Construction of an extended three-dimensional idiotope map by electron microscopic analysis of idiotope-anti-idiotope complexes

Epitopes, paratopes, and other topes 30 years on: Understanding what we are talking about

The question of which protein antigens, such as HLA class I or class II molecules, will bind, and how well, to a given antibody is often assumed to depend exclusively on the details of protein surface structure. These structures are usually based on static models resulting from X-ray crystallography. While these notions are useful, the ultimate causal factors determining how well a given antigen binds a given antibody are based in thermodynamics and can include atomic mobility and the time-varying conformations of proteins. In this article, fundamental biophysical principles of antibody-antigen interaction are discussed, concepts critical for a deeper understanding of the pertinent molecular phenomena are highlighted, and common misunderstandings are identified and debunked.

IgE Trimers Drive SPE-7 Cytokinergic Activity

Degranulation of mast cells and basophils, with release of agents of the allergic response, ensues when multivalent antigens bind to and cross-link the cells' receptor-bound IgE antibodies. A widely used commercial monoclonal IgE antibody, SPE-7 IgE from Sigma, was found to possess the radically anomalous property, termed "cytokinergic", of inducing basophil degranulation without the intervention of an antigen. We show here that the IgE monomer, freed of protein contaminants, is devoid of this activity, and that the source of the anomaly is a trace impurity, identified as a dissociation-resistant IgE trimer. Possible models for the formation of IgE trimers and the manner in which they cross-link cell surface receptors are suggested herein.

Site-Specifically Labeled Immunoconjugates for Molecular Imaging--Part 1: Cysteine Residues and Glycans

Due to their remarkable selectivity and specificity for cancer biomarkers, immunoconjugates have emerged as extremely promising vectors for the delivery of diagnostic radioisotopes and fluorophores to malignant tissues. Paradoxically, however, these tools for precision medicine are synthesized in a remarkably imprecise way. Indeed, the vast majority of immunoconjugates are created via the random conjugation of bifunctional probes (e.g., DOTA-NCS) to amino acids within the antibody (e.g., lysines). Yet antibodies have multiple copies of these residues throughout their macromolecular structure, making control over the location of the conjugation reaction impossible. This lack of site specificity can lead to the formation of poorly defined, heterogeneous immunoconjugates with suboptimal in vivo behavior. Over the past decade, interest in the synthesis and development of site-specifically labeled immunoconjugates—both antibody-drug conjugates as well as constructs for in vivo imaging—has increased dramatically, and a number of reports have suggested that these better defined, more homogeneous constructs exhibit improved performance in vivo compared to their randomly modified cousins. In this two-part review, we seek to provide an overview of the various methods that have been developed to create site-specifically modified immunoconjugates for positron emission tomography, single photon emission computed tomography, and fluorescence imaging. We will begin with an introduction to the structure of antibodies and antibody fragments. This is followed by the core of the work: sections detailing the four different approaches to site-specific modification strategies based on cysteine residues, glycans, peptide tags, and unnatural amino acids. These discussions will be divided into two installments: cysteine residues and glycans will be detailed in Part 1 of the review, while peptide tags and unnatural amino acids will be addressed in Part 2. Ultimately, we sincerely hope that this review fosters interest and enthusiasm for site-specific immunoconjugates within the nuclear medicine and molecular imaging communities.

IgE epitope proximity determines immune complex shape and effector cell activation capacity

Background

IgE-allergen complexes induce mast cell and basophil activation and thus immediate allergic inflammation. They are also important for IgE-facilitated allergen presentation to T cells by antigen-presenting cells.

Objective

To investigate whether the proximity of IgE binding sites on an allergen affects immune complex shape and subsequent effector cell activation in vitro and in vivo.

Methods

We constructed artificial allergens by grafting IgE epitopes in different numbers and proximity onto a scaffold protein. The shape of immune complexes formed between artificial allergens and the corresponding IgE was studied by negative-stain electron microscopy. Allergenic activity was determined using basophil activation assays. Mice were primed with IgE, followed by injection of artificial allergens to evaluate their in vivo allergenic activity. Severity of systemic anaphylaxis was measured by changes in body temperature.

Results

We could demonstrate simultaneous binding of 4 IgE antibodies in close vicinity to each other. The proximity of IgE binding sites on allergens influenced the shape of the resulting immune complexes and the magnitude of effector cell activation and in vivo inflammation.

Conclusions

Our results demonstrate that the proximity of IgE epitopes on an allergen affects its allergenic activity. We thus identified a novel mechanism by which IgE-allergen complexes regulate allergic inflammation. This mechanism should be important for allergy and other immune complex–mediated diseases.

The immunoglobulin constant region contributes to affinity and specificity

A central dogma in immunology is that antibody specificity is solely the result of variable (V)-region interactions with an antigen. However, this view is not tenable in light of numerous reports that constant heavy (C(H)) domains can affect binding affinity and specificity and V-region structure. Kinetic and thermodynamic proof for the occurrence of this phenomenon is now available. C(H)-region effects on affinity and specificity suggest new mechanisms for generating antibody diversity and polyreactivity (multispecificity) that impact current views on idiotype regulation, autoimmunity, and B cell selection and change our understanding of vaccine responses.

Electron microscopic and immunochemical analysis of the broadly neutralizing HIV-1-specific, anti-carbohydrate antibody, 2G12

2G12 is one of only a few cloned antibodies with broadly neutralizing specificity to HIV-1 envelope proteins. Crystallographic and electron microscopic (EM) data showed that the Fab arms are locked together via a novel VH domain exchange. Both the conventional and the unprecedented additional VH-VH antigen binding sites show specificity for high mannose oligosaccharides on the silent face of gp120. We have now extended the EM and biochemical analysis of 2G12. Unligated 2G12 IgG1 molecules clearly show paired (parallel attached) Fab arms in the "doughnut" configuration attached to the Fc both in individual and computationally averaged images. A minority of the IgG molecules in the 2G12 prep showed the open "Y" configuration of conventional IgG. The averaged EM image compares well to the atomic structure model of 2G12. Papain digests of 2G12 yielded paired Fab arms (Fab dimer), as observed by EM, which dissociated into Fab-sized fragments in non-reducing SDS-PAGE. Purified 2G12 reduced and alkylated H and L chains can reassociate to form IgG molecules with the Fab dimer configuration and can combine with L and H chains from conventional human IgG to form hybrid molecules. 2G12 is heavily aggregated following brief acid exposure possibly as a result of its unique structure. A model of the aggregation process is proposed. An anti-Id MAb was shown by EM to react with neither the conventional nor additional antigen binding sites, but bound to the lateral faces of the Fab arms of intact, reduced and alkylated, and reconstructed 2G12 molecules. Efforts to identify IgG molecules with a similar intertwined Fab dimer structure in a large IgG pool were unsuccessful.

A molecular model of type I allergy: identification and characterization of a nonanaphylactic anti-human IgE antibody fragment that blocks the IgE-FcepsilonRI interaction and reacts with receptor-bound IgE

BACKGROUND

The IgE-mediated activation of effector cells and antigen-presenting cells through the high-affinity receptor for IgE (FcepsilonRI) represents a key pathomechanism in type I allergy and many forms of asthma.

OBJECTIVE

We sought to establish an in vitro molecular model for the interaction of human FcepsilonRI, IgE, and the corresponding allergen and to identify monoclonal anti-human IgE antibodies with a therapeutic profile different from previously established anti-IgE antibodies.

METHODS

Human FcepsilonRI alpha chain, a human monoclonal allergen-specific IgE antibody (chimeric Bip 1), and the corresponding allergen, the major birch pollen allergen Bet v 1, were produced as recombinant proteins and analyzed by means of circular dichroism and native overlays, respectively. Using this molecular model, as well as negative stain immunoelectron microscopic analysis, and in vitro cultivated human basophils, we characterized mouse anti-human IgE antibodies.

RESULTS

We established a molecular model for the interaction of human IgE with FcepsilonRI. Using this molecular model, we identified a nonanaphylactic anti-human IgE antibody fragment (Fab12), which blocked the IgE-FcepsilonRI interaction and reacted with effector cell-bound IgE.

CONCLUSION

Fab12 represents a candidate molecule for therapy of atopy and asthma because it can be used for the depletion of circulating IgE antibodies, as well as for the depletion of IgE-bearing cells.

Inhibition of HLA antibody cytotoxicity by intravenous immunoglobulin G F(ab')2 dimers, monomers, and monovalent F(ab)

IVIgG preparations are clinically relevant to sensitized transplant candidates because they inhibit HLA alloantibody in vitro and in vivo. We hypothesized that IVIgG F(ab')2 idiotypic-antiidiotypic dimers may possess a greater immunomodulatory capacity when remonomerized than non-dimerizable F(ab')2 monomers in IVIgG. We reasoned that when 60-75% of potential antiidiotypic IVIgG monomers fail to bind to IVIgG molecules in a large pool of plasma donors (>10,000), IVIgG monomers may fail to inhibit HLA idiotypic antibodies of sensitized transplant candidates. In the first series of AHG T cell crossmatches, non-fractionated IVIgG F(ab')2 was found to inhibit titered HLA antibodies in 13 out of 29 (45%) crossmatch combinations. Crossmatch inhibition was incomplete, i.e., a particular titered HLA antibody specificity was not always inhibited by IVIgG F(ab')2 in every HLA antigen-matched target cell crossmatch. Next, the IVIgG F(ab')2 product was fractionated into F(ab')2 dimers, F(ab')2 monomers and Fab monovalent components by size exclusion high pressure liquid chromatography (HPLC) and retested in crossmatches which previously demonstrated inhibition. The percent of crossmatches that were inhibited by HPLC F(ab')2 IVIgG fractions in three separate experiments was statistically similar for pH 4.0 remonomerized dimers, 82%; pH 6.0 dimers, 50%; monomers, 64%; and monovalent Fab, 64% (p = 0.50). Soluble class I HLA antigen was undetectable in IVIgG F(ab')2 by an ELISA assay. In conclusion, IVIgG dimers and monomers appear to have similar immunomodulatory capacities, and separation of whole IVIgG products into dimer and monomer fractions does not appear to be warranted. Further, IVIgG products should be tested for optimal HLA antibody inhibition in vitro prior to in vivo therapy.

All-D peptides recognized by an anti-carbohydrate antibody identified from a positional scanning library

Monoclonal antibodies recognize antigens with high affinity and specificity, but the structural basis for molecular mimicry remains unclear. It is often assumed that cross-reactive antigens share some structural similarity that is specifically recognized by a monoclonal antibody. Recent studies using combinatorial libraries, which are composed of millions of sequences, have examined antibody cross-reactivity in a manner entirely different from traditional epitope mapping approaches. Here, peptide libraries were screened against an anti-carbohydrate monoclonal antibody for the identification of peptide mimics. Positional scanning libraries composed of all-l or all-d hexapeptides were screened for inhibition of monoclonal antibody HGAC 39.G3 binding to an antigen displaying N-acetyl-d-glucosamine (GlcNAc) residues on a polyrhamnose backbone. Inhibitory activity by mixtures from the all-d hexapeptide library was greater than the activity from the all-l libraries. The most active d-amino acid residues defined in each of the six positions of the library were selected to prepare 27 different individual hexapeptides. The sequence Ac-yryygl-NH2 was specifically recognized by mAb HGAC 39.G3 with a relative affinity of 300 nM when measured in a competitive binding assay. The contributions to overall specificity of the residues of the all-d peptide (Ac-yryygl-NH2) in binding to mAb HGAC 39.G3 were examined with a series of truncation, l and d-amino acid substitution, and retro analogs. Dimeric forms of the all-d peptide were recognized with tenfold to 100-fold greater affinities relative to the monomer. The all-d peptide was found to inhibit mAb HGAC 39.G3 binding to an anti-idiotype antibody with approximately 1000-fold greater affinity than GlcNAc. As demonstrated here, the study of immune recognition using combinatorial chemistry may offer new insights into the molecular basis of cross-reactivity.

IgG3 cryoglobulins in autoimmune MRL-lpr/lpr mice: immunopathogenesis, therapeutic approaches and relevance to similar human diseases

MRL-lpr/lpr mice spontaneously develop an autoimmune disease resembling systemic lupus erythematosus and rheumatoid arthritis. One of the unique serological abnormalities in this strain is remarkably high concentrations of cryoglobulins. Analysis of immunoglobulin components in their cryoglobulins has shown selective enrichment of a particular IgG subclass, IgG3. As IgG3 enrichment is also found in two other cryoglobulins, which are induced after injection with bacterial lipopolysaccharides or infection with malaria, IgG3 apparently represents a major source of murine cryoglobulins. Studies on murine IgG3 monoclonal antibodies (mAbs) have clearly shown that murine IgG3 have the unique physiochemical property to self associate through non-specific IgG3 Fc-Fc interaction, and that most of them can generate monoclonal cryoglobulins. Most strikingly, IgG3 monoclonal cryoglobulins with rheumatoid factor (RF) activity induce extensive pathological manifestations: skin vascular purpura and glomerulonephritis with 'wire loop' lesions. Although the cryoglobulin activity of IgG3 RF mAb is solely responsible for the generation of glomerular lesions (both RF and cryoglobulin activities are necessary for skin vascular lesions), the absence of nephritogenic activity by some IgG3 cryoglobulins supports the idea that qualitative features of cryoglobulins are critical to determine their pathogenic activity. The demonstration of a positive correlation between the production of IgG3 cryoglobulins and the development of lupus nephritis in MRL-lpr/lpr mice further substantiates the pathological importance of cryogenic autoantibodies. On the other hand, it should be emphasised that non-cryogenerating IgG3 autoantibodies may not be harmful, but even protective, as a result of their interaction with pathogenic IgG3 cryoglobulins. Finally, the development of an experimental model of cryoglobulinaemia associated with vascular and glomerular disease certainly represents an invaluable opportunity to study the molecular mechanisms responsible for the generation of cryoglobulins and their associated tissue lesions, and also to assess various therapeutic approaches. Our demonstration that anti-idiotypic mAb can prevent the pathogenic effects of the cryoprecipitable IgG3 RF mAb suggests strongly that such a therapeutic approach might be successful in similar diseases in man.

Molecular heterogeneity of auto-anti-idiotypic antibodies in MLR-lpr/lpr mice

The VH and V kappa gene families expressed by 20 monoclonal auto-anti-idiotypes (Ab2) derived from unmanipulated MLR-lpr/lpr mice were determined by Northern blotting. Complete variable region sequences of six Ab2, along with three additional V kappa-JH Ab2 sequences, were obtained. These auto-anti-idiotypes arose spontaneously in the animals, and they bound specifically to an idiotypic determinant (Id/r) on mAb 28/12, a monoclonal IgG2b MLR-lpr/lpr anti-small nuclear ribonucleoprotein antibody. The 16 Ab2 heavy chains belonged to 7 different VH gene families, and the 10 Ab2 light chains were derived from 8 V kappa families. The light chains of two Ab2 were approximately 99% identical; the remaining variable region sequences were highly heterogeneous. There was no correlation between primary amino acid sequence of either heavy or light chain and idiotypic properties of the auto-anti-idiotypes. Six Ab2 used VH or V kappa genes that are identical to known germ-line genes. A high proportion of the spontaneous auto-anti-idiotypes was shown to have autoantibody activity (anti-DNA, anti-ribonucleoprotein), or specific binding reactions with lipopolysaccharide of Salmonella RE, or both properties. The structural diversity of spontaneous MLR-lpr/lpr auto-anti-idiotypes differs sharply from the structural homogeneity reported for Ab2 induced in normal animals against syngeneic Ab1. Our results suggest that auto-anti-idiotypes might arise independently of an immunogenic stimulus from an Ab1.

Dual conformations of an immunoglobulin light-chain dimer: heterogeneity of antigen specificity and idiotope profile may result from multiple variable-domain interaction mechanisms

The structure of an immunoglobulin antigen-binding fragment (Fab) has been thought to be invariantly defined by well-conserved amino acid residues in the variable domains of the heavy and light chains. These conserved residues enable folding of the polypeptide segments into the characteristic immunoglobulin fold domains and are the major controllers of interactions between domains. However, crystallographic studies of some immunoglobulin light-chain dimers have suggested and the crystallographic structure of the Fab in an Fab-neuraminidase complex may have proven that antibodies are not restricted to a single, invariant relative positioning of the two variable domains. We propose that in some cases the detailed quaternary structural relationships between the variable domains of heavy and light chains are not restricted to those of the canonical Fab. It is unclear whether alterations of these relationships occur only after complex formation with antigen or, if in ligand-free solution, Fab conformers might coexist in relative concentrations determined by isomerization rates. In the latter case, antibody-presenting lymphocytes may be polyspecific, and the specificity of lymphocytes might be modulated by anti-idiotopic antibodies complexed to cell surface receptors. In either case, the idiotopic repertoire displayed by an antibody or lymphocyte surface receptor might be changed by the presence or absence of antigen.

On the structure of polymeric IgM

The cysteine at position 575 of the immunoglobulin mu heavy chain is thought to provide the only disulfide bonds joining the monomer subunits of mouse polymeric IgM. The importance of this cysteine in the assembly of polymeric IgM was investigated by using site-directed mutagenesis to produce mu chains with serine at position 575. Thirty percent of the secreted mutant IgM was covalently assembled polymer implying that cysteines other than Cys575 can form inter-subunit disulfide bonds. The polymeric IgM lacked J chain, mediated complement-dependent cytolysis and appeared to have a higher molecular weight than conventional IgM pentamers, as judged by sucrose gradient sedimentation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis mobility. Electron microscopy revealed that the mutant IgM molecule contained six subunits. Wild-type IgM, while synthesized predominantly as a pentameric molecule, was assembled in at least two other forms, which were distinguished by their electrophoretic mobility. The apparently higher molecular weight forms of wild-type IgM include hexameric molecules which, like the hexameric mutant IgM, contained much less J chain that the pentameric form and were 20-fold more efficient at activating complement-dependent cytolysis.

Anti-IgM-mediated B cell signaling. Molecular analysis of ligand binding requisites for human B cell clonal expansion and tolerance

The ligand binding requisites for membrane IgM-mediated signaling of human B lymphocyte clonal expansion and B cell tolerance were investigated with a well-characterized set of soluble murine anti-human IgM mAbs. Evaluation of the impact of mu chain domain specificity, affinity, and binding stoichiometry for membrane IgM on antibody-induced regulation of normal and leukemic B cell DNA synthesis revealed that the ligand binding requisites for inducing or, alternatively, suppressing B cell DNA synthesis are significantly different. First, while the induction of S phase entry required micrograms/ml concentrations of ligand, orders of magnitude lower concentrations of ligand sufficed for inhibitory signaling. Second, while an upper affinity threshold for achieving maximal stimulation of B cell DNA synthesis was never detected, inhibitory signaling by bivalent ligands appeared to become relatively affinity independent at Fab binding affinities greater than 7.0 x 10(6) M-1. Third, while a C mu 1-specific mAb with an enhanced incidence of monogamous binding to mIgM was ineffective at inducing B cell DNA synthesis, the antibody was not significantly compromised in ability to initiate inhibitory signals. These differences could be observed in a clonal B cell population which positively or negatively responded to mIgM ligation depending upon its state of activation. The accumulated observations indicate that the ligand binding requisites for inhibitory signal transduction in human B lymphocytes are much less rigorous than those for stimulatory signal transduction and suggest that many physiologically relevant anti-Ig antibodies are more likely to function in the negative feedback regulation of B cell responses than in the direct triggering of human B cell clonal expansion.

Inhibition of self-binding antibodies (autobodies) by a VH-derived peptide

The self-binding properties of a dominant idiotypic antibody (T15) and a minor idiotypic antibody (M603), both specific for phosphorylcholine, were examined as models of self-binding antibodies (autobodies). Observed differences in the self-binding affinity of T15 and M603 relate to variable sequence differences in their respective heavy and light chains. A molecular recognition theory based on the translation of coding and noncoding DNA strands was used to identify complementary amino acid sequences responsible for self-binding. The second hypervariable region of the heavy chain domain, extending into the third framework region, was predicted as the primary self-binding locus. Among peptides synthesized with different variable heavy and light chain regions, a 24-residue peptide spanning the second hypervariable and third framework regions of the heavy chain of T15 was nearly as effective as phosphorycholine in inhibiting the self-binding complexes.