Unfolding and refolding of the constant fragment of the immunoglobulin light chain

The manufacturing considerations of bispecific antibodies

INTRODUCTION

Antibody therapies have made huge strides in providing safe and efficacious drugs for autoimmune, cancer and infectious disease. These bispecific antibodies can be assembled from the basic building blocks of IgGs, resulting in dozens of formats.

AREAS COVERED

It is important to consider the manufacturability of these formats early in the antibody discovery phases. Broadly categorizing bispecific antibodies into IgG-like, fragment-based, appended and hybrid formats can help in looking at early manufacturability considerations.

EXPERT OPINION

Ideally, bispecific antibody manufacturing should contain a minimal number of steps, with processes that give high yields of protein with no contaminants. Many of these have been determined for the fragment-based bispecific blinatumomab and the IgG-like bispecifics from hybridomas. However, for new formats, these need to be considered early in the research and development pipeline. The hybrid formats offer an unusual alternative in generating high pure yields of bispecific molecules if the engineering challenges can be deciphered.

Domain Interactions Determine the Amyloidogenicity of Antibody Light Chain Mutants

In antibody light chain amyloidosis (AL), mutant light chains (LCs) or their variable domains (V_Ls) form fibrils, which accumulate in organs and lead to their failure. The molecular mechanism of this disease is still poorly understood. One of the key open issues is whether the mutant V_Ls and LCs differ in fibril formation. We addressed this question studying the effects of the V_L mutations S20N and R61A within the isolated V_L domain and in the full-length LC scaffold. Both V_L variants readily form fibrils. Here, we find that in the LC context, the S20N variant is protected from fibril formation while for LC R61A fibril formation is even accelerated compared to V_L R61A. Our analyses revealed that the partially unfolded state of the V_L R61A domain destabilizes the C_L domain by non-native interactions, in turn leading to a further unfolding of the V_L domain. In contrast, the folded mutant V_L S20N and V_L wt form native interactions with C_L. These are beneficial for LC stability and promote amyloid resistance. Thus the effects of specific mutations on the V_L fold can have opposing effects on LC domain interactions, stability and amyloidogenicity.

Effect of Heat-treatment on Accuracy of Infrared Spectroscopy and Digital and Optical Brix Refractometers for Measuring Immunoglobulin G Concentration in Bovine Colostrum

BACKGROUND

Heat-treatment of colostrum is a method developed to reduce calf exposure to pathogens. Infrared (IR) spectroscopy and Brix refractometers can be used for measuring colostral IgG concentration and assessing colostrum quality.

OBJECTIVES

To determine the impact of heat-treatment on accuracy of IR spectroscopy and Brix refractometers for measuring colostral IgG concentration and assessing colostrum quality before and after heat-treatment.

ANIMALS

A total of 60 Holstein dairy cows on 8 commercial dairy farms.

METHODS

A cross-sectional study was designed to determine the effect of heat-treatment at 60°C and 63°C each for 30 and 60 minutes duration on colostral IgG concentration measured by the reference radial immunodiffusion (RID) assay, IR spectroscopy, and digital and optical refractometers.

RESULTS

Colostrum IgG concentration significantly decreased after heat-treatment at 63°C for 30 or 60 minutes as measured by RID, but the IgG values remained unchanged when measured by IR spectroscopy and refractometers. The lowest correlation coefficient found between IR spectroscopy (r = 0.70) and RID results was in colostrum heat-treated at 63°C for 60 minutes. For digital (r = 0.48) and optical (r = 0.50) refractometers, the lowest correlation coefficient was at 63°C for 30 minutes when compared to RID. The accuracy of the IR spectroscopy, digital and optical Brix refractometers was decreased from 91.7 to 80%, 81.7 to 45%, and 80 to 45%, respectively, when colostrum heat-treated at 63°C for 60 minutes.

CONCLUSIONS AND CLINICAL IMPORTANCE

Radial immunodiffusion, IR spectroscopy, and Brix refractometers exhibit utility for measuring IgG concentration when colostrum heat-treated at 60°C but does not detect decrease IgG concentrations when heat-treated at 63°C.

Sequence composition predicts immunoglobulin superfamily members that could share the intrinsically disordered properties of antibody CH1 domains

Antibodies are central to the growing sector of protein therapeutics, and increasingly they are being manipulated as fragments and combinations. An improved understanding of the properties of antibody domains in isolation would aid in their engineering. We have conducted an analysis of sequence and domain interactions for IgG antibodies and Fab fragments in the structural database. Of sequence-related properties studied, relative lysine to arginine content was found to be higher in CH1 and CL than in variable domains. As earlier work shows that lysine is favoured over arginine in more soluble proteins, this suggests that individual domains may not be optimised for greater solubility, giving scope for fragment engineering. Across other sequence-based features, CH1 is anomalous. A sequence-based scheme predicts CH1 to be folded, although it is known that CH1 folding is linked to IgG assembly and secretion. Calculations indicate that charge interactions in CH1 domains contribute less to folded state stability than in other Fab domains. Expanding to the immunoglobulin superfamily reveals that a subset of non-antibody domains shares sequence composition properties with CH1, leading us to suggest that some of these may also couple folding, assembly and secretion.

Kinetic stability and sequence/structure studies of urine-derived Bence-Jones proteins from multiple myeloma and light chain amyloidosis patients

It is now accepted that the ability of a protein to form amyloid fibrils could be associated both kinetic and thermodynamic protein folding parameters. A recent study from our laboratory using recombinant full-length (encompassing the variable and constant domain) immunoglobulin light chains found a strong kinetic control of the protein unfolding for these proteins. In this study, we are extending our analysis by using urine-derived Bence Jones proteins (BJPs) from five patients with light chain (AL) amyloidosis and four patients with multiple myeloma (MM). We observed lower stability in κ proteins compared to λ proteins (for both MM and AL proteins) in agreement with previous studies. The kinetic component of protein stability is not a universal feature of BJPs and the hysteresis observed during refolding reactions could be attributed to the inability of the protein to refold all domains. The most stable proteins exhibited 3-state unfolding transitions. While these proteins do not refold reversibly, partial refolding shows 2-state partial refolding transitions, suggesting that one of the domains (possibly the variable domain) does not refold completely. Sequences were aligned with their respective germlines and the location and nature of the mutations were analyzed. The location of the mutations were analyzed and compared with the stability and amyloidogenic properties for the proteins in this study, increasing our understanding of light chain unfolding and amyloidogenic potential.

Unusual denaturation trajectory of bovine gamma globulin studied by fluorescence correlation spectroscopy

Non-native and denatured states of proteins have received increasing attention because of their relevance to issues such as protein folding and stability. In this context, the pathway of polypeptide collapse and random coil formation in a denatured protein is a subject of much interest. Most proteins so far studied have shown monotonic expansion of their hydrodynamic radius (RH) in the presence of increasing concentration of chaotropes. We have studied GdnHCl-induced folding transitions and conformational states of a multi-domain protein, bovine gamma globulin, using fluorescence, circular dichroism and fluorescence correlation spectroscopy (FCS). FCS measurements showed that for gamma globulin, contrary to the observed trend, RH decreases with increasing GdnHCl concentration up to 3 M. At higher GdnHCl concentration, RH starts to increase but exhibits complicated behavior in the form of two sharp maxima at 4 M and 7 M. Further experiments suggest that the maximum at 4 M GdnHCl arises due to electrostatic interaction, whereas the one at 7 M GdnHCl corresponds to the usual expanded conformation due to denaturation. Beyond 7 M GdnHCl, RH decreases drastically and is shown to result from fragmentation of the protein caused by rupture of disulphide bonds by the high GdnHCl concentration. Our results demonstrate the capability of FCS in revealing intricate details of the unfolding trajectory that eludes conventional ensemble techniques such as fluorescence and CD.

Principles and engineering of antibody folding and assembly

Antibodies are uniquely suited to serve essential roles in the human immune defense as they combine several specific functions in one hetero-oligomeric protein. Their constant regions activate effector functions and their variable domains provide a stable framework that allows incorporation of highly diverse loop sequences. The combination of non-germline DNA recombination and mutation together with heavy and light chain assembly allows developing variable regions that specifically recognize essentially any antigen they may encounter. However, this diversity also requires tailor-made mechanisms to guarantee that folding and association of antibodies is carefully this diversity also requires tailor-made mechanisms to guarantee that folding and association of antibodies is carefully controlled before the protein is secreted from a plasma cell. Accordingly, the generic immunoglobulin fold β-barrel structure of antibody domains has been fine-tuned during evolution to fit the different requirements. Work over the past decades has identified important aspects of the folding and assembly of antibody domains and chains revealing domain specific variations of a general scheme. The most striking is the folding of an intrinsically disordered antibody domain in the context of its partner domain as the basis for antibody assembly and its control on the molecular level in the cell. These insights have not only allowed a better understanding of the antibody folding process but also provide a wealth of opportunities for rational optimization of antibody molecules. In this review, we summarize current concepts of antibody folding and assembly and discuss how they can be utilized to engineer antibodies with improved performance for different applications. This article is part of a Special Issue entitled: Recent advances in the molecular engineering of antibodies.

The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins

Sharks and other cartilaginous fish are the phylogenetically oldest living organisms that rely on antibodies as part of their adaptive immune system. They produce the immunoglobulin new antigen receptor (IgNAR), a homodimeric heavy chain-only antibody, as a major part of their humoral adaptive immune response. Here, we report the atomic resolution structure of the IgNAR constant domains and a structural model of this heavy chain-only antibody. We find that despite low sequence conservation, the basic Ig fold of modern antibodies is already present in the evolutionary ancient shark IgNAR domains, highlighting key structural determinants of the ubiquitous Ig fold. In contrast, structural differences between human and shark antibody domains explain the high stability of several IgNAR domains and allowed us to engineer human antibodies for increased stability and secretion efficiency. We identified two constant domains, C1 and C3, that act as dimerization modules within IgNAR. Together with the individual domain structures and small-angle X-ray scattering, this allowed us to develop a structural model of the complete IgNAR molecule. Its constant region exhibits an elongated shape with flexibility and a characteristic kink in the middle. Despite the lack of a canonical hinge region, the variable domains are spaced appropriately wide for binding to multiple antigens. Thus, the shark IgNAR domains already display the well-known Ig fold, but apart from that, this heavy chain-only antibody employs unique ways for dimerization and positioning of functional modules.

Proteins improving recombinant antibody production in mammalian cells

Mammalian cells have been successfully used for the industrial manufacture of antibodies due to their ability to synthesize antibodies correctly. Nascent polypeptides must be subjected to protein folding and assembly in the ER and the Golgi to be secreted as mature proteins. If these reactions do not proceed appropriately, unfolded or misfolded proteins are degraded by the ER-associated degradation (ERAD) pathway. The accumulation of unfolded proteins or intracellular antibody crystals accompanied by this failure triggers the unfolded protein response (UPR), which can considerably attenuate the levels of translation, folding, assembly, and secretion, resulting in reduction of antibody productivity. Accumulating studies by omics-based analysis of recombinant mammalian cells suggest that not only protein secretion processes including protein folding and assembly but also translation are likely to be the rate-limiting factors for increasing antibody production. Here, this review describes the mechanism of antibody folding and assembly and recent advantages which could improve recombinant antibody production in mammalian cells by utilizing proteins such as ER chaperones or UPR-related proteins.

Understanding the complex mechanisms of β2-microglobulin amyloid assembly

Several protein misfolding diseases are associated with the conversion of native proteins into ordered protein aggregates known as amyloid. Studies of amyloid assemblies have indicated that non-native proteins are responsible for initiating aggregation in vitro and in vivo. Despite the importance of these species for understanding amyloid disease, the structural and dynamic features of amyloidogenic intermediates and the molecular details of how they aggregate remain elusive. This review focuses on recent advances in developing a molecular description of the folding and aggregation mechanisms of the human amyloidogenic protein β(2)-microglobulin under physiologically relevant conditions. In particular, the structural and dynamic properties of the non-native folding intermediate I(T) and its role in the initiation of fibrillation and the development of dialysis-related amyloidosis are discussed.

Effect of heat treatment of bovine colostrum on bacterial counts, viscosity, and Immunoglobulin G concentration

A study was conducted to identify the optimal temperature and time at which heat treatment of bovine colostrum would least change viscosity and IgG concentrations yet reduce bacterial count. First-milking colostrum with >50g of immunoglobulins/L (measured by colostrometer) was collected from 30 Holstein cows. Aliquots of colostrum were heated for 0, 30, 60, or 90min at 57, 60, or 63 degrees C in a water bath. Samples were examined for viscosity, IgG(1), and IgG(2) concentrations, standard plate count, coagulase-negative staphylococci, environmental streptococci, coliform, gram-negative noncoliform, Streptococcus agalactiae, and Staphylococcus aureus counts. All heat treatments reduced counts of all bacteria groups measured compared with untreated colostrum samples. Heat treatment at >or=60 degrees C denatured IgG(1) compared with untreated colostrum; however, colostral IgG(2) levels were not reduced when temperature was held at 60 degrees C for <60min. Viscosity was not affected when temperature was held at 60 degrees C for <60min. In this study, heat treatment of bovine colostrum at 60 degrees C for 30 or 60min reduced bacterial count, slightly reduced IgG concentration, and did not affect viscosity.

How antibodies fold

B cells use unconventional strategies for the production of a seemingly unlimited number of antibodies from a very limited amount of DNA. These methods dramatically increase the likelihood of producing proteins that cannot fold or assemble appropriately. B cells are therefore particularly dependent on 'quality control' mechanisms to oversee antibody production. Recent in vitro experiments demonstrate that Ig domains have evolved diverse folding strategies ranging from robust spontaneous folding to intrinsically disordered domains that require assembly with their partner domains to fold; in vivo experiments reveal that these different folding characteristics form the basis for cellular checkpoints in Ig transport. Taken together, these reports provide a detailed understanding of how B cells monitor and ensure the functional fidelity of Ig proteins.

The folding pathway of the antibody V(L) domain

Antibodies are modular proteins consisting of domains that exhibit a beta-sandwich structure, the so-called immunoglobulin fold. Despite structural similarity, differences in folding and stability exist between different domains. In particular, the variable domain of the light chain V(L) is unusual as it is associated with misfolding diseases, including the pathologic assembly of the protein into fibrillar structures. Here, we have analysed the folding pathway of a V(L) domain with a view to determine features that may influence the relationship between productive folding and fibril formation. The V(L) domain from MAK33 (murine monoclonal antibody of the subtype kappa/IgG1) has not previously been associated with fibrillisation but is shown here to be capable of forming fibrils. The folding pathway of this V(L) domain is complex, involving two intermediates in different pathways. An obligatory early molten globule-like intermediate with secondary structure but only loose tertiary interactions is inferred. The native state can then be formed directly from this intermediate in a phase that can be accelerated by the addition of prolyl isomerases. However, an alternative pathway involving a second, more native-like intermediate is also significantly populated. Thus, the protein can reach the native state via two distinct folding pathways. Comparisons to the folding pathways of other antibody domains reveal similarities in the folding pathways; however, in detail, the folding of the V(L) domain is striking, with two intermediates populated on different branches of the folding pathway, one of which could provide an entry point for molecules diverted into the amyloid pathway.

An unfolded CH1 domain controls the assembly and secretion of IgG antibodies

A prerequisite for antibody secretion and function is their assembly into a defined quaternary structure, composed of two heavy and two light chains for IgG. Unassembled heavy chains are actively retained in the endoplasmic reticulum (ER). Here, we show that the C(H)1 domain of the heavy chain is intrinsically disordered in vitro, which sets it apart from other antibody domains. It folds only upon interaction with the light-chain C(L) domain. Structure formation proceeds via a trapped intermediate and can be accelerated by the ER-specific peptidyl-prolyl isomerase cyclophilin B. The molecular chaperone BiP recognizes incompletely folded states of the C(H)1 domain and competes for binding to the C(L) domain. In vivo experiments demonstrate that requirements identified for folding the C(H)1 domain in vitro, including association with a folded C(L) domain and isomerization of a conserved proline residue, are essential for antibody assembly and secretion in the cell.

A remote prolyl isomerization controls domain assembly via a hydrogen bonding network

Prolyl cis/trans isomerizations determine the rates of protein folding reactions and can serve as molecular switches and timers. In the gene-3-protein of filamentous phage, Pro-213 trans --> cis isomerization in a hinge region controls the assembly of the 2 domains N1 and N2 and, in reverse, the activation of the phage for infection. We elucidated the structural and energetic basis of this proline-limited domain assembly at the level of individual residues by real-time 2D NMR. A local cluster of inter-domain hydrogen bonds, remote from Pro-213, is stabilized up to 3,000-fold by trans --> cis isomerization. This network of hydrogen bonds mediates domain assembly and is connected with Pro-213 by rigid backbone segments. Thus, proline cis/trans switching is propagated in a specific and directional fashion to change the protein structure and stability at a distant position.

Molecular determinants of a native-state prolyl isomerization

Prolyl cis/trans isomerizations determine the rates of many protein-folding reactions, and they can serve as molecular switches and timers. The energy required to shift the prolyl cis/trans equilibrium during these processes originates from conformational reactions that are linked structurally and energetically with prolyl isomerization. We used the N2 domain of the gene-3-protein of phage fd to elucidate how such an energetic linkage develops in the course of folding. The Asp160-Pro161 bond at the tip of a beta hairpin of N2 is cis in the crystal structure, but in fact, it exists as a mixture of conformers in folded N2. During refolding, about 10 kJ mol(-1) of conformational energy becomes available for a 75-fold shift of the cis/trans equilibrium constant at Pro161, from 7/93 in the unfolded to 90/10 in the folded form. We combined single- and double-mixing kinetic experiments with a mutational analysis to identify the structural origin of this proline shift energy and to elucidate the molecular path for the transfer of this energy to Pro161. It originates largely, if not entirely, from the two-stranded beta sheet at the base of the Pro161 hairpin. The two strands improve their stabilizing interactions when Pro161 is cis, and this stabilization is propagated to Pro161, because the connector peptides between the beta strands and Pro161 are native-like folded when Pro161 is cis. In the presence of a trans-Pro161, the connector peptides are locally unfolded, and thus, Pro161 is structurally and energetically uncoupled from the beta sheet. Such interrelations between local folding and prolyl isomerization and the potential modulation by prolyl isomerases might also be used to break and reestablish slow communication pathways in proteins.

The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity

Folding intermediates play a key role in defining protein folding and assembly pathways as well as those of misfolding and aggregation. Yet, due to their transient nature, they are poorly accessible to high-resolution techniques. Here, we made use of the intrinsically slow folding reaction of an antibody domain to characterize its major folding intermediate in detail. Furthermore, by a single point mutation we were able to trap the intermediate in equilibrium and characterize it at atomic resolution. The intermediate exhibits the basic beta-barrel topology, yet some strands are distorted. Surprisingly, two short strand-connecting helices conserved in constant antibody domains assume their completely native structure already in the intermediate, thus providing a scaffold for adjacent strands. By transplanting these helical elements into beta(2)-microglobulin, a highly homologous member of the same superfamily, we drastically reduced its amyloidogenicity. Thus, minor structural differences in an intermediate can shape the folding landscape decisively to favor either folding or misfolding.

Denaturant-induced expansion and compaction of a multi-domain protein: IgG

It is generally believed that unfolded or denatured proteins show random-coil statistics and hence their radius of gyration simply scales with solvent quality (or concentration of denaturant). Indeed, nearly all proteins studied thus far have been shown to undergo a gradual and continuous expansion with increasing concentration of denaturant. Here, we use fluorescence correlation spectroscopy (FCS) to show that while protein A, a multi-domain and predominantly helical protein, expands gradually and continuously with increasing concentration of guanidine hydrochloride (GdnHCl), the F(ab')2 fragment of goat anti-rabbit antibody IgG, a multi-subunit all beta-sheet protein does not show such continuous expansion behavior. Instead, it first expands and then contracts with increasing concentration of GdnHCl. Even more striking is the fact that the hydrodynamic radius of the most expanded F(ab')2 ensemble, observed at 3-4 M GdnHCl, is approximately 3.6 times that of the native protein. Further FCS measurements involving urea and NaCl show that the unusually expanded F(ab')2 conformations might be due to electrostatic repulsions. Taken together, these results suggest that specific interactions need to be considered while assessing the conformational and statistical properties of unfolded proteins, particularly under conditions of low solvent quality.

Influence of the Internal Disulfide Bridge on the Folding Pathway of the CL Antibody Domain

Disulfide bridges are one of the most important factors stabilizing the native structure of a protein. Whereas the basis for their stabilizing effect is well understood, their role in a protein folding reaction still seems to require further attention. We used the constant domain of the antibody light chain (C(L)), a representative of the ubiquitous immunoglobulin (Ig)-superfamily, to delineate the kinetic role of its single buried disulfide bridge. Independent of its redox state, the monomeric C(L) domain adopts a typical Ig-fold under native conditions and does not retain significant structural elements when unfolded. Interestingly, its folding pathway is strongly influenced by the disulfide bridge. The more stable oxidized protein folds via a highly structured on-pathway intermediate, whereas the destabilized reduced protein populates a misfolded off-pathway species on its way to the native state. In both cases, the formation of the intermediate species is shown to be independent of the isomerization state of the Tyr(141)-Pro(142) bond. Our results demonstrate that the internal disulfide bridge in an antibody domain restricts the folding pathway by bringing residues of the folding nucleus into proximity thus facilitating the way to the native state.

Biophysical characterization of insoluble aggregates of a multi-domain protein: an insight into the role of the various domains

Insoluble (visible) aggregates of a homodimer fusion glycoprotein, consisting of the first extracellular domain of a human protein, fused to the hinge, C(H)2, and C(H)3 domains of a human immunoglobulin G(1) (IgG(1)), were observed during early formulation development. The soluble fraction of the fusion protein was compared to the visible aggregates by various biophysical techniques such as intrinsic and ANS fluorescence emission, reducing and nonreducing SDS-PAGE, equilibrium folding and refolding experiments in urea and guanidine hydrochloride in the absence and presence of mercaptoethanol. Significant differences were observed between the visible aggregates and the supernatant. Partial unfolding of the aggregated molecules was detected by intrinsic and ANS fluorescence. Using urea and guanidine hydrochloride unfolding/solubilization and refolding curves, it was possible to extrapolate that (i) the aggregates were not covalently linked but tightly associated, (ii) the fused domains of the protein were unfolded but not involved in the aggregation process, (iii) the C(H)2 domains were native-like, and (iv) the C(H)3 domains were involved in the aggregation process.

A Stable Disulfide-free Gene-3-protein of Phage fd Generated by In vitro Evolution

Disulfide bonds provide major contributions to the conformational stability of proteins, and their cleavage often leads to unfolding. The gene-3-protein of the filamentous phage fd contains two disulfides in its N1 domain and one in its N2 domain, and these three disulfide bonds are essential for the stability of this protein. Here, we employed in vitro evolution to generate a disulfide-free variant of the N1-N2 protein with a high conformational stability. The gene-3-protein is essential for the phage infectivity, and we exploited this requirement for a proteolytic selection of stabilized protein variants from phage libraries. First, optimal replacements for individual disulfide bonds were identified in libraries, in which the corresponding cysteine codons were randomized. Then stabilizing amino acid replacements at non-cysteine positions were selected from libraries that were created by error-prone PCR. This stepwise procedure led to variants of N1-N2 that are devoid of all three disulfide bonds but stable and functional. The best variant without disulfide bonds showed a much higher conformational stability than the disulfide-containing wild-type form of the gene-3-protein. Despite the loss of all three disulfide bonds, the midpoints of the thermal transitions were increased from 48.5 degrees C to 67.0 degrees C for the N2 domain and from 60.0 degrees C to 78.7 degrees C for the N1 domain. The major loss in conformational stability caused by the removal of the disulfides was thus over-compensated by strongly improved non-covalent interactions. The stabilized variants were less infectious than the wild-type protein, probably because the domain mobility was reduced. Only a small fraction of the sequence space could be accessed by using libraries created by error-prone PCR, but still many strongly stabilized variants could be identified. This is encouraging and indicates that proteins can be stabilized by mutations in many different ways.

Nuclear Magnetic Resonance Characterization of the Refolding Intermediate of β2-Microglobulin Trapped by Non-native Prolyl Peptide Bond

beta(2)-Microglobulin (beta2-m), a light chain of the major histocompatibility complex type I, is also found as a major component of amyloid fibrils formed in dialysis-related amyloidosis. Denaturation of beta2-m is considered to initiate the formation of fibrils. To clarify the mechanism of fibril formation, it is important to characterize the intermediate conformational states at the atomic level. Here, we investigated the refolding of beta2-m from the acid-unfolded state by heteronuclear magnetic resonance and circular dichroism spectroscopies. At low temperature, beta2-m refolded slowly, accumulating a rate-limiting intermediate with non-native chemical shift dispersions for several residues, but with compactness and secondary structures similar to those of the native protein. beta2-m has a cis proline residue at Pro32, located on the turn connecting the betaB and betaC strands. The slow refolding phase disappeared upon mutation of Pro32 to Val, indicating that Pro32 is responsible for the accumulation of the intermediate. The distribution of the perturbed residues in the intermediate suggests that the non-native prolyl peptide bond of Pro32 affects large areas of the molecule. A cis proline residue is common to various immunoglobulin domains involved in amyloidosis, implying that a non-native prolyl peptide bond that might occur under physiological conditions is related to the amyloidogenicity of these immunoglobulin domains.

Folding Mechanism of the CH2 Antibody Domain

The immunoglobulin C(H)2 domain is a simple model system suitable for the study of the folding of all-beta-proteins. Its structure consists of two beta-sheets forming a greek-key beta-barrel, which is stabilized by an internal disulfide bridge located in the hydrophobic core. Crystal structures of various antibodies suggest that the C(H)2 domains of the two heavy chains interact with their sugar moieties and form a homodimer. Here, we show that the isolated, unglycosylated C(H)2 domain is a monomeric protein. Equilibrium unfolding was a two-state process, and the conformational stability is remarkably low compared to other antibody domains. Folding kinetics of C(H)2 were found to consist of several phases. The reactions could be mapped to three parallel pathways, two of which are generated by prolyl isomerizations in the unfolded state. The slowest folding reaction, which was observed only after long-term denaturation, could be catalyzed by a prolyl isomerase. The majority of the unfolded molecules, however, folded more rapidly, on a time-scale of minutes. Presumably, these molecules also have to undergo prolyl isomerization before reaching the native state. In addition, we detected a small number of fast-folding molecules in which all proline residues appear to be in the correct conformation. On both prolyl isomerization limited pathways, the formation of partly structured intermediates could be observed.

How additives influence the refolding of immunoglobulin-folded proteins in a stepwise dialysis system. Spectroscopic evidence for highly efficient refolding of a single-chain Fv fragment

The gradual removal of the denaturing reagent guanidine HCl (GdnHCl) using stepwise dialysis with the introduction of an oxidizing reagent and l-arginine resulted in the highly efficient refolding of various denatured single-chain Fv fragments (scFvs) from inclusion bodies expressed in Escherichia coli. In this study, the influence of the additives on the intermediates in scFv refolding was carefully analyzed on the basis of the stepwise dialysis, and it was revealed that the additive effect critically changes the pathway of scFv refolding. Circular dichroism and tryptophan fluorescence emission spectroscopies demonstrated that distinct secondary and tertiary structures were formed upon dialysis from 2 m GdnHCl to 1 m GdnHCl, and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid dipotassium salt binding analysis indicated that the addition of l-arginine to the stepwise dialysis system effectively stabilized the exposed hydrophobic area on the scFv. Quantification of the free thiol groups in the scFv by means of Ellman's assay revealed that there was a particular stage in which most of the free thiol groups were oxidized and that adding an oxidizing reagent (the oxidized form of glutathione, GSSG) at that stage was important for complete refolding of the scFv. The particular stage depended on the nature of the refolding solution, especially on whether l-arginine was present. Spontaneous folding at the 1 m GdnHCl stage resulted in a structure in which a free thiol group accessed to the proper one for correct disulfide linkage; however, the addition of l-arginine resulted in the formation of a partially folded intermediate without disulfide linkages. Mass spectrometry experiments on alkylated scFv were carried out at each stage to determine the effects of l-arginine. The spectroscopic studies revealed two different pathways for scFv refolding in the stepwise dialysis system, pathways that depended on whether l-arginine was present. Controlled coupling of the effects of GSSG and l-arginine led to the complete refolding of scFv in the stepwise dialysis.

Kinetic mechanism and catalysis of a native-state prolyl isomerization reaction

Folding of tendamistat is a rapid two-state process for the majority of the unfolded molecules. In fluorescence-monitored refolding kinetics about 8% of the unfolded molecules fold slowly (lambda=0.083s(-1)), limited by peptidyl-prolyl cis-trans isomerization. This is significantly less than expected from the presence of three trans prolyl-peptide bonds in the native state. In interrupted refolding experiments we detected an additional very slow folding reaction (lambda=0.008s(-1) at pH 2) with an amplitude of about 12%. This reaction is caused by the interconversion of a highly structured intermediate to native tendamistat. The intermediate has essentially native spectroscopic properties and about 2% of it remain populated in equilibrium after folding is complete. Catalysis by human cyclophilin 18 identifies this very slow reaction as a prolyl isomerization reaction. This shows that prolyl-isomerases are able to efficiently catalyze native state isomerization reactions, which allows them to influence biologically important regulatory conformational transitions. Folding kinetics of the proline variants P7A, P9A, P50A and P7A/P9A show that the very slow reaction is due to isomerization of the Glu6-Pro7 and Ala8-Pro9 peptide bonds, which are located in a region that makes strong backbone and side-chain interactions to both beta-sheets. In the P50A variant the very slow isomerization reaction is still present but native state heterogeneity is not observed any more, indicating a long-range destabilizing effect on the alternative native state relative to N. These results enable us to include all prolyl and non-prolyl peptide bond isomerization reactions in the folding mechanism of tendamistat and to characterize the kinetic mechanism and the energetics of a native-state prolyl isomerization reaction.

The alternatively folded state of the antibody C(H)3 domain

The C(H)3 domain of antibodies is characterized by two antiparallel beta-sheets forming a disulfide-linked sandwich-like structure. At acidic pH values and low ionic strength, C(H)3 becomes completely unfolded. The addition of salt transforms the acid-unfolded protein into an alternatively folded state exhibiting a characteristic secondary structure. The transition from native to alternatively folded C(H)3 is a fast reaction. Interestingly, this reaction involves the formation of a defined oligomer consisting of 12-14 subunits. Association is completely reversible and the native dimer is quantitatively reformed at neutral pH. This alternatively folded protein is remarkably stable against thermal and chemical denaturation and the unfolding transitions are highly cooperative. With a t(m) of 80 degrees C, the stability of the alternatively folded state is comparable to that of the native state of C(H)3. The defined oligomeric structure of C(H)3 at pH 2 seems to be a prerequisite for the cooperative unfolding transitions.

The scFv fragment of the antibody hu4D5-8: evidence for early premature domain interaction in refolding

Fluorescence spectroscopy and 1H/2H-exchange techniques have been applied to characterize the folding of an scFv fragment, derived from the humanized anti-HER2 antibody hu4D5-8. A stable intermediate, consisting of a native VL domain and an unfolded VH domain, is populated under equilibrium unfolding conditions. A partially structured intermediate, with 1H/2H-exchange protection significantly less than that of the two isolated domains together, is detectable upon refolding the equilibrium-denatured scFv fragment. This means that the domains in the heterodimer do not fold independently. Rather, they associate prematurely before full 1H/2H-exchange protection can be gained. The formation of the native heterodimer from the non-native intermediate is a slow, cooperative process, which is rate-limited by proline cis/trans-isomerization. Unproductive domain association is also detectable after short-term denaturation, i.e. with the proline residues in native conformation. Only a fraction of the short-term denatured protein folds into the native protein in a fast, proline-independent reaction, because of spontaneous proline cis/trans-reisomerization in the early non-native intermediate. The comparison with the previously studied antibody McPC603 has now allowed us to delineate similarities in the refolding pathway of scFv fragments.

Chromatographic purification of the C(H)2 domain of the monoclonal antibody MAK33

The C(H)2 domain, one of the constant domains of the murine monoclonal antibody MAK33 (immunoglobulin subtype K/IgG1) was expressed in Escherichia coli forming insoluble inclusion bodies (IBs) and purified by a three-step process including a denaturation-renaturation step, hydrophobic interaction and gel permeation chromatography. After disrupting the cells, the soluble protein fraction was removed by several centrifugation steps. The isolation of the IBs from the cell fragments was achieved by solubilizing the IBs with 6 M guanidinium hydrochloride (GdmCl) and 0.1 M 1,4-dithioerythrit (DTE) to reduce all disulfide bonds. After refolding the C(H)2 domain, 1.5 M (NH4)2SO4 was added to the protein solution in order to precipitate contaminations. Then the protein was loaded on a Butyl-Sepharose fast flow column and eluted with a linear gradient [1.5-0 M (NH4)2SO4]. As the last purification step a gel permeation chromatography was run on a Superdex 75 prep grade. Finally, the purity of the C(H)2 protein was determined by a silver-stained sodium dodecyl sulfate polyacrylamide gel. We achieved a typical yield of 0.5 mg pure protein per 1 g of wet cells.

Folding and association of the antibody domain CH3: prolyl isomerization preceeds dimerization

The simplest naturally occurring model system for studying immunoglobulin folding and assembly is the non-covalent homodimer formed by the C-terminal domains (CH3) of the heavy chains of IgG. Here, we describe the structure of recombinant CH3 dimer as determined by X-ray crystallography and an analysis of the folding pathway of this protein. Under conditions where prolyl isomerization does not contribute to the folding kinetics, formation of the beta-sandwich structure is the rate-limiting step. beta-Sheet formation of CH3 is a slow process, even compared to other antibody domains, while the subsequent association of the folded monomers is fast. After long-time denaturation, the majority of the unfolded CH3 molecules reaches the native state in two serial reactions, involving the re-isomerization of the Pro35-peptide bond to the cis configuration. The species with the wrong isomer accumulate as a monomeric intermediate. Importantly, the isomerization to the correct cis configuration is the prerequisite for dimerization of the CH3 domain. In contrast, in the Fab fragment of the same antibody, prolyl isomerization occurs after dimerization demonstrating that within one protein, comprised of highly homologous domains, both the kinetics of beta-sandwich formation and the stage at which prolyl isomerization occurs during the folding process can be completely different.

Protein folding in the ER

The endoplasmic reticulum (ER) is a major protein folding compartment for secreted, plasma membrane and organelle proteins. Each of these newly-synthesized polypeptides folds in a deterministic process, affected by the unique conditions that exist in the ER. An understanding of protein folding in the ER is a fundamental biomolecular challenge at two levels. The first level addresses how the amino acid sequence programs that polypeptide to efficiently arrive at a particular fold out of a multitude of alternatives, and how different sequences obtain similar folds. At the second level are the issues introduced by folding not in the cytosol, but in the ER, including the risk of aggregation in a molecularly crowded environment, accommodation of post-translational modifications and the compatibility with subsequent intracellular trafficking. This review discusses both the physicochemical and cell biological constraints of folding, which are the challenges that the ER molecular chaperones help overcome.

Conformation, pH-induced conformational changes, and thermal unfolding of anti-p24 (HIV-1) monoclonal antibody CB4-1 and its Fab and Fc fragments

Conformation, acid-induced conformational changes and stability of the murine monoclonal antibody CB4-1 directed against the human immunodeficiency virus type 1 capsid protein p24, and its Fab and Fc fragments, were analysed by circular dichroism (CD), fluorescence, and differential scanning calorimetry (DSC) measurements. CD spectra show the characteristics expected for beta-proteins. Lowering the pH to 3.5 reduces the stability, but does not change the conformation. Between pH 3.5 and 2.0 conformational changes and the formation of new structures are indicated. Deconvolution of the bimodal DSC curves of CB4-1 reveals five 'two-state' transitions at pH 7.5. At pH 5 and below, only four transitions are found. Half transition temperatures Tm and molar enthalpy changes DeltaHm gradually decrease at pH 4 and 3.4. At pH 2.1, two low-temperature (Tm=36.9 and 44.1 degrees C) and two high-temperature (Tm=74.6 and 76.8 degrees C) transitions are identified. The Fab and Fc fragments behave similarly. Deconvolution of their monophasic DSC curves yields two 'two-state' transitions for each fragment. Tm and DeltaHm values gradually decrease at pH 4.0 and 3.4; and at pH 2.1 and 2.8 for Fab and Fc, respectively, one of the transitions is found at high temperature (Tm=67.2 and 75.9 degrees C for Fab and Fc, respectively).

Folding and assembly of an antibody Fv fragment, a heterodimer stabilized by antigen

The folding and assembly of the Fv fragment of the phosphorylcholine binding antibody McPC603, a non-covalent heterodimer of the variable domains VH and VL, was investigated. Since both domains, each engineered for stability and folding efficiency, could now be obtained in native and soluble form by themselves, fluorescence spectra of VH and VL in unfolded, folded and associated states can be reported. VH and VL only associate when they are native, and the stability of the heterodimer is strongly increased in the presence of antigen. VH rapidly folds into an hyperfluorescent intermediate, and the native state is reached in two parallel, proline-independent reactions. VL displays two fast refolding reactions, which are followed by two slower phases, limited by proline cis/trans-isomerization. The rate-limiting step for both the Fv and the scFv (single-chain Fv) fragment is the formation of the native VH-VL interface, which depends on ProL95 being in cis. The folding of the Fv fragment is fast after short-term denaturation or in the presence of proline cis/trans-isomerase catalysis, but the scFv fragment falls into a kinetic trap, observed by the persistence of the slow phases under all conditions. Furthermore, the scFv fragment, but not the Fv fragment, gives rise to premature interface formation, indicated by the fluorescence spectra and a much higher transient binding of 8-anilino-1-naphthalene sulfonate. The analysis of the folding pathway of the domains VH and VL in isolation and in non-covalent and covalent assemblies should provide helpful insights into the folding of multimeric proteins in general, and for the further engineering of stable and well-folding antibody fragments in particular.

Enhanced secretory production of a single-chain antibody fragment from Bacillus subtilis by coproduction of molecular chaperones

Formation of inclusion bodies is a major limiting factor for secretory production of an antidigoxin single-chain antibody (SCA) fragment from Bacillus subtilis. To address this problem, three new strains with enhanced production of molecular chaperones were constructed. WB600BHM constitutively produces the major intracellular molecular chaperones in an appropriate ratio without any heat shock treatment. This strain reduced the formation of insoluble SCA by 45% and increased the secretory production yield by 60%. The second strain, WB600B[pEPP], overproduces an extracytoplasmic molecular chaperone, PrsA. An increase in the total yield of SCA was observed. The third strain, WB600BHM[pEPP], coproduces both intracellular and extracytoplasmic molecular chaperones. This led to a further reduction in inclusion body formation and a 2.5-fold increase in the secretory production yield. SCA fragments secreted by this strain were biologically active and showed affinity to digoxin comparable to the affinity of those secreted by strains without overproduction of molecular chaperones. Interestingly, accumulation of a pool of periplasmic SCA was observed in the PrsA-overproducing strains. This pool is suggested to represent the secreted folding intermediates in the process of achieving their final configuration.

Parallel pathways in the folding of a short-term denatured scFv fragment of an antibody

BACKGROUND

Antibodies are prototypes of multimeric proteins and consist of structurally similar domains. The two variable domains of an antibody (VH and VL) interact through a large hydrophobic interface and can be expressed as covalently linked single-chain Fv (scFv) fragments. The in vitro folding of scFv fragments after long-term denaturation in guanidinium chloride is known to be slow. In order to delineate the nature of the rate-limiting step, the folding of the scFv fragment of an antibody after short-term denaturation has been investigated.

RESULTS

Secondary structure formation, measured by H/D-exchange protection, of a mutant scFv fragment of an antibody after short incubation in 6 M guanidinium chloride was shown to be multiphasic. NMR analysis shows that an intermediate with significant proton protection is observed within the dead time of the manual mixing experiments. Subsequently, the folding reaction proceeds via a biphasic reaction and mass spectrometry analyses of the exchange experiments confirm the existence of two parallel pathways. In the presence of cyclophilin, however, the faster of the two phases vanishes (when followed by intrinsic tryptophan fluorescence), while the slower phase is not significantly enhanced by equimolar cyclophilin.

CONCLUSIONS

The formation of an early intermediate, which shows amide-proton exchange protection, is independent of proline isomerization. Subsequently, a proline cis-trans isomerization reaction in the rapidly formed intermediate, producing 'non-native' isomers, competes with the fast formation of native species. Interface formation in a folding intermediate of the scFv fragment is proposed to prevent the back-isomerization of these prolines from being efficiently catalyzed by cyclophilin.

Fractionation and characterization of polyclonal antibodies using three progressively more chaotropic solvents

In the previous paper we described the effect of several different solvents on the structure of antibodies and demonstrated that 0.1 M glycine, pH 2.9, 7 M urea, pH 4.0, and 6 M guanidine-HCl, pH 4.0, unfold the antibodies to different degrees. Antibodies can be refolded from all of these solvents by dialysis. Polyclonal antibodies (pAbs) are a mixture of antibodies which recognize and bind different epitopes on the same antigen, with the strength of the antigen-antibody binding varying with each subpopulation. When rabbit antisera to the extracellular domain of Her2 receptor (sHer2), derived from Chinese hamster ovary cells, was applied to an antigen column, bound pAbs were recovered with a step-wise elution of 0.1 M glycine, pH 2.9 (44% of the total recovered pAb), 7 M urea, pH 4.0 (29%), and 6 M guanidine-HCl, pH 4.0 (27%), with baseline resolution between them. Fluorescence spectra of the pAbs confirmed that the 0. 1 M glycine pH 2.9 sample had near-native structure, the pAbs in 7 M urea, pH 4.0, were partially unfolded, and the pAbs in the 6 M guanidine-HCl, pH 4.0, were totally unfolded. The glycine- or urea-eluted sample was refolded by dialysis into PBS, while the guanidine-HCl-eluted sample was first dialyzed into the 7 M urea pH 4.0 buffer and then into PBS. The refolded material from glycine or urea had native-like spectra, while the spectrum of the protein refolded from 6 M guanidine-HCl was slightly perturbed. All three of these subpopulations of pAbs formed antigen-antibody complexes which could be isolated by gel-filtration chromatography, precipitated sHer2 during immunoprecipitation, and recognized sHer2 in Western blots. The guanidine-HCl-eluted material was most sensitive for Western blotting. Identical results were obtained with pAbs applied either in the batch mode or to the top of the column, indicating that antibody aggregation which may occur when applied from the top of the column is not responsible for the distribution of pAbs into different subpopulations. These results indicate that the sequential use of these three increasingly chaotropic solvents to elute antibodies results in both increased recovery of antibodies and fractionation of pAbs into subpopulations with potentially different antigen binding characteristics.

Folding of the Fab fragment within the intact antibody

At present it is not clear to which extent the Fab fragment and the Fc part of an antibody interact in the intact immunoglobulin structure. To determine such potential interactions the unfolding and refolding of an isolated Fab fragment and the respective antibody MAK 33 (kappa/IgG1) are compared. It could be shown that the proline independent renaturation kinetics of both an unfolding intermediate and the fully denatured form of both proteins are identical. Upon denaturation, the loss of antigen binding activity occurs with the same rate for both the Fab fragment and the intact antibody. However, the complete structural unfolding of the Fab part of the antibody is significantly slower than that of the isolated Fab fragment. These kinetic data suggest that the structure of the Fab fragment within the intact antibody is stabilized by interactions, presumably with the Fc part, missing in the isolated Fab.

The role of a trans-proline in the folding mechanism of ribonuclease T1

Protein folding is often retarded by the cis reversible trans isomerizations of prolyl peptide bonds both in vitro and in vivo. An important role for the folding mechanism is well established for the prolyl peptide bonds that are cis in the native protein, but not for those that are trans. Here we investigated the role of trans-Pro73 for the folding of ribonuclease T1 (which additionally contains two cis-prolines) by comparing the wild-type protein with the Pro73-->Val variant. The Pro-->Val substitution led to a destabilization of the folded protein by 8.5 kJ/mol, which is explained by the strong, 25-fold increase in the rate of unfolding. In contrast, the rates and amplitudes of the fast and slow refolding reactions were virtually unchanged. trans-Proline residues remain largely trans after unfolding, and therefore their contributions to the observed folding kinetics should indeed be insignificant for proteins which also contain one or more cis prolines. The cis-proline residues dominate the kinetics of refolding, because almost all slow-folding molecules contain the respective incorrect (trans) isomers, and because trans-->cis isomerizations are slower than cis-->trans isomerizations. The inability to detect contributions from a trans-proline to the kinetics of folding does not imply that this proline is non-essential for folding in the sense that its cis reversible trans isomerization is energetically uncoupled from conformational folding.

Investigation of the folding pathway of the TEM-1 beta-lactamase

The TEM-1 beta-lactamase is a globular protein containing 12 proline residues. The folding mechanism of this enzyme was investigated by kinetic and equilibrium experiments with the help of fluorescence spectroscopy and circular dichroism. The equilibrium denaturation of the protein induced by guanidine hydrochloride occurs in two discrete steps, indicating the existence of a thermodynamically stable intermediate state. This state is 5.2 +/- 0.4 kcal/mol less stable than the native conformation and 5.7 +/- 0.2 kcal/mol more stable than the fully denatured protein. This intermediate state exhibits a high content of native secondary structure elements but is devoid of specific tertiary organization; its relation to the "molten globule" is discussed. Refolding kinetic experiments revealed the existence of a transient intermediate conformation between the thermodynamically stable intermediate and the native protein. This transient intermediate appears rapidly during the folding reaction. It exhibits a secondary structure content very similar to that of the native protein and has also recovered a significant amount of tertiary organisation. The final refolding step of the TEM-1 beta-lactamase, leading to the native enzyme, is dominated by two major slow kinetic phases which probably reflect a very complex process kinetically limited by proline cis/trans isomerization.

Molecular chaperones and the biosynthesis of antigen receptors

Oligomeric antigen receptors must fold and assemble in the endoplasmic reticulum (ER) before they can be expressed on the surface of lymphocytes. It is increasingly evident that these processes are facilitated by molecular chaperones. Here, Jeffrey Melnick and Yair Argon review the known ER chaperones, summarize their roles in the maturation of antigen receptors, and discuss how they may affect lymphocyte differentiation and function.

Characterization of a quaternary-structured folding intermediate of an antibody Fab-fragment

Antibody folding is a complex process comprising folding and association reactions. Although it is usually difficult to characterize kinetic folding intermediates, in the case of the antibody Fab fragment, domain-domain interactions lead to a rate-limiting step of folding, thus accumulating folding intermediates at a late step of folding. Here, we analyzed a late folding intermediate of the Fab fragment of the monoclonal antibody MAK 33 from mouse (kappa/IgG1). As a strategy for accumulation of this intermediate we used partial denaturation of the native Fab by guanidinium chloride. This denaturation intermediate, which can be populated to about 90%, is indistinguishable from a late-folding intermediate with respect to denaturation and renaturation kinetics. The spectroscopic analysis reveals a native-like secondary structure of this intermediate with aromatic side chains only slightly more solvent exposed than in the native state. The respective partner domains are weekly associated. From these data we conclude that the intramolecular association of the two chains during folding, with all domains in a native-like structure, follows a two-step mechanism. In this mechanism, presumably hydrophobic interactions are followed by rearrangements leading to the exact complementarity of the contact sites of the respective domains.

Non-prolyl cis-trans peptide bond isomerization as a rate-determining step in protein unfolding and refolding

In wild-type ribonuclease T1 the peptide bond between Tyr38 and Pro39 is in the cis conformation. When Pro39 is replaced by an alanine this cis conformation is retained, and a non-prolyl cis Tyr38-Ala39 peptide bond is generated. We employed a stopped-flow double-mixing technique to investigate the kinetics of the cis-->trans isomerization of this peptide bond in the unfolding and the trans-->cis isomerization in the refolding of Pro39Ala-ribonuclease T1. In 6.0 M GdmCl (pH 1.6) and 25 degrees C the protein unfolds rapidly with a time constant of 20 ms, followed by Tyr38-Ala39 cis-->trans isomerization. This reaction shows a time constant of 730 ms and is about 60-fold faster than the isomerization of the Tyr38-Pro39 bond in the wild-type protein. Unfolded molecules with the Tyr38-Ala39 bond still in the native-like cis conformation accumulate transiently for a short time after unfolding is initiated, and they can refold very rapidly to the native state with a time constant of 290 ms (in 1.0 M GdmCl, pH 4.6, 25 degrees C). After more than three seconds of unfolding virtually all protein molecules contain an incorrect trans Tyr38-Ala39 bond and refolding is decelerated approximately 1000-fold, because Tyr38-Ala39 trans-->cis re-isomerization is very slow and, with its time constant of 480 s, determines the overall rate of refolding. Due to the coupling of the cis-trans equilibrium with protein folding it was possible to measure the kinetic parameters of the isomerization of a non-prolyl peptide bond in a protein. Previously this could not be accomplished, because the trans isomer is strongly preferred for unsubstituted peptide bonds in oligopeptides under virtually all conditions. Our data indicate that the kinetics of Tyr38-Pro39 and of Tyr38-Ala39 isomerization differ predominantly in the rate of the cis-->trans, rather than of the trans-->cis reaction. The rate of the trans-->cis reaction is, however, measured during refolding and may be influenced by the formation of ordered protein structure.

Quantitative analysis of the kinetics of denaturation and renaturation of barstar in the folding transition zone

The fluorescence-monitored kinetics of folding and unfolding of barstar by guanidine hydrochloride (GdnHCl) in the folding transition zone, at pH 7, 25 degrees C, have been quantitatively analyzed using a 3-state mechanism: U(S)<-->UF<-->N. U(S) and UF are slow-refolding and fast-refolding unfolded forms of barstar, and N is the native protein. U(S) and UF probably differ in possessing trans and cis conformations, respectively, of the Tyr 47-Pro 48 bond. The 3-state model could be used because the kinetics of folding and unfolding of barstar show 2 phases, a fast phase and a slow phase, and because the relative amplitudes of the 2 phases depend only on the final refolding conditions and not on the initial conditions. Analysis of the observed kinetics according to the 3-state model yields the values of the 4 microscopic rate constants that describe the transitions between the 3 states at different concentrations of GdnHCl. The value of the equilibrium unfolded ratio U(S):UF (K21) and the values of the rate constants of the U(S)-->UF and UF-->U(S) reactions, k12 and k21, respectively, are shown to be independent of the concentration of GdnHCl. K21 has a value of 2.1 +/- 0.1, and k12 and k21 have values of 5.3 x 10(-3) s-1 and 11.2 x 10(-3) s-1, respectively. Double-jump experiments that monitor reactions that are silent to fluorescence monitoring were used to confirm the values of K21, k12, and k21 obtained from the 3-state analysis and thereby the validity of the 3-state model.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetic characterization of the chemotactic protein from Escherichia coli, CheY. Kinetic analysis of the inverse hydrophobic effect

CheY, the 129 amino acid chemotactic protein from Escherichia coli, is a good model for studying the folding process of the parallel alpha/beta family of proteins. A study of the folding kinetics of CheY using fluorescence and far-UV circular dichroism (CD) stopped-flow measurements is reported. CheY has three prolines, two of them in the trans conformation and one, Pro110, with a cis Lys-Pro peptide bond. This protein presents a unimolecular, but complex, kinetic mechanism that is dominated by a slow phase compatible with a trans-cis isomerization. Mutation of Pro110 to Gly results in the disappearance of this slow phase, indicating that this cis prolyl bond is responsible for it. The slow phase is catalyzed in a very inefficient way by prolyl isomerase, indicating that the cis bond is poorly accessible to the enzyme during refolding. In agreement with this is the fact that the isomerization of the Lys109-Pro110 bond occurs in an intermediate which contains 96% of the native far-UV CD signal and 80% of the native fluorescence signal. Analysis of the unfolded protein with all its prolines in the native conformation shows the existence of a very stable intermediate in the folding reaction. Mutation of a hyperexposed hydrophobic residue, Phe14, to Asn results in an increase in the free energy of unfolding of the protein of approximately 3 kcal mol-1. Kinetic analysis of the unfolding and refolding reactions of this mutant indicates that the major stabilization effect comes from the relative destabilization of the unfolded state and the kinetic intermediate with respect to the transition state, providing kinetic evidence for the inverse hydrophobic effect. This could also indicate the existence of nonnative interactions in folding intermediates.