineering mammalian cell lines for increased viability and productivity

The generation of new host cell lines for the production of foreign proteins can be achieved by cell engineering. This approach can be used to enhance the cell's ability to produce proteins that are properly processed and secreted at elevated levels and consequently can increase the overall productivity of an expression system. One potential target for cell engineering is the modification of the cell's protein folding capacity. The appropriate folding, assembly, localization and secretion of newly synthesized proteins is dependent upon the action of a group of proteins known as molecular chaperones. Improving the host cell's chaperoning capacity might increase the yield of properly folded recombinant proteins by preventing the formation of insoluble aggregates. Another potentially beneficial cell engineering goal is the inhibition of physiological cell death. The productivity of genetically engineered cells is dependent upon the maintenance of high levels of cell viability throughout the bioprocess period. Fluctuations in a cell's environment can trigger a deliberate form of cell death known as apoptosis. The proteins that mediate this self-destruction are currently being characterized. Regulating the expression of these death genes by cellular engineering could limit the loss of productivity that results from the physiological death of the recombinant cell line.

Physical characterization of a reactivatable liposome-bound rhodanese folding intermediate

Recently, we described the formation of a complex between liposomes and the unfolded protein rhodanese (thiosulfate:cyanide sulfurtransferase, EC 2.8.1.1), which could be liberated and efficiently reactivated after treatment of the complex with detergents [Zardeneta, G., & Horowitz, P. M. (1992) Eur. J. Biochem. 210, 831-837]. Previous data suggested that liposome-bound rhodanese was in the form of a folding intermediate. We have characterized in greater detail the nature of the conformation of the bound rhodanese. Physical characterization of the bound rhodanese intermediate was carried out using proteolysis, fluorescence studies with 1,8-anilinonapthalene-8-sulfonic acid, a probe for hydrophobic site exposure, intrinsic fluorescence to determine tryptophan accessibility using the quenchers acrylamide and iodide, and circular dichroism to detect extent of secondary structure. These studies show that the rhodanese intermediates bound to either cardiolipin or phosphatidylserine liposomes are not identical, the former being in a less compact conformation yet having more secondary structure than the latter, an observation which may explain why the reactivation of the former intermediate is more effective. Finally, turbidimetric and proteolytic studies raise the possibility that each rhodanese intermediate binds to several liposomes. This finding suggests that a possible reason for the differential reactivation yields obtained may be due to the fact that unfolded rhodanese has more binding sites for cardiolipin than for phosphatidylserine liposomes. A greater number of binding sites would result in better anchoring of rhodanese's interactive surfaces and thus reduce the likelihood of misfolding.

Suppression of temperature-sensitive assembly mutants of heat-labile enterotoxin B subunits

Deletions or substitutions of amino acids at the carboxyl-terminus of the heat-labile enterotoxin B subunit (EtxB) affect its assembly into pentamers in a temperature-dependent manner. At 42 degrees C, the mutations prevent the B subunits from achieving their final pentameric structure resulting in membrane association of the monomers. However, mutant B subunits produced at 30 degrees C assemble, in the periplasm, into pentamers that remain stable when transferred to 42 degrees C, indicating that the mutant pentamers are stable under conditions where their formation is inhibited. The mutant pentamers are, similarly to wild-type pentamers, SDS-resistant and stable, in vitro, at temperatures up to 65 degrees C. This suggests that although the C-terminal amino acids are part of the subunit interface, they appear not to contribute significantly to the stability of the final pentameric complex, but are instead essential for the formation or stabilization of an assembly intermediate in the pentamerization process. Single second site mutations suppress the assembly defect of mutant EtxB191.5, which carries substitutions at its C-terminus. The Thr-->Ile replacement at position 75 in the alpha 2-helix probably restores the van der Waals contact between residues 75 and 101, which had been greatly reduced by the Met-->Leu substitution at position 101 in the beta 6-strand of EtxB191.5. Interaction between the alpha 2-helix and beta 6-strand which contains the C-terminus probably stabilizes a conformation essential for assembly and is therefore required for the formation of pentamers.

Partially structured self-associating states of acidic fibroblast growth factor

A combination of near- and far-UV circular dichroism, Fourier-transform infrared spectroscopy, tryptophan fluorescence, size-exclusion chromatography, and a fluorescent extrinsic hydrophobic probe has been employed to characterize partially structured states of human recombinant acidic fibroblast growth factor (aFGF). At low pH, the addition of specific polyanionic ligands or moderate amounts of salts induces states with high secondary but low tertiary structure content. At neutral pH, intermediate amounts of chaotropic agents impose similar partially structured conformational states which also display noncooperative unfolding transitions. Kinetic evidence indicates that similar forms of the protein exist in the first few hundred milliseconds in the refolding pathway of aFGF. The kinetics of their formation appear to be temperature-independent, implying lack of an energy barrier, which is characteristic for further slow folding into the native state. Unlike the native and fully unfolded states, these partially structured conformations exhibit very low solubility, resulting in irreversible aggregation. Potential physiological implications of the existence of such "molten globule" states with regard to the growth factor's transport and biological activity are considered.

Inclusion bodies and crystals of Bacillus sphaericus mosquitocidal proteins expressed in various bacterial hosts

Mosquitocidal proteins of 42 and 51 kDa from Bacillus sphaericus were produced in acrystallogenic B. sphaericus and B. subtilis strains. In both species, transformants containing each protein expressed individually were non-toxic for mosquito larvae and produced small inclusions which did not have a crystalline ultrastructure. When both components of the binary toxin were expressed together, toxicity was restored: oval and round amorphous inclusions were produced in B. subtilis, and typical native-type crystals were synthesized in B. sphaericus. In B. subtilis, native-type crystals were produced only when the two components of the binary toxin were synthesized as a 93-kDa fusion protein.

Aggregation and denaturation of apomyoglobin in aqueous urea solutions

The effects of urea on apomyoglobin solubility have been investigated. Apomyoglobin precipitation was found to be a thermodynamically reversible process independent of the pathway of aggregation. A liquid-solid phase diagram was constructed for the precipitation of apomyoglobin as a function of urea and protein concentration. Apomyoglobin solubility decreases by an order of magnitude between 0 and 1.5 M urea, reaching a minimum near 2.4 M urea and increasing at higher urea concentrations (the denaturation midpoint is at approximately 2.6 M urea). This decrease in protein solubility is opposite to that expected based on amino acid solubilities, since both polar and nonpolar molecules become more soluble with increasing urea concentration. Solubility minima for proteins have been rationalized in terms of folding intermediates. However, our structural studies show no evidence for folding intermediates in apomyoglobin under the experimental conditions, apart from small predenaturation changes. Our data are consistent with an alternative hypothesis, namely, that the primary aggregating species are denatured protein molecules, rather than intermediate states. Consistent with recent thermodynamic and statistical mechanical models, the solubility minimum may be described as the result of two competing effects of urea: (1) urea denatures the protein, and (2) urea makes the solvent more favorable for the native and any denatured state. At low urea concentration, solubility decreases with increasing urea concentration due to the domination of the solubility behavior by the increase in the population of aggregation-competent (denatured) protein molecules. However, at high urea concentration, the increasingly favorable nature of the solvent dominates, resulting in increasing solubility with urea concentration. The phase diagram provides guidance for the best experimental conditions (pathway) to use to avoid aggregation during the refolding of denaturant-unfolded protein.

Characterization of inclusion bodies in recombinant Escherichia coli producing high levels of porcine somatotropin

The protein composition of inclusion bodies (IBs) formed in recombinant Escherichia coli producing high levels of porcine somatotropin (pST) was analyzed by one- and two-dimensional protein gel electrophoresis. Recombinant pST is exclusively recovered from the insoluble cell fraction. Results indicate that, in addition to the main species of pST, subspecies with different isoelectric points and degradative fragments are contained within IBs. The presence of outer membrane proteins in IB fractions results from coprecipitation of cell debris during IB preparation and not from specific in vivo or in vitro interaction of these proteins with IBs. Cells producing pST contain up to three IBs located in the cytoplasm. The implication of high level gene expression on the uniformity of the desired product is discussed.

Folding and assembly of oligomeric proteins in Escherichia coli

High levels of expression of oligomeric proteins in heterologous systems are frequently associated with misfolding and accumulation of the polypeptides in inclusion bodies. This reflects aspects of the folding and assembly pathways of oligomeric proteins, which generally proceed from either folding intermediates or native-like metastable species that are not in their final conformation. Methods for optimizing the yield of correctly assembled oligomers are discussed.

Isolation of inclusion bodies from vegetative Clostridium perfringens: partial purification of a 47 kDa inclusion protein

A refractile inclusion body produced by vegetative cells of Clostridium perfringens at temperatures above 40 degrees C was isolated and partially characterized. The inclusion was composed of protein and could be solubilized by sodium dodecyl sulphate plus either dithiothreitol or beta-mercaptoethanol. The solubilized inclusion showed no antigenic relationship with Cl. perfringens enterotoxin. One major band with an apparent MW of 47 kDa was demonstrated after polyacrylamide gel electrophoresis of the solubilized inclusion. Both enterotoxin-positive and enterotoxin-negative strains produced the inclusion body. No effect on the morphology of several eucaryotic cell lines was observed when solubilized or intact inclusion was added to the cell cultures.

A rapid procedure for production of human basic fibroblast growth factor in Escherichia coli cells

Human basic fibroblast growth factor has been expressed in Escherichia coli cells at a level of 2-3 mg/l culture, using a rapid procedure which requires only simple DNA manipulative work. The recombinant material has the same potency as natural basic fibroblast growth factor from bovine pituitary glands.

De novo design, synthesis and study of albebetin, a polypeptide with a predetermined three-dimensional structure. Probing the structure at the nanogram level

The de novo polypeptide named albebetin was designed to form the tertiary fold that has not yet been observed in natural proteins. The design was based on the molecular theory of protein structures. The gene coding for this polypeptide was chemically synthesized. For the initial characterization of a protein structure, a new approach has been developed that uses only nanogram amounts of a polypeptide without its previous purification. This approach includes the biosynthesis of radiolabeled protein in a cell-free translation system with subsequent analysis of its compactness and structure by size-exclusion chromatography, urea-gradient electrophoresis and limited proteolysis. According to all tests used, albebetin has a compact stable structure.

Control of in vivo proteolysis in the production of recombinant proteins

Proteolytic degradation of protein products causes many problems in the bioprocess industry. The increasing production of proteins in heterologous hosts through the use of recombinant DNA technology, has recently brought the problem into focus, since it seems that heterologous proteins are more prone to proteolysis. The result of proteolytic attack may vary from complete hydrolysis of the product to minor truncation of the protein without impairment of its biological function. The degree to which such partial proteolysis is a problem depends on the requirements of the ultimate use of the protein product.

Routes to active proteins from transformed microorganisms

Over-expression of recombinant proteins in microbial hosts results in the formation of active soluble protein or of insoluble aggregates (inclusion bodies). Efficient in vitro refolding strategies have been developed to reactivate inactive proteins from inclusion bodies. Co-expression of molecular chaperones may provide a tool to promote correct structure formation of recombinant proteins in vivo.

Response of Escherichia coli cell membranes to induction of lambda cl857 prophage by heat shock

Heat shock induces protein aggregation in Escherichia coli and E. coli (lambda cl857). The aggregates (S fraction) appear 15 min post-induction and are separable from membranes by sucrose density-gradient centrifugation. The S fraction quickly disappears in wild type strains but persists in rpoH mutant with concomitant quick inner membrane destruction. We propose that: (1) the disappearance of the S fraction reflects a rpoH-dependent processing, (2) the membrane destruction explains the lethality of the rpoH mutation at elevated temperatures; and (3) the protection of the inner membrane integrity is an important physiological function of the heat-shock response. We assume that the S fraction of aggregated proteins represents the signal inducing the heat-shock response. The prophage thermo-induction results in an increase (35 min post-induction) in the A fraction resembling that of the adhesion zones of the membranes. This fraction is greater than the corresponding fraction from uninduced cells. The increase is mediated by the lambda late genes, since it is absent in the induced E. coli (lambda cl857 Qam21). Since heat shock is widely used for induction of the lambda promoters in expression vectors it is possible that the formation of the protein aggregates (though transient in WT strains) and/or the fragility of membranes in rpoH mutants may be the cause of poor expression of cloned genes or may lead to mistaken localization of their expression products.

Conformational stability, folding, and ligand-binding affinity of single-chain Fv immunoglobulin fragments expressed in Escherichia coli

A fluorescein-binding single-chain Fv (scFv) was chosen as a model for the study of the physicochemical parameters associated with synthetic IgG fragments. Three such scFv proteins were designed from the primary sequences of one anti-fluorescyl monoclonal antibody (Mab 4.4.20). These were constructed with varying-length interdomain peptide linkers of between 12 and 25 residues, expressed in Escherichia coli, and the protein folding, stability, and antigen-binding characteristics were assessed. Efficient renaturation could be accomplished in vitro to yield approximately 26 mg of active scFv/L of fermentation. Scatchard analysis for fluorescein ligand binding revealed that the scFv designs come within 2-fold of the Ka = 1.99 (+/- 0.18) x 10(9) observed for the parental 4.4.20 Fab and have identical stoichiometries (n approximately 0.99). Reversible solvent denaturation studies demonstrated that the unfolding/refolding equilibria for the scFv proteins can be fit to a simple two-state model and that two of the scFv designs were found to be slightly more stable than single IgG domains (VL and CL) when assessed in terms of the free energy of unfolding, delta Gon-u, or nearly identical to other multiple domain immunoglobulin proteins such as light chains and Fab's when relative transition midpoints, Cm, are compared. Linkers which conferred conformational flexibility beyond the minimally required length of 12 residues were found to have a stabilizing effect. By these criteria of ligand-binding function and protein stability, the scFv proteins were found to be bona fide minimal replicas of their parental IgG molecules.

Expression in Escherichia coli: purification and properties of the yeast general transcription factor TFIID

A T7 RNA polymerase expression system has been used for the efficient expression of the yeast RNA polymerase general transcription factor TFIID (TFIIDY), the TATA-box factor (previously called BTF1) in Escherichia coli. Expression of the gene was performed at 25 degrees C instead of 37 degrees C to increase the total amount of soluble TFIIDY. Soluble TFIIDY was purified in three chromatographic steps and was eluted from the final column, a heparin-5PW HPLC column, in two peaks at 0.38 M (peak I) and 0.42 M (peak II) KCl in which this protein was 52% and greater than 95% pure, respectively. The protein in both peaks was active in an in vitro transcription assay. However, while TFIIDY from peak II was essentially indistinguishable from the material isolated from yeast, the protein of peak I differed in a number of biochemical characteristics, having a lower specific activity in an in vitro transcription assay and displaying an altered pattern of bands in a DNA band shift assay. Despite these differences, the proteins in both peaks have identical molecular weights on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, have indistinguishable N-terminal amino acid sequences, and apparently exist as monomers under the conditions used for the heparin-5PW chromatography.

Physicochemical and immunological characterization of recombinant host-protective antigen (VP2) of infectious bursal disease virus

Small fusions to the N-terminal end of the host-protective antigen (VP2) of infectious bursal disease virus lead to stable expression of VP2 in Escherichia coli and yeast, and reduce the levels of inclusion body formation in E. coli in comparison to VP2 constructs with larger N-terminal fusions. VP2 produced with small N-terminal fusions, like native viral VP2, can be fractionated into a high molecular weight 'multimeric' form and a monomeric form. A virus-neutralizing monoclonal antibody that only recognizes undenatured VP2 preferentially reacts with multimeric forms of recombinant VP2. Both native and recombinant monomeric forms of VP2 are non-immunogenic. The multimeric forms of viral and yeast-derived VP2 are highly immunogenic, while those produced in E. coli are not.

Thermal unfolding pathway for the thermostable P22 tailspike endorhamnosidase

The conditions in which protein stability is biologically or industrially relevant frequently differ from those in which reversible denaturation is studied. The trimeric tailspike endorhamnosidase of phage P22 is a viral structural protein which exhibits high stability to heat, proteases, and detergents under a range of environmental conditions. Its intracellular folding pathway includes monomeric and trimeric folding intermediates and has been the subject of detailed genetic analysis. To understand the basis of tailspike thermostability, we have examined the kinetics of thermal and detergent unfolding. During thermal unfolding of the tailspike, a metastable unfolding intermediate accumulates which can be trapped in the cold or in the presence of SDS. This species is still trimeric, but has lost the ability to bind to virus capsids and, unlike the native trimer, is partially susceptible to protease digestion. Its N-terminal regions, containing about 110 residues, are unfolded whereas the central regions and the C-termini of the polypeptide chains are still in the folded state. Thus, the initiation step in thermal denaturation is the unfolding of the N-termini, but melting of the intermediate represents a second kinetic barrier in the denaturation process. This two-step unfolding is unusually slow at elevated temperature; for instance, in 2% SDS at 65 degrees C, the unfolding rate constant is 1.1 x 10(-3) s-1 for the transition from the native to the unfolding intermediate and 4.0 x 10(-5) s-1 for the transition from the intermediate to the unfolded chains. The sequential unfolding pathway explains the insensitivity of the apparent Tm to the presence of temperature-sensitive folding mutations [Sturtevant, J. M., Yu, M.-H., Haase-Pettingell, C., & King, J. (1989) J. Biol. Chem. 264, 10693-10698] which are located in the central region of the chain. The metastable unfolding intermediate has not been detected in the forward folding pathway occurring at lower temperatures. The early stage of the high-temperature thermal unfolding pathway is not the reverse of the late stage of the low-temperature folding pathway.

Signal peptidase I overproduction results in increased efficiencies of export and maturation of hybrid secretory proteins in Escherichia coli

The effects of 25-fold overproduction of Escherichia coli signal peptidase I (SPase I) on the processing kinetics of various (hybrid) secretory proteins, comprising fusions between signal sequence functions selected from the Bacillus subtilis chromosome and the mature part of TEM-beta-lactamase, were studied in E. coli. One precursor (pre[A2d]-beta-lactamase) showed an enhanced processing rate, and consequently, a highly improved release of the mature enzyme into the periplasm. A minor fraction of a second hybrid precursor (pre[A13i]-beta-lactamase), which was not processed under standard conditions of SPase I synthesis, was shown to be processed under conditions of SPase I overproduction. However, this did not result in efficient release of the mature beta-lactamase into the periplasm. In contrast, the processing rates of wild-type pre-beta-lactamase and pre(A2)-beta-lactamase, already high under standard conditions, were not detectably altered by SPase I overproduction. These results demonstrate that the availability of SPase I can be a limiting factor in protein export in E. coli, in particular with respect to (hybrid) precursor proteins showing low (SPase I) processing efficiencies.

Applications of simulated annealing to the multiple-minima problem in small peptides

A Simulated Annealing method has been implemented to overcome the multiple minima problem inherent in finding the global minimum of small peptides with 2, 3, 5, 10 and 24 dihedral angles. The algorithm works much better if one introduces the anticorrelations observed in Molecular Dynamics.