Monoclonal antibodies as probes of conformational changes in protein-engineered cytochrome c

Correlation between antigenicity and variability in the vls antigenic variation system of Borrelia burgdorferi

Many parasites have evolved antigenic variation systems that alter surface proteins in order to evade recognition by presently expressed antibodies and subsequent death. Although the amino acid positions in antigens to which antibodies most commonly target are expected to be the most variable, this assumption has not been investigated. Using the vls antigenic variation system of Borrelia burgdorferi as a model, we first investigated this assumption computationally and then developed a sensitive immunoassay to experimentally validate the computational results. There was a strong correlation between variability at an amino acid position and each of the computational metrics associated with antibody reactivity. However, empirical measures of antibody reactivity were not consistently greater at the variable amino acid positions than at the invariant amino acid positions. The inconsistent experimental support for this hypothesis suggests that the biological effect of variability at an amino acid position is obfuscated by other factors.

Distribution of the c-MYC gene product in colorectal neoplasia

AIMS

Recent attempts to study MYC distribution in human samples have been confounded by a lack of agreement in immunohistochemical staining between antibodies targeting the N-terminus and those targeting the C-terminus of the MYC protein. The aim of this study was to use a novel in-situ hybridization (ISH) approach to detect MYC mRNA in clinically relevant samples, and thereby determine the reliability of MYC-targeting antibodies.

METHODS AND RESULTS

We performed immunohistochemistry on human formalin-fixed paraffin embedded normal colon (n = 15), hyperplastic polyp (n = 4) and neoplastic colon samples (n = 55), using the N-terminally directed antibody Y69, and the C-terminally directed antibody 9E10. The MYC protein distributions were then compared with the location of MYC mRNA, determined by ISH. We found that the localization of MYC mRNA correlated well with the protein distribution determined with the N-terminally directed antibody Y69, and was also associated with expression of the proliferation marker Ki67. The protein distribution determined with the C-terminally directed antibody 9E10 was not always associated with MYC mRNA, Y69, or Ki67, and indeed often showed a reciprocal pattern of expression, with staining being strongest in non-proliferating cells.

CONCLUSIONS

The observed discrepancy between the staining patterns suggests that the significance of 9E10 in immunohistochemical staining is currently uncertain, and therefore should be interpreted with caution.

A structurally based approach to determine HLA compatibility at the humoral immune level

HLAMatchmaker is a structurally based matching program. Each HLA antigen is viewed as a string of epitopes represented by short sequences (triplets) involving polymorphic amino acid residues in antibody-accessible positions. HLAMatchmaker determines which triplets are different between donor and recipient, and this algorithm is clinically useful in determining HLA mismatch acceptability. Triplets provide however an incomplete description of the HLA epitope repertoire and expanded criteria must be used including longer sequences and polymorphic residues in discontinuous positions. Such criteria should consider the structural basis of antibody-antigen interactions including contact areas and binding energy, the essence of antigenicity. This report describes the development of a structurally defined HLA epitope repertoire based on stereochemical modeling of crystallized complexes of antibodies and different protein antigens. This analysis considered also data in the literature about contributions of amino acid residues to antigen-antibody binding energy. The results have led to the concept that HLA antigens like other antigenic proteins have structural epitopes consisting of 15-22 residues that constitute the binding face with alloantibody. Each structural epitope has a functional epitope of about 2-5 residues that dominate the strength and specificity of binding with antibody. The remaining residues of a structural epitope provide supplementary interactions that increase the stability of the antigen-antibody complex. Each functional epitope has one or more non-self residues and the term "eplet" is used to describe polymorphic HLA residues within 3.0-3.5 A of a given sequence position on the molecular surface. Many eplets represent short linear sequences identical to those referred to as triplets but others have residues in discontinuous sequence positions that cluster together on the molecular surface. Serologically defined HLA determinants correspond well to eplets. The eplet version of HLAMatchmaker represents therefore a more complete repertoire of structurally defined HLA epitopes and provides a more detailed assessment of HLA compatibility.

Monoclonal Antibody Epitope Mapping Describes Tailspike β-Helix Folding and Aggregation Intermediates

There is growing interest in understanding how the cellular environment affects protein folding mechanisms, but most spectroscopic methods for monitoring folding in vitro are unsuitable for experiments in vivo or in other complex mixtures. Monoclonal antibody binding represents a sensitive structural probe that can be detected against the background of other cellular components. A panel of antibodies has been raised against Salmonella typhimurium phage P22 tailspike. In this report, nine alpha-tailspike antibody binding epitopes were characterized by measuring the binding of these monoclonal antibodies to tailspike variants bearing surface point mutations. These results reveal that the antibody epitopes are distributed throughout the tailspike structure, with several clustered in the central parallel beta-helix domain. The ability of each antibody to distinguish between tailspike conformational states was assessed by measuring antibody binding to tailspike in vitro refolding intermediates. Interestingly, the binding of all but one of the nine antibodies is sensitive to the tailspike conformational state. Whereas several antibodies bind preferentially to the tailspike native structure, the structural features that comprise the binding epitopes form with different rates. In addition, two antibodies preferentially recognize early refolding intermediates. Combined with the epitope mapping, these results indicate portions of the beta-helix form early during refolding, perhaps serving as a scaffold for the formation of additional structure. Finally, three of the antibodies show enhanced binding to non-native, potentially aggregation-prone tailspike conformations. The refolding results indicate these non-native conformations form early during the refolding reaction, long before the appearance of native tailspike.

Amino acid residue substitution at T-cell determinant-flanking sites in beta-lactoglobulin modulates antigen presentation to T cells through subtle conformational change

We compared T-cell responses to regions in residues 21-40 of A and B variants of bovine milk beta-lactoglobulin (beta-LG) that vary by two different amino acid residues at 64 and 118. Results showed that T cells from C57/BL6 and C3H/HeN mice immunized with peptide 21-40 or BALB/c mice immunized with peptide 21-32 or 25-40 responded more vigorously to beta-LG B than to beta-LG A. This difference in response to 25-40 in BALB/c mice was not observed when beta-LGs B and A were denatured, suggesting that the conformation difference affects display of the determinant 25-40. Reactivity of anti-beta-LG monoclonal antibodies and molecular modeling using molecular dynamics calculations revealed subtle differences in the three-dimensional structure of these two variants. Furthermore, substitution of two amino acid residues at sites distant from the T-cell determinant induced differential determinant display on antigen-presenting cells, possibly due to subtle conformational changes in beta-LG.

Characterization of anti-irradiation-denatured ovalbumin monoclonal antibodies. Immunochemical and structural analysis of irradiation-denatured ovalbumin

Five monoclonal antibodies (OVA-01, -02, -03, -04, -06) produced against irradiated ovalbumin were investigated in relation to the conformational change in the ovalbumin molecule induced by irradiation with Cobalt-60 gamma-rays. Four antibodies (OVA-01, -02, -04, -06) recognized both native and irradiated ovalbumin, but OVA-03 reacted only with irradiated ovalbumin. These antibodies were classified by modified competitive ELISA, and their K(d) values were determined by the Klotz equation. Epitope analyses were also performed on OVA-03 using CNBr-cleaved peptide fragments from ovalbumin, and it was confirmed that OVA-03 bound to the fragment corresponding to residues Val173-Met196 of the ovalbumin molecule that consists of internal beta-sheet strand 3A and helix F1 containing one open turn. These results demonstrate that dramatic conformational changes in proteins can be induced or that some tertiary or secondary structures can be broken down by gamma-ray irradiation, producing new antigenic sites.

Monoclonal antibodies as probes for the changes in antigenicity of bovine and porcine aspartyl proteases with pH

Two monoclonal antibodies, 918(4) and 139(7), directed against either bovine or porcine pepsin, respectively, were retained among 365 positive hybridoma clones. These monoclonal antibodies were characterized by using both indirect and sandwich ELISA. Characterization of these monoclonal antibodies was further performed by the biospecific interaction analysis (BIA-core analysis). Then, they were used as antigenic probes to study the changes in antigenicity of both bovine and porcine pepsins induced by pH. The results demonstrated the importance of the conformational change in both catalytic activities and antigenic determinant accessibility of bovine and porcine pepsins. Furthermore, our results suggest that changes in the conformation due to pH can be detected by specific monoclonal antibodies.

Active concentration measurements of recombinant biomolecules using biosensor technology

Whereas the concentration of a biomolecule simply refers to the amount of chemical substance per unit of volume, its active concentration refers to a relational parameter that has meaning only with respect to the molecule's ability to interact specifically with one particular ligand. When proteins are studied in a biological context, it is the biologically active concentration that is relevant, and not the total concentration of correctly and incorrectly folded molecules. Using a biosensor instrument the concentration of active biomolecules in a preparation can be measured by injecting the preparation at different flow rates onto a sensor chip surface presenting a high concentration of a specific ligand. The method can be used under conditions of partial mass transport limitation and does not require a pre-established standard curve. When the method was used to measure the active concentration of several recombinant proteins it was found that the active concentration was much lower than the nominal concentration determined by conventional methods. The active concentration also depended on the ligand used in the binding assay, reflecting the fact that active concentration can only be defined with respect to one specific probe. Such discrepancies in concentration values, if undetected, may lead to erroneous conclusions regarding the properties and behaviour of recombinant proteins tested in different assays.

Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution

A complete understanding of antibody-antigen association and specificity requires the stereochemical description of both antigen and antibody before and upon complex formation. The structural mechanism involved in the binding of the IgG1 monoclonal antibody E8 to its highly charged protein antigen horse cytochrome c (cyt c) is revealed by crystallographic structures of the antigen-binding fragment (Fab) of E8 bound to cyt c (FabE8-cytc), determined to 1.8 A resolution, and of uncomplexed Fab E8 (FabE8), determined to 2.26 A resolution. E8 antibody binds to three major discontiguous segments (33 to 39; 56 to 66; 96 to 104), and two minor sites on cyt c opposite to the exposed haem edge. Crystallographic definition of the E8 epitope complements and extends biochemical mapping and two-dimensional nuclear magnetic resonance with hydrogen-deuterium exchange studies. These combined results demonstrate that antibody-induced stabilization of secondary structural elements within the antigen can propagate locally to adjacent residues outside the epitope. Pre-existing shape complementarity at the FabE8-cytc interface is enhanced by 48 bound water molecules, and by local movements of up to 4.2 A for E8 antibody and 8.9 A for cyt c. Glu62, Asn103 and the C-terminal Glu104 of cyt c adjust to fit the pre-formed VL "hill" and VH "valley" shape of the grooved E8 paratope. All six E8 complementarity determining regions (CDRs) contact the antigen, with CDR L1 forming 46% of the total atomic contacts, and CDRs L1 (29%) and H3 (20%) contributing the highest percentage of the total surface area of E8 buried by cyt c (550 A2). The E8 antibody covers 534 A2 of the cyt c surface. The formation of five ion pairs between E8 and flexible cyt c residues Lys60, Glu62 and Glu104 suggests the importance of mobile regions and electrostatic interactions in providing the exquisite specificity needed for recognition of this extremely conserved protein antigen. The highly homologous VL domains of E8 and anti-lysozyme antibody D1. 3 achieve their distinct antigen-binding specificities by expanding the impact of their limited sequence differences through the recruitment of different sets of conserved residues and distinctly different CDR L3 conformations.

Probing intramolecular electron transfer within flavocytochrome b2 with a monoclonal antibody

Flavocytochrome b2 or L-lactate dehydrogenase from yeast is a tetrameric enzyme which oxidizes lactate at the expense of cytochrome c or artificial electron acceptors. The prosthetic group FMN is reduced by the substrate and then transfers sequentially the reducing equivalents to heme b2 in the same subunit. The latter is reoxidized by cytochrome c. The crystal structure of the enzyme indicates that each subunit is composed of a flavodehydrogenase domain (FDH) and a cytochrome b2 domain; the latter, which encompasses the first 99 residues of the peptide chain, is mobile relative to the tetrameric FDH assembly. We describe here the properties of a monoclonal antibody elicited against the holoenzyme. It only recognizes the heme-binding domain, with a Kd lower than 10(-7) M, and its epitope is conformational. In the enzyme-IgG complex, flavin is reduced normally and can be reoxidized by ferricyanide, but no longer by heme b2. Stopped-flow experiments in the absence of electron acceptors give no indication of flavin to heme electron transfer in the enzyme-antibody complex. In other words, the two domains are functionally uncoupled. The binding stoichiometry is 1/1 for the Fab fragment with respect to the isolated, monomeric, heme-binding domain, but 2/4 with respect to the enzyme tetramer; furthermore, binding of two Fab fragments per tetramer is sufficient to cause inhibition of intra-subunit flavin to heme electron transfer in all four subunits. Altogether these results can only be rationalized by considering that mobility of the cytochrome domain with respect to the FDH is an essential component of the catalytic cycle. The first experiment designed to locate the epitope shows it does not encompass the interdomain peptide linker (so-called hinge region, centered on residues 99-100).

Conformational changes in MHC class I molecules. Antibody, T-cell receptor, and NK cell recognition in an HLA-B7 model system

In this article we review the role of MHC conformation, including peptide-induced MHC conformation, in forming antibody (Ab), T-cell receptor (TCR), and natural killer (NK) cell receptor epitopes. Abs recognize conformational major histocompatibility (MHC) epitopes that often are influenced by the identity of MHC-bound peptide. Diverse TCRs recognize a common docking site on peptide/MHC complexes and directly contact peptide. Human NK cell inhibitory receptors (KIR) appear to recognize limited regions of the HLA alpha (1) helix. DX9+ KIR specifically focus on HLA-B residues 82 and 83. However, NK cells recognize much broader regions of HLA class I molecules and are sensitive to bound peptides. Thus, several classes of lymphocyte receptors are peptide-specific. Peptide specificity could be the result of direct contact with the receptor, or to conformational shifts in MHC residues that interact with both receptor and bound peptide.

Structural analysis of bovine somatotropin using monoclonal antibodies and the conformation-sensitive immunoassay

Bovine somatotropin was studied with respect to thermal stability, quantitative thermal denaturation kinetics, and refolding potential following thermal denaturation using a panel of 6 monoclonal antibodies and the Conformation-Sensitive Immunoassay (CSI). The antibody panel consisted of 4 conformation-dependent and 2 sequence-specific antibodies. Each of the antibodies revealed unique thermal stability profiles for their respective epitopes suggesting that they each recognize different antigenic determinants. Comparing the thermal stability profiles generated with these antibodies allowed the stability of bovine somatotropin to be "dissected" based on individual structural features. The degree to which bovine somatotropin is stabilized by disulfide bonds was examined using CSI-based quantitative thermal denaturation kinetics profiles generated under reducing and nonreducing conditions. All of the conformational epitopes unfolded faster under reducing conditions indicating that the two disulfide bonds within the somatotropin molecule impart some degree of global stabilization. The ability of bovine somatotropin to refold after reducing or nonreducing thermal denaturation was also examined using the antibody panel and the CSI. The results show that, although significant refolding was evident for some epitopes, bovine somatotropin cannot refold to the native state following thermal denaturation under either reducing or nonreducing conditions.

Refolding of riboflavin carrier protein as probed by biochemical and immunological parameters

The unfolding of the chicken egg white riboflavin carrier protein by disulfide reduction with dithiothreitol led to aggregation with concomitant loss of ligand binding characteristics and the capacity to interact with six monoclonal antibodies directed against surface-exposed discontinuous epitopes. The reduced protein could, however, bind to a monoclonal antibody recognizing sequential epitope. Under optimal conditions of protein refolding, the vitamin carrier protein regained its folded structure with high efficiency with simultaneous complete restoration of hydrophobic flavin binding site as well as the epitopic conformations exposed at the surface in a manner comparable to its native form.

The self antigen heme evades immune recognition by sequestration in some hemoproteins

Heme is a non-protein autoantigen which is ubiquitous in vivo, primarily complexed in various hemoproteins or bound to specialized carrier molecules. Nevertheless, heme is able to stimulate a high frequency of CD4+, class II-restricted T cells, freshly explanted from unprimed mice, to proliferate in vitro. In this study, we show that heme incorporated into various species of mammalian cytochrome c (cyt c), including murine cyt c, represents a facultative cryptic determinant, able to be recalled only at high doses of native cyt c. By contrast, avian cyt c is of comparable antigenicity to free heme. Artificially denatured carboxymethylated (CM) mammalian cyt c exhibited greatly increased antigenicity, comparable to that of heme and avian cyt c, indicating that the crypticity of heme in native mammalian cyt c is due to the resistance of the native conformation of this molecule to antigen processing within murine antigen-presenting cells. Thus, tolerance to the heme group of at least some hemoproteins, may be maintained by the crypticity of the heme, rather than by deletion of heme-reactive T cells. Given the high frequency of heme-reactive T cells in unprimed mice, these findings suggest that heme may become an important modulator during an inflammatory response.

Configurational effects in antibody-antigen interactions studied by microcalorimetry

In this paper we study the binding of two monoclonal antibodies, E3 and E8, to cytochrome c using high-sensitivity isothermal titration calorimetry. We combine the calorimetric results with empirical calculations which relate changes in heat capacity to changes in entropy which arise from the hydrophobic effect. The change in heat capacity for binding E3 is -350 +/- 60 cal K-1 mol-1 while for E8 it is -165 +/- 40 cal K-1 mol-1. This result indicates that the hydrophobic effect makes a much larger contribution for E3 than for E8. Since the total entropy change at 25 degrees C is very similar for both antibodies, it follows that the configurational entropy cost for binding E3 is much larger than for binding E8 (-77 +/- 15 vs. -34 +/- 11 cal K-1 mol-1). These results illustrate a case of entropy compensation in which the cost of restricting conformational degrees of freedom is to a large extent compensated by solvent release. We also show that the thermodynamic data can be used to make estimates of the surface area changes that occur upon binding. The results of the present study are consistent with previous hydrogen-deuterium exchange data, detected using 2D NMR, on the two antibody-antigen interactions. The NMR study indicated that protection from exchange is limited to the binding epitope for E8, but extends beyond the epitope for E3.(ABSTRACT TRUNCATED AT 250 WORDS)

Mutagenesis of the human interleukin-6 fourth predicted alpha-helix: involvement of the Arg168 in the binding site

Random substitutions of amino acid 161-184 of human interleukin-6 (hIL-6) have been generated at the cDNA level using oligonucleotide-directed mutagenesis. Among the majority of the mutant proteins showing a reduced biological activity on murine hybridoma cells, only those having a substitution of Met161, Arg168, Arg179 or Met184, retained a tertiary structure similar to the IL-6 folding. These residues are thus probably involved in the interaction with the IL-6 receptor. However, the contacts established by Arg168 and Arg179 seem far more important for the biological activity. According to Bazan's model of cytokine folding and the receptor binding site on the fourth alpha-helix, based on growth hormone similarity, we propose that Arg168 and Arg179 are located on the exposed surface of this presumed helix.

HLA-B*0702 antibody epitopes are affected indirectly by distant antigen residues

We examine the effect of mutations in the HLA-B*0702 alpha 1 domain on the binding of several well-characterized monoclonal antibodies. BB7.1 recognizes the alpha-helix, with a special requirement for residue 67. Combined with an established requirement for the alpha 2 alpha-helix, BB7.1 appears to span the B*0702 peptide-binding groove. Alternatively, BB7.1 epitope conformation may be altered by distant B*0702 sites. ME1 and B27M1 recognize connecting loop residues 41 and 43 and alpha 1 alpha-helical residues 67-71. Instead of contacting residue 67-71 side chains directly, however, ME1 appears to recognizes a B*0702 configuration that depends upon the proper interaction of these and other HLA residues. In addition to solvent-accessible residues 41 and 43, the B27M1 epitope depends on solvent-inaccessible residue 32 at the bottom of the peptide-binding groove. MB40.2, known to require residues 169-182 near the alpha 2-alpha 3 junction, also requires the proper combination of distant residues in the alpha 1 beta-strand and alpha-helix. The effect of mutations near the peptide-binding groove suggests that bound peptides may directly or indirectly affect HLA epitopes. These results illustrate that HLA epitope conformation is very sensitive to changes at distant HLA sites and forecast that epitope models based on sequential amino acid residues will often fail to predict HLA epitopes.

Involvement of the Arg179 in the active site of human IL-6

Three internal-amino acid deletions of amino acids 171-179 of human interleukin 6 (IL-6) were introduced at the cDNA level. While all deletion proteins were biologically inactive, immunoprecipitations with a set of conformation-specific anti-(IL-6) monoclonal antibodies showed that only mutant delta 177-179 does not present major alterations in folding. This finding, together with the observation that delta 177-179 is not able to compete with IL-6 for binding to the soluble human IL-6 receptor, suggested that some or all of these three residues participate to the composition of the receptor-binding site of human IL-6. A large number of single-amino-acid-substitution mutants were generated in residues 177, 178 and 179. Their detailed analysis revealed that Arg179 is crucial for activity in mouse cells, because all amino acid substitutions in this position cause a dramatic drop of biological activity on murine hybridoma cells without affecting the overall protein folding. The only substitution which preserved some residual activity was the conservative Arg to Lys change. This demonstrates the absolute requirement for a positive charge in position 179 for the interaction of human IL-6 with its receptor.

Kinetics of inter-heavy chain disulfide bond formation of liganded and unliganded human immunoglobulin G by radioimmunoassay

Monoclonal antibodies (mAbs) to the hinge region of human IgG1 immunoglobulins were prepared by immunization with a proteolytic fragment of hinge segment coupled to keyhole limpet hemocyanin. A mAb, 4G3, was obtained capable of binding to intact IgG but not to partially reduced IgG. Using this mAb, inter-heavy (H) chain disulfide bond formation from partially reduced anti-tetanus antibodies (Abs) in the presence or absence of antigens (Ags) was studied by solid phase radioimmunoassay. When the Abs were partially reduced in solution and then coated to plastic plates, only 10% regeneration of inter-H chain disulfide bonds occurred after reoxidation, although 100% formation occurred in solution [Kishida et al., J. Biochem. (Tokyo) 79, 91-105 (1976)]. This difference in the extent of disulfide bond formation can be explained by the fact that there are two convertible isomers in solution, Conformer I and II, one of which (Conformer I) can form disulfide bonds but is present as a minor component. Since the motion of IgG molecules on plates is restricted by hydrophobic interactions, the two conformers are not convertible as in solution. Therefore only Conformer I which existed before coating formed inter-H chain disulfide bonds. Similar kinetic measurements were performed using plates coated with tetanus toxoid. Abs, partially reduced in solution and then allowed to react with Ags on the plate were able to completely regenerate their inter-H chain disulfide bonds, although the rate of reaction was slow. These results can also be explained by the fact that the two isomers are convertible since Ag-Ab complexes are dissociable. Ag-binding therefore did not significantly perturb conformation of the hinge segments. In addition, no difference between liganded and unliganded Abs was observed in the binding of anti-hinge mAbs. These results imply little or no contribution of the hinge region to transmission of the signal produced by Ag-binding to Fc.

Structure-function relationships of the hematopoietic growth factors

The hematopoietic growth factors are a family of glycoproteins involved in the production of blood cells from their bone marrow precursors and in the activation of mature blood cells. Much has been learned about the structural features of these molecules responsible for their characteristic biological activities. Most studies have been based upon mutagenesis strategies of intact polypeptides and on epitope mapping of informative monoclonal antibodies to the growth factors. A more limited amount of physical data is available. This review will summarize these findings, highlight the growing body of evidence suggesting that many of these proteins share common evolutionary origins and structural elements, and hopefully point to the directions being taken for further investigations of these scientifically informative and clinically useful group of proteins.

Investigating protein conformation, dynamics and folding with monoclonal antibodies

Monoclonal antibodies with thoroughly characterized target specificities can be used as powerful probes of protein conformation. In addition to providing information on the relative arrangement of the domains in the native molecule, they can also be used to monitor both early and late stages of protein folding and conformational changes related to enzyme action.

Biochemical implications from the variable gene sequences of an anti-cytochrome c antibody and crystallographic characterization of its antigen-binding fragment in free and antigen-complexed forms

To study the nature of antibody-antigen interactions, we have determined the variable gene sequences of the anti-cytochrome c immunoglobulin G1 (IgG1) monoclonal antibody E8, and obtained diffraction-quality crystals of the E8 antigen-binding fragment (Fab), both free and bound to its antigen, horse cytochrome c. The FabE8 crystals belong to space group P21 with unit cell dimensions of a = 45.0 A, b = 85.1 A, c = 63.3 A and beta = 105.5 degrees, have one FabE8 molecule per asymmetric unit and diffract to at least 2.1 A resolution. Crystals of the FabE8-cytochrome c complex belong to space group P212121 with unit cell dimensions of a = 84.3 A, b = 73.3 A and c = 94.9 A, accommodate one complex per asymmetric unit and diffract to 2.4 A resolution. In the nucleotide-derived amino acid sequences, the light-chain variable domain (VL) but not the heavy-chain variable domain (VH) of E8 is nearly identical to that of the anti-lysozyme antibody D1.3, differing by only five amino acid residues. Only one of these interacts with lysozyme in the D1.3-lysozyme crystal structure. Six negative and four positive charges in the VH complementarity determining regions of E8 complement four positive and three negative charges in the E8 epitope on cytochrome c. These data suggest that only a subset of the residues in an antibody-protein interface may be critical for binding and that the VH may play a dominant role in antigenic recognition.

An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR

The interaction of a protein antigen, horse cytochrome c (cyt c), with a monoclonal antibody has been studied by hydrogen-deuterium (H-D) exchange labeling and two-dimensional nuclear magnetic resonance (2D NMR) methods. The H-exchange rate of residues in three discontiguous regions of the cyt c polypeptide backbone was slowed by factors up to 340-fold in the antibody-antigen complex compared with free cyt c. The protected residues, 36 to 38, 59, 60, 64 to 67, 100, and 101, and their hydrogen-bond acceptors, are brought together in the three-dimensional structure to form a contiguous, largely exposed protein surface with an area of about 750 square angstroms. The interaction site determined in this way is consistent with prior epitope mapping studies and includes several residues that were not previously identified. The hydrogen exchange labeling approach can be used to map binding sites on small proteins in antibody-antigen complexes and may be applicable to protein-protein and protein-ligand interactions in general.

The conformation-sensitive immunoassay: a membrane based ELISA system for identifying antibodies sensitive to alterations of protein conformation

A Conformation-Sensitive Immunoassay (CSI) has been developed for identification of antibodies that are sensitive to alterations in protein conformation. The method involves covalently coupling proteins to an activated hydrophilic membrane support. The membrane bound proteins are then treated under conditions known to alter protein conformation, immobilized in a non-native state via additional covalent interactions with the support, and subsequently probed using conventional ELISA techniques. This method has been validated using several well characterized conformation-sensitive antibodies to horse cytochrome c and sperm whale myoglobin. A panel of monoclonal antibodies directed against bovine somatotropin (bSt) has been partially characterized using this validated CSI procedure. Each of these antibodies to bSt has been shown to detect conformational alterations of bSt structure. Data are also presented that demonstrates that the accuracy of CSI analysis is superior to that of Western blotting for characterizing conformation-sensitive antibodies.

Structural changes in myosin subfragment 1 by mild denaturation and proteolysis probed by antibodies

The perturbations in the structure of myosin subfragment 1 (S1) by mild denaturation or proteolysis were investigated by measuring the inhibition of the binding of antibodies to immobilized S1 by treated S1 in a solution-phase competitive immunochemical assay. The structural changes in S1 were probed by using anti-50-kDa segment, anti-N-terminus, anti-27-kDa segment, and anti-A1 light chain monoclonal antibodies (MAbs). Methanol and heat denaturation increased MAb binding to the 50-kDa segment. MAb binding to regions in the 27-kDa segment was also promoted, slightly by methanol and more drastically by heat. Proteolysis also induced structural alterations in 50- and 27-kDa segments as shown by increased MAb binding to these regions in cleaved S1. These results indicate that mild denaturation and proteolysis induce structural perturbations which alter the epitope accessibility in 50- and 27-kDa segments of S1 and that antibody binding studies afford a sensitive probe to such perturbations.

Monoclonal antibodies as probes for monitoring the denaturation process of bovine beta-lactoglobulin

Five monoclonal antibodies (MAbs) of different idiotypes were produced against bovine beta-lactoglobulin (beta-LG). Among them, MAbs 61B4 and 62A6 reacted preferentially to native beta-LG, while MAbs 21B3 and 31A4 reacted more strongly to the reduced carboxymethylated (denatured) beta-LG than to the native material. These two types of MAb were used to analyze the denaturation process of a beta-LG molecule during heating. The binding affinity of MAbs 21B3 and 31A4 with beta-LG was increased by increasing the heating temperature, the transition temperature being 67-68 degrees C, while that of MAbs 61B4 and 62A6 was reduced by increasing the temperature, this transition temperature being about 80 degrees C. Epitopes recognized by MAbs 31A4 and 61B4 were shown to be included in the segments, Lys8-Trp19 (mostly in the random-coil region) and Thr125-Lys135 (helical region), respectively. The heat-induced conformational change of the beta-LG molecule is, therefore, likely to start in random-coil region as Lys8-Trp19, and to be followed by a structural change in a helical region as Thr125-Lys135. This study demonstrates that MAb is a useful probe to monitor local conformational changes of a protein molecule during denaturation.

Mapping of four discontiguous antigenic determinants on horse cytochrome c

The epitopes (antigenic determinants) recognized by four different monoclonal antibodies on horse cytochrome c have been partially characterized by differential acetylation of lysine residues of free and antibody-bound cytochrome c. The degree of acetylation in the bound and free antigen molecule was assessed by a double-labeling procedure with [3H]acetic anhydride and [14C]acetic anhydride. Out of the 19 lysine residues of cytochrome c only very few were less reactive in the antigen-antibody complex, i.e. presumably located at the epitope for the antibody under study. The protection varied from 1.5-fold to over 20-fold lower reactivity in antibody-bound cytochrome c. The present results are complemented by previous data obtained by cross-reactivity analysis with cytochromes c from different species, with chemically modified cytochrome c derivatives, and by inhibition of proteolysis of cytochrome c in the presence of the antibodies. From the combined data we conclude that each of the four epitopes depends on the precise spatial folding of the antigen and contains residues which are brought together by the folding of the polypeptide chain. This work exemplifies that mapping of conformation-dependent epitopes can be achieved by applying a combination of mapping procedures of which each by itself provides partial information.

Receptor and antibody epitopes in human growth hormone identified by homolog-scanning mutagenesis

A strategy, termed homolog-scanning mutagenesis, was used to identify the epitopes on human growth hormone (hGH) for binding to its cloned liver receptor and eight different monoclonal antibodies (Mab's). Segments of sequences (7 to 30 residues long) that were derived from homologous hormones known not to bind to the hGH receptor or Mab's, were systematically substituted throughout the hGH gene to produce a set of 17 chimeric hormones. Each Mab or receptor was categorized by a particular subset of mutant hormones was categorized by a particular subset of mutant hormones that disrupted binding. Each subset of the disruptive mutations mapped within close proximity on a three-dimensional model of hGH, even though the residues changed within each subset were usually distant in the primary sequence. The mapping analysis correctly predicted those Mab's which could or could not block binding of the receptor to hGH and further suggested (along with other data) that the folding of these chimeric hormones is like that of HGH. By this analysis, three discontinuous polypeptide determinants in hGH--the loop between residues 54 and 74, the central portion of helix 4 to the carboxyl terminus, and to a lesser extent the amino-terminal region of helix 1--modulate binding to the liver receptor. Homolog-scanning mutagenesis should be of general use in identifying sequences that cause functional variation among homologous proteins.

Size-exclusion high-performance liquid chromatography in analysis of protein and peptide epitopes

Size-exclusion HPLC provides direct observation of antibody-antigen interactions in free solution without chemical modification of either component. HPLC data collection systems are now a routine resource in both academic and industrial research laboratories. Monoclonal antibodies are, in principle, homogeneous reagents whose interactions with epitope are suitable for unambiguous quantitative characterization. HPLC-based methods, therefore, have the potential to contribute significantly to efficient quantitative characterization of monoclonal antibodies in studies directed to the fundamental physiological roles of these molecules as well as to the optimized selection and quality control of these reagents in biotechnical applications such as represented by the immunodiagnostic industry. In many cases, HPLC-based methods may represent the simplest and most rapid approach for evaluation of relative epitope specificities and affinity/kinetic characteristics of interaction.