The three-dimensional structure of a phosphorylcholine-binding mouse immunoglobulin Fab and the nature of the antigen binding site

Core fucosylation within the Fc-FcγR degradation pathway promotes enhanced IgG levels via exogenous L-fucose

α1,6-Fucosyltransferase (Fut8) is the enzyme responsible for catalyzing core fucosylation. Exogenous L-fucose upregulates fucosylation levels through the GDP-fucose salvage pathway. This study investigated the relationship between core fucosylation and immunoglobulin G (IgG) amounts in serum utilizing WT (Fut8+/+), Fut8 heterozygous knockout (Fut8+/-), and Fut8 knockout (Fut8-/-) mice. The IgG levels in serum were lower in Fut8+/- and Fut8-/- mice compared with Fut8+/+ mice. Exogenous L-fucose increased IgG levels in Fut8+/- mice, while the ratios of core fucosylated IgG versus total IgG showed no significant difference among Fut8+/+, Fut8+/-, and Fut8+/- mice treated with L-fucose. These ratios were determined by Western blot, lectin blot, and mass spectrometry analysis. Real-time PCR results demonstrated that mRNA levels of IgG Fc and neonatal Fc receptor, responsible for protecting IgG turnover, were similar among Fut8+/+, Fut8+/-, and Fut8+/- mice treated with L-fucose. In contrast, the expression levels of Fc-gamma receptor Ⅳ (FcγRⅣ), mainly expressed on macrophages and neutrophils, were increased in Fut8+/- mice compared to Fut8+/+ mice. The effect was reversed by administrating L-fucose, suggesting that core fucosylation primarily regulates the IgG levels through the Fc-FcγRⅣ degradation pathway. Consistently, IgG internalization and transcytosis were suppressed in FcγRⅣ-knockout cells while enhanced in Fut8-knockout cells. Furthermore, we assessed the expression levels of specific antibodies against ovalbumin and found they were downregulated in Fut8+/- mice, with potential recovery observed with L-fucose administration. These findings confirm that core fucosylation plays a vital role in regulating IgG levels in serum, which may provide insights into a novel mechanism in adaptive immune regulation.

The mosaic puzzle of the therapeutic monoclonal antibodies and antibody fragments - A modular transition from full-length immunoglobulins to antibody mimetics

The use of monoclonal antibodies represents an important and efficient diagnostic and therapeutic tool in disease management and modern science but remains limited by several factors including the uneven distribution in diseased tissues as well as undesired activation of side immune reactions. Major scientific advancements including Recombinant DNA Technology, Hybridoma Technology, and Polymerase Chain Reaction have considerably impacted the use of monoclonal antibodies providing technical and effective solutions to overcome the shortcomings encountered with conventional antibodies. Initially, the introduction of antibody fragments allowed a more uniform and deeper penetration of the targeted tissue and reduced unwanted activation of Fc-mediated immune reactions. On another level, the immunogenicity of murine-derived antibodies was overcome by humanizing their encoding genes with specific sequences of human origin andtransgenic mice able to synthesize fully human antibodies were successfully created. Moreover, the advancement of genetic engineering techniques supported by the modular structure of antibody coding genes paved the way for the development of a new generation of antibody fragments with a wide spectrum of monospecific and bispecific agents. These later could be monovalent, bivalent, or multivalent, and either expressed as a single chain, assembled in multimeric forms or stringed in tandem. This has conferred improved affinity, stability, and solubility to antibody targetting. Lately, a new array of monoclonal antibody fragments was introduced with the engineering of nanobody and antibody mimetics as non-immunoglobulin-derived fragments with promising diagnostic and therapeutic applications. In this review, we decipher the molecular basis of monoclonal antibody engineering with a detailed screening of the antibody derivatives that provides new perspectives to expand the use of monoclonal fragments into previously unexplored fields.

The Impact of the Hybridoma Technology on the R&D of Idiotypic Antibodies

The PubMed data set was scanned with the title and abstract term "Idiotype" followed by secondary searches with "Vaccine" and "Clinical trial." The retrieved references were analyzed from the period before and after hybridoma technology (1975). In 1963, Oudin and Kunkel discovered that antibodies against antibodies can be raised to identify determinants unique to an antibody termed idiotype or individual antigenic determinant. Two laboratories reported that anti-idiotypic antibodies can suppress specific antibody responses in mice. In 1974, Jerne proposed a network of idiotypes and anti-idiotypes and the functionality of the idiotype network was confirmed. This prompted the proposal of a symmetrical regulatory immune response. By 1989, the concept and the functional parameters of the immune idiotype network were established in the prehybridoma period. It was not until 1981 that monoclonal anti-idiotypic antibodies were used as tools to study the expression of idiotypic determinants on antibodies and to categorize functional properties in the immune network as network antigens in 1989. Hybridoma-generated monoclonal anti-idiotypic antibodies provided the tools to precisely identify different idiotypic regions on antibodies and test these as targets to induce network cascades. The initial distinction of Ab2s as alpha and beta were expanded to include gamma and delta. The initial concept of Ab2beta being an antigen internal image, used as vaccine, was challenged showing that targeting all idiotopes on B cell receptors can induce specific antibodies. After the discovery of the hybridoma technology a wave of idiotype topic publications occurred, that declined by 2015. In 1985, in this wave of reports on anti-idiotypes, their importance to vaccines dominated. These vaccines targeted in animal models parasite, bacterial, and viral diseases, and cancer. The reported data indicated a therapeutic response in inbred mice. The issue of idiotype matching between mouse haplotypes of vaccine origin and treated mice were raised. In 1995, the human clinical trials in different cancers using anti-Id vaccines were reported. Only one such vaccine received conditional approval in Argentina and Cuba, whereas the other trials failed in phase II and III. The reasons for this failure were subsequently discussed. Although the use of the Milstein and Kohler hybridoma technology and subsequently alternative methods to produce monoclonal animal and human antibodies created a new class of drugs, commonly referred as "Biological," it failed on the promise therapeutic of anti-Id vaccines.

50 Years of structural immunology

Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.

Antibody Epitope Specificity for dsDNA Phosphate Backbone Is an Intrinsic Property of the Heavy Chain Variable Germline Gene Segment Used

Analysis of protein sequences by the informational spectrum method (ISM) enables characterization of their specificity according to encoded information represented with defined frequency (F). Our previous data showed that F(0.367) is characteristic for variable heavy chain (VH) domains (a combination of variable (V), diversity (D) and joining (J) gene segments) of the anti-phosphocholine (PC) T15 antibodies and mostly dependent on the CDR2 region, a site for PC phosphate group binding. Because the T15 dsDNA-reactive U4 mutant also encodes F(0.367), we hypothesized that the same frequency may also be characteristic for anti-DNA antibodies. Data obtained from an analysis of 60 spontaneously produced anti-DNA antibody VH domain sequences supported our hypothesis only for antibodies, which use V gene segment in germline configuration, such as S57(VH31), MRL-DNA22, and VH11, members of the VH1 (J558) and VH7 (S107) gene families. The important finding is that out of seven V gene segments used by spontaneous anti-DNA antibodies, F(0.367) is only expressed by the germline configuration of these three V gene segments. The data suggest that antibody specificity for the phosphate group moiety delineated as F(0.367) is the intrinsic property of the V germline gene segments used, whereas paratope/epitope interaction with antigens bearing this epitope, such as PC or dsDNA, requires corresponding antibody VH conformation that is susceptible to somatic mutation(s).

Engineered hapten-binding antibody derivatives for modulation of pharmacokinetic properties of small molecules and targeted payload delivery

Hapten‐binding antibodies have for more than 50 years played a pivotal role in immunology, paving the way to antibody generation (as haptens are very important and robust immunogens), to antibody characterization (as the first structures generated more than 40 years ago were those of hapten binders), and enabled and expanded antibody engineering technologies. The latter field of engineered antibodies evolved over many years and many steps resulting in recombinant humanized or human‐derived antibody derivatives in multiple formats. Today, hapten‐binding antibodies are applied not only as reagents and tools (where they still play an important part) but evolved also to engineered targeting and pretargeting vehicles for disease diagnosis and therapy. Here we describe recent applications of hapten‐binding antibodies and of engineered mono‐ and bispecific hapten‐binding antibody derivatives. We have designed and applied these molecules for the modulation of the pharmacokinetic properties of small compounds or peptides. They are also integrated as additional binding entities into bispecific antibody formats. Here they serve as non‐covalent or covalent coupling modules to haptenylated compounds, to enable targeted payload delivery to disease tissues or cells.

Ig Constant Region Effects on Variable Region Structure and Function

The adaptive humoral immune response is responsible for the generation of antimicrobial proteins known as immunoglobulin molecules or antibodies. Immunoglobulins provide a defense system against pathogenic microbes and toxins by targeting them for removal and/or destruction. Historically, antibodies have been thought to be composed of distinct structural domains known as the variable and constant regions that are responsible for antigen binding and mediating effector functions such as opsonization and complement activation, respectively. These domains were thought to be structurally and functionally independent. Recent work has revealed however, that in some families of antibodies, the two regions can influence each other. We will discuss the body of work that led to these observations, as well as the mechanisms that have been proposed to explain how these two different antibody regions may interact in the function of antigen binding.

Human L-ficolin recognizes phosphocholine moieties of pneumococcal teichoic acid

Human L-ficolin is a soluble protein of the innate immune system able to sense pathogens through its fibrinogen (FBG) recognition domains and to trigger activation of the lectin complement pathway through associated serine proteases. L-Ficolin has been previously shown to recognize pneumococcal clinical isolates, but its ligands and especially its molecular specificity remain to be identified. Using solid-phase binding assays, serum and recombinant L-ficolins were shown to interact with serotype 2 pneumococcal strain D39 and its unencapsulated R6 derivative. Incubation of both strains with serum triggered complement activation, as measured by C4b and C3b deposition, which was decreased by using ficolin-depleted serum. Recombinant L-ficolin and its FBG-like recognition domain bound to isolated pneumococcal cell wall extracts, whereas binding to cell walls depleted of teichoic acid (TA) was decreased. Both proteins were also shown to interact with two synthetic TA compounds, each comprising part structures of the complete lipoteichoic acid molecule with two PCho residues. Competition studies and direct interaction measurements by surface plasmon resonance identified PCho as a novel L-ficolin ligand. Structural analysis of complexes of the FBG domain of L-ficolin and PCho revealed that the phosphate moiety interacts with amino acids previously shown to define an acetyl binding site. Consequently, binding of L-ficolin to immobilized acetylated BSA was inhibited by PCho and synthetic TA. Binding of serum L-ficolin to immobilized synthetic TA and PCho-conjugated BSA triggered activation of the lectin complement pathway, thus further supporting the hypothesis of L-ficolin involvement in host antipneumococcal defense.

From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display

Antibodies are the most versatile binding proteins in nature with six loops creating a flexible continuous interaction surface. However, in some molecular formats, antibodies are aggregation prone. Designed ankyrin repeat proteins (DARPins) were successfully created as alternative design solutions. Nevertheless, their concave shape, rigidity and incompletely randomized binding surface may limit the epitopes that can be targeted by this extremely stable scaffold. Combining conformational diversity and a continuous convex paratope found in many antibodies with the beneficial biophysical properties of DARPins, we created LoopDARPins, a next generation of DARPins with extended epitope binding properties. We employed X-ray structure determination of a LoopDARPin for design validation. Biophysical characterizations show that the introduction of an elongated loop through consensus design does not decrease the stability of the scaffold,consistent with molecular dynamics simulations. Ribosome-display selections against extracellular signal-regulated kinase 2 (ERK2) and four members of the BCL-2 family (BCL-2, BCL-XL, BCL-W and MCL-1) of anti-apoptotic regulators yielded LoopDARPins with affinities in the mid-picomolar to low nanomol arrange against all targets. The BCL-2 family binders block the interaction with their natural interaction partner and will be valuable reagents to test the apoptotic response in functional assays. With the LoopDARPin scaffold, binders for BCL-2 with an affinity of 30 pM were isolated with only a single round of ribosome display,an enrichment that has not been described for any scaffold. Identical stringent one-round selections with conventional DARPins without loop yielded no binders. The LoopDARPin scaffold may become a highly valuable tool for biotechnological high-throughput applications.

Structure of a human IgA1 Fab fragment at 1.55 Å resolution: potential effect of the constant domains on antigen-affinity modulation

Despite being the most abundant class of immunoglobulins in humans and playing central roles in the adaptive immune response, high-resolution structural data are still lacking for the antigen-binding region of human isotype A antibodies (IgAs). The crystal structures of a human Fab fragment of IgA1 in three different crystal forms are now reported. The three-dimensional organization is similar to those of other Fab classes, but FabA1 seems to be more rigid, being constrained by a hydrophobic core in the interface between the variable and constant domains of the heavy chain (VH-CH1) as well as by a disulfide bridge that connects the light and heavy chains, influencing the relative heavy/light-chain orientation. The crystal structure of the same antibody but with a G-isotype CH1 which is reported to display different antigen affinity has also been solved. The differential structural features reveal plausible mechanisms for constant/variable-domain long-distance effects whereby antibody class switching could alter antigen affinity.

Defining a protective epitope on factor H binding protein, a key meningococcal virulence factor and vaccine antigen

Mapping of epitopes recognized by functional monoclonal antibodies (mAbs) is essential for understanding the nature of immune responses and designing improved vaccines, therapeutics, and diagnostics. In recent years, identification of B-cell epitopes targeted by neutralizing antibodies has facilitated the design of peptide-based vaccines against highly variable pathogens like HIV, respiratory syncytial virus, and Helicobacter pylori; however, none of these products has yet progressed into clinical stages. Linear epitopes identified by conventional mapping techniques only partially reflect the immunogenic properties of the epitope in its natural conformation, thus limiting the success of this approach. To investigate antigen-antibody interactions and assess the potential of the most common epitope mapping techniques, we generated a series of mAbs against factor H binding protein (fHbp), a key virulence factor and vaccine antigen of Neisseria meningitidis. The interaction of fHbp with the bactericidal mAb 12C1 was studied by various epitope mapping methods. Although a 12-residue epitope in the C terminus of fHbp was identified by both Peptide Scanning and Phage Display Library screening, other approaches, such as hydrogen/deuterium exchange mass spectrometry (MS) and X-ray crystallography, showed that mAb 12C1 occupies an area of ∼1,000 Å(2) on fHbp, including >20 fHbp residues distributed on both N- and C-terminal domains. Collectively, these data show that linear epitope mapping techniques provide useful but incomplete descriptions of B-cell epitopes, indicating that increased efforts to fully characterize antigen-antibody interfaces are required to understand and design effective immunogens.

Antigen-antibody interactions and structural flexibility of a femtomolar-affinity antibody

The femtomolar-affinity mutant antibody (4M5.3) generated by directed evolution is interesting because of the potential of antibody engineering. In this study, the mutant and its wild type (4-4-20) were compared in terms of antigen-antibody interactions and structural flexibility to elucidate the effects of directed evolution. For this purpose, multiple steered molecular dynamics (SMD) simulations were performed. The pulling forces of SMD simulations elucidated the regions that form strong attractive interactions in the binding pocket. Structural analysis in these regions showed two important mutations for improving attractive interactions. First, mutation of Tyr102(H) to Ser (sequence numbering of Protein Data Bank entry 1FLR ) played a role in resolving the steric hindrance on the pathway of the antigen in the binding pocket. Second, mutation of Asp31(H) to His played a role in resolving electrostatic repulsion. Potentials of mean force (PMFs) of both the wild type and the mutant showed landscapes that do not include obvious intermediate states and go directly to the bound state. These landscapes were regarded as funnel-like binding free energy landscapes. Furthermore, the structural flexibility based on the fluctuations of the positions of atoms was analyzed. It was shown that the fluctuations in the positions of the antigen and residues in contact with antigen tend to be smaller in the mutant than in the wild type. This result suggested that structural flexibility decreases as affinity is improved by directed evolution. This suggestion is similar to the relationship between affinity and flexibility for in vivo affinity maturation, which was suggested by Romesberg and co-workers [Jimenez, R., et al. (2003) Proc. Natl. Acad. Sci. U.S.A.100, 92-97]. Consequently, the relationship was found to be applicable up to femotomolar affinity levels.

Solid phase synthesis of the protected 27--42 hexadecapeptide of the heavy chain from myeloma immunoglobulin M603. Elimination of side reactions associated with glycyl-2-oxypropionyl-resin

A fully protected 27--42 hexadecapeptide of the variable region of myeloma immunoglobulin M603 was synthesized on a 2-bromopropionyl-resin by the solid phase method. Side reactions due to cyclization of glycyl-2-oxypropionyl-resin were studied under different reaction conditions. The loss of peptide chains at the dipeptide and tripeptide stages due to diketopeperazine formation was also examined. These side reactions were circumvented by using a combination of fragment and stepwise coupling methods. The synthesized protected peptide was removed from the resin in 85% yield by photolysis, and purified by crystallization and by chromatography on a Sephadex LH-60 column.

Structural features of T cell receptor variable regions that enhance domain stability and enable expression as single-chain ValphaVbeta fragments

The variable (V) domains of antibodies and T cell receptors (TCRs) share sequence homology and striking structural similarity. Single-chain antibody V domain constructs (scFv) are routinely expressed in a variety of heterologous systems, both for production of soluble protein as well as for in vitro engineering. In contrast, single-chain T cell receptor V domain constructs (scTCR) are prone to aggregation and misfolding and are refractory to display on phage or yeast in their wild-type form. However, through random mutagenesis and yeast display engineering, it has been possible to isolate scTCR mutants that are properly folded and displayed on the yeast surface. These displayed mutants can serve not only as a scaffold for further engineering but also as scTCR variants that exhibit favorable biophysical properties in Escherichia coli expression. Thus, a more comprehensive understanding of the V domain mutations that allowed display would be beneficial. Our goal here was to identify generalizable patterns of important mutations that can be applied to different TCRs. We compared five different scTCRs, four from mice and one from a human, for yeast surface display. Analysis of a collection of mutants revealed four distinct regions of TCR V domains that were most important for enabling surface expression: the Valpha-Vbeta interface, the HV4 of Vbeta, and the region of the Valpha and Vbeta domains normally apposed against the constant (C) domains. Consistent with the role of the V-C interface in surface display, reconstitution of this interface, by including the constant domains of each chain, allowed V domain display and alphabeta chain association on the yeast surface, thus providing an alternative TCR scaffold. However, the surface levels of TCR achieved with engineered scTCR mutants were superior to that of the ValphaCalpha/VbetaCbeta constructs. Therefore, we describe further optimization of the current strategy for surface display of the single-chain format in order to facilitate yeast display engineering of a broader range of scTCRs.

Flexibility in Tobacco Mosaic Virus

Tobacco mosaic virus (TMV) particles are rod-like, 300 nm long and 18 nm in diameter. TMV consists of 2140 protein subunits, each with a relative molecular mass of 17420 (158 residues), arranged on a helix of pitch 2.3 nm with 16 1/3 subunits per turn. Winding through this helix is a single strand of RNA 6400 nucleotides long. Three bases are bound to each protein subunit. TMV has a central hole of diameter 4.0 nm. Assembly of TMV occurs by the threading of the RNA through the central hole of the growing rodlet of viral coat protein and involves a preassembled double disk as intermediate. Given the structure of the subunit, such a mechanism requires that the segment of polypeptide chain which separates the nucleic acid binding site from the lumen of the cylinder should be able to move out of the way during the assembly process. Evidence from diffraction studies and from proton nuclear magnetic resonance spectroscopy points to a segment of about 20 amino acid residues being very flexible in the disk. In the helical virus these residues take on a well-defined conformation which completely shields the nucleic acid from the central channel.

Catalytic antibodies: contributions from engineering and expression in Escherichia coli

Antibodies have been raised against the transition state of many reactions and shown to catalyse the relevant reaction. Their moderate catalytic efficiencies can be increased by protein engineering, if ways can be found to express the engineered antibody. We have developed a system by which fully functional Fv and Fab fragments can be expressed in Escherichia coli. The Fv fragment dissociates at low concentrations; we therefore devised methods to stabilize the fragment. We showed that the Fv fragment of the antibody McPC603, a phosphorylcholine-binding immunoglobulin A, binds the antigen with the same affinity as does the intact antibody isolated from mouse ascites. Phosphorylcholine is an analogue of the transition state for the hydrolysis of choline carboxylate ester. The Fv fragment of McPC603 catalysed this hydrolysis. Mutational analysis of the residues in the binding site of the antibody has shown which are essential for binding and for catalysis, and the importance of charged residues in certain positions. The E. coli expression system combined with protein engineering and screening methods will facilitate understanding of enzyme catalysis and the development of new catalytic antibodies.

A synthetic receptor for phosphocholine esters

A bifunctional Zn-salen modified cavitand, reminiscent of the enzyme phospholipase C, shows high efficiency and synergic effect in the binding of the phospholipid DOPC.

Structure of the male determinant factor for Brassica self-incompatibility

Many flowering plants possess a self-incompatibility system to prevent inbreeding. In Brassica rapa, self/non-self recognition in mating is established through S-haplotype-specific interactions between stigma receptors and S-locus protein 11 (SP11, also called S-locus cysteine-rich protein) that is encoded at the highly polymorphic S-locus. Here we describe the solution structure of the SP11 protein of the S8-haplotype (S8-SP11), which specifically binds to the stigma factor of the same haplotype. It folds into an alpha/beta sandwich structure that resembles those of plant defensins. Residues important for structural integrity are highly conserved among the allelic SP11s, suggesting the existence of a common folding pattern. Structure-based sequence alignment and homology modeling of allelic SP11 identified a hyper-variable (HV) region, which is thought to form a loop that bulges out from the body of the protein that is amenable to solvent exposure. We suggest that the HV region could serve as a specific binding site for the stigma receptor.

Evolution of catalytic antibody repertoire in autoimmune mice

We have attempted to efficiently obtain catalytic antibodies (catAbs) with amidase/esterase activity in the expanded sequence space of the antibody repertoire. In doing so, we used an autoimmune mouse strain, MRL/lpr, that is known to produce enhanced levels of autoantibodies. We applied different types of haptens, such as, and, that are supposed to mimic the transition state of the substrate in the ester/amide hydrolysis. Among them, hapten (2) could not be used, as it was readily broken down after synthesis. Upon immunization with hapten (1), catAbs preferentially evolved in MRL/lpr mice, but this did not happen upon immunization with haptens (3) and (4). Independently, immunization to MRL/lpr mice with successfully elicited the catAbs with the ability to activate vitamin B(6) prodrugs. The common observation seen in these two cases is that most of the catAbs derived from MRL/lpr mice by hapten (1) and half of them by hapten (5) had a Lys at H95, which is at the junctional N region between the V(H) and J(H) gene segments. Despite the conservation of Lys (H95), analyses of the N-region and utilization of the D gene segment in the heavy chain gene showed that these catAbs were from several independent clones of the same family. Studies of site-directed mutagenesis suggest that, in the catAbs elicited from hapten (1), a Lys (H95) and a His (L91) are involved in the catalytic function. Both residues are known to interact with the phosphonate moiety of hapten (1). Such studies also suggest that, in the catAbs elicited from hapten (5), a Lys (H95) and a His (H35) are involved in the catalytic function. These basic amino acids seem to be important for binding to the phosphonate hapten, as they were not changed even after extensive evolution following multiple mutations. By contrast, in normal BALB/c mice, immunization of hapten (1) resulted in eliciting catAbs in lower yield and the majority were the non-catAbs, whose sequences were quite different from those of the catAbs from MRL/lpr mice. They were clonally related to one another and most of them originated from a single clone. The positions of the interacting key residues in the CDRs that interact with the phosphorus moiety strongly differ between our catAbs and other reported catAbs with esterase/amidase activity, which were elicited by the phosphonate/phosphonamidate haptens from normal mice. Further comparison of antibodies elicited by the phosphorus haptens, such as DNA, RNA, phosphocholine, and phosphotyrosine, indicated that none of them had sequence similarity in the basic amino acids and their positions in the CDRs, except for one example, which is anti-DNA antibody elicited from C3H-lpr mice. Analysis based on the classification of canonical structures of the antibodies again suggested that our catAbs derived from MRL/lpr mice belong to an unusual class that is not listed in the literature. Taken together, the above evidence suggests that the unique catalytic subsets that existed in the initial repertoire in the MRL/lpr mice could effectively be captured by the phosphonate haptens through the interaction with the Lys at H95. In the BALB/c mice, however, another noncatalytic subset with an ability to bind only to a moiety other than the phosphonate moiety alternatively evolved, because of the lowest abundance or elimination of the catalytic subsets.

Regulating the isotypic and idiotypic profile of an anti-PC antibody response: lessons from peptide mimics

Protection against microbial invasion depends not only on the host's ability to mount an immune response, but on its ability to mount the correct immune response. Whether an antibody response is protective or not depends on both the fine antigenic specificity, that may be associated with particular idiotypes and epitope binding characteristics, and the isotype, determining antibody effector function. Thus, both the variable and the constant region of the antibodies induced by a peptide mimotope must be considered when assessing the success of any immunization. Phosphorylcholine (PC), an epitope present on the cell-wall C-polysaccharide of all pneumococcal serotypes, is capable of eliciting a protective antibody response to pneumococcal infection in mice and provides an attractive model system for understanding the immune response generated by peptide mimics. In this system, both the idiotype and isotype of protective antibodies have been determined and the characteristics of the in vivo response are well described and highly reproducible. We describe here the immune response generated by two peptide mimics of PC. Mice immunized with the peptides developed antibodies binding PC and C-polysaccharide. The idiotypic profile of the response differed depending on the peptide, but never included canonical T15(+) antibodies. The isotype of the response to peptide mimics differed depending on a combination of peptide and adjuvant, and included both IgG2a and IgG2b antibodies which are not typically seen in the response to PC. Thus, peptide mimotopes may elicit anti-polysaccharide responses, but fail to elicit the idiotypes and isotypes observed in the protective response to the microbial antigen.

Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products

Sequencing of all human immunoglobulin (Ig) germline gene segments has recently been completed. However, our first glimpses of the recombined products of this combinatorial gene system were in the 1970s, in landmark publications, reporting the crystal structures of two human myeloma proteins, the Mcg lambda light chain dimer and the New IgG1(lambda) Fab. Although numerous crystal structures of murine and human antibodies have now been determined, only a relatively small proportion of the human germline genes have had their corresponding protein three-dimensional structures resolved. Therefore, further structural investigations are required before the inherent diversity of the antibody repertoire can be fully appreciated. We discuss the detailed structural information available for human antibodies with regard to their immune functions. Also discussed, is how the structural information is finding application in the 'humanization' of murine antibodies as part of their development as 'biopharmaceuticals' for the treatment of human disease.

Third complementarity-determining region of mutated VH immunoglobulin genes contains shorter V, D, J, P, and N components than non-mutated genes

The third complementarity-determining region (CDR3) of immunoglobulin variable genes for the heavy chain (VH) has been shown to be shorter in length in hypermutated antibodies than in non-hypermutated antibodies. To determine which components of CDR3 contribute to the shorter length, and if there is an effect of age on the length, we analysed 235 cDNA clones from human peripheral blood of VH6 genes rearranged to immunoglobulin M (IgM) constant genes. There was similar use of diversity (D) and joining (JH) gene segments between clones from young and old donors, and there was similar use of D segments among the mutated and non-mutated heavy chains. However, in the mutated heavy chains, there was increased use of shorter JH4 segments and decreased use of longer JH6 segments compared to the non-mutated proteins. The overall length of CDR3 did not change with age within the mutated and non-mutated categories, but was significantly shorter by three amino acids in the mutated clones compared to the non-mutated clones. Analyses of the individual components that comprise CDR3 indicated that they were all shorter in the mutated clones. Thus, there were more nucleotides deleted from the ends of VH, D, and JH gene segments, and fewer P and N nucleotides added. The results suggest that B cells bearing immunoglobulin receptors with shorter CDR3s have been selected for binding to antigen. A smaller CDR3 may allow room in the antibody binding pocket for antigen to interact with CDRs 1 and 2 as well, so that as the VDJ gene undergoes hypermutation, substitutions in all three CDRs can further contribute to the binding energy.

Natural antibodies with the T15 idiotype may act in atherosclerosis, apoptotic clearance, and protective immunity

The immune response to oxidized LDL (OxLDL) may play an important role in atherogenesis. Working with apoE-deficient mice, we isolated a panel of OxLDL-specific B-cell lines that secrete IgM Abs that specifically bind to oxidized phospholipids such as 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphorylcholine (POVPC). These Abs block uptake of OxLDL by macrophages, recognize similar oxidation-specific epitopes on apoptotic cells, and are deposited in atherosclerotic lesions. The Abs were found to be structurally and functionally identical to classic "natural" T15 anti-PC Abs that are of B-1 cell origin and are reported to provide optimal protection from virulent pneumococcal infection. These findings suggest that there has been natural selection for B-1 cells secreting oxidation-specific/T15 antibodies, both for their role in natural immune defense and for housekeeping roles against oxidation-dependent neodeterminants in health and disease.

The structural basis of repertoire shift in an immune response to phosphocholine

The immune response to phosphocholine (PC)-protein is characterized by a shift in antibody repertoire as the response progresses. This change in expressed gene combinations is accompanied by a shift in fine specificity toward the carrier, resulting in high affinity to PC-protein. The somatically mutated memory hybridoma, M3C65, possesses high affinity for PC-protein and the phenyl-hapten analogue, p-nitrophenyl phosphocholine (NPPC). Affinity measurements using related PC-phenyl analogues, including peptides of varying lengths, demonstrate that carrier determinants contribute to binding affinity and that somatic mutations alter this recognition. The crystal structure of an M3C65-NPPC complex at 2.35-A resolution allows evaluation of the three light chain mutations that confer high-affinity binding to NPPC. Only one of the mutations involves a contact residue, whereas the other two have indirect effects on the shape of the combining site. Comparison of the M3C65 structure to that of T15, an antibody dominating the primary response, provides clear structural evidence for the role of carrier determinants in promoting repertoire shift. These two antibodies express unrelated variable region heavy and light chain genes and represent a classic example of the effect of repertoire shift on maturation of the immune response.

Natural antibodies with the T15 idiotype may act in atherosclerosis, apoptotic clearance, and protective immunity

The immune response to oxidized LDL (OxLDL) may play an important role in atherogenesis. Working with apoE-deficient mice, we isolated a panel of OxLDL-specific B-cell lines that secrete IgM Abs that specifically bind to oxidized phospholipids such as 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphorylcholine (POVPC). These Abs block uptake of OxLDL by macrophages, recognize similar oxidation-specific epitopes on apoptotic cells, and are deposited in atherosclerotic lesions. The Abs were found to be structurally and functionally identical to classic "natural" T15 anti-PC Abs that are of B-1 cell origin and are reported to provide optimal protection from virulent pneumococcal infection. These findings suggest that there has been natural selection for B-1 cells secreting oxidation-specific/T15 antibodies, both for their role in natural immune defense and for housekeeping roles against oxidation-dependent neodeterminants in health and disease.

Crystal structure of a ternary complex between human chorionic gonadotropin (hCG) and two Fv fragments specific for the alpha and beta-subunits

Human chorionic gonadotropin (hCG), is a placental hormone which exerts its major effect by stimulating progesterone production, crucially sustaining the early weeks of pregnancy. Detection of hCG with specific monoclonal antibodies (mAbs) has become the chosen means for pregnancy diagnosis. We have used antibody Fv fragments derived from two high-affinity mAbs, one against the alpha and the other against the beta-hCG subunit to enable the crystallisation of intact or desialylated hCG. Crystals of a ternary complex composed of Fv anti-alpha/hCG/Fv anti-beta were found to diffract to 3.5 A resolution, and the structure was solved by molecular replacement. In the crystal, the two Fvs keep hCG as in a molecular cage, providing good protein-protein contacts and leaving enough space for the saccharides to be accommodated in the cell solvent. The two Fvs were found not to interact directly through their complementary-determining regions with the hCG saccharides, but only with the protein. The hCG structure in the ternary complex was very close to that of the HF partially deglycosylated hormone, thus indicating that neither the saccharides nor the Fvs had any substantial influence on hormone structure.

Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation

In this paper, a method of simulating the docking of small flexible ligands to flexible receptors in water is reported. The method is based on molecular dynamics simulations and is an extension of an algorithm previously reported by Di Nola et al. (Di Nola et al., Proteins 1994;19:174-182). The method allows a fast exploration of the receptor surface, using a high temperature of the center of mass translational motion, while the ligand internal motions, the solvent, and the receptor are simulated at room temperature. In addition, the method allows a fast center of mass motion of the ligand, even in solution. The dampening effect of the solvent can be overcome by applying different weights to the interactions between system subsets (solvent, receptor, and ligand). Specific ligand-receptor distances have been used to compare the results of the simulations with the crystal structure. The method is applied, as a test system, to the docking of the phosphocholine to the immunoglobulin McPC603. The results show the similarity of structure between the complex in solution and in the crystal.

Production and characterization of recombinant IgA

Existence of secretory immunity at the mucosal surfaces was first postulated in 1919. Since then experimental and clinical studies have indicated that it is immunoglobulin A (IgA) that provides the first line of immune defense at the mucosal surfaces. While a number of expression systems--including viral, plant and mammalian cells--have been used to produce recombinant IgA, we used the mammalian expression system to produce IgA1 and the three allotypes of IgA2. By introducing the gene coding for human secretory component (SC) into transfectants producing IgA1, we have generated a single mammalian cell system that produces covalently assembled secretory IgA (sIgA). Using pulse-chase analysis, we determined the covalent assembly pathways of IgA1, IgA2 and sIgA and identified some of the structural differences leading to the different assembly patterns. Using affinity purified proteins, we have shown that neither IgA1 nor any of the allotypes of IgA2 activate either the classical or the alternative complement pathways, but modulate the complement activity of IgG or IgM. The two N-linked glycosylation sites in IgA1 are not required for its binding to the polymeric Ig receptor (pIgR). Finally, we have shown that sIgA1 was more stable than dIgA1 in the gastrointestinal tract of mice, suggesting that SC provides resistance to IgA in the gastrointestinal tract.

Do active site conformations of small ligands correspond to low free-energy solution structures?

We compare the low free energy structures of ten small, polar ligands in solution to their conformations in their respective receptor active sites. The solution conformations are generated by a systematic search and the free energies of representative structures are computed with a continuum solvation model. Based on the values of torsion angles, we find little similarity between low energy solution structures of small ligands and their active site conformations. However, in nine out of ten cases, the positions of 'anchor points' (key atoms responsible for tight binding) in the lowest energy solution structures are very similar to the positions of these atoms in the active site conformations. A metric that more closely captures the essentials of binding supports the basic premise underlying pharmacophore mapping, namely that active site conformations of small flexible ligands correspond to their low energy structures in solution. This work supports the efforts of building pharmacophore models based on the information present in solution structures of small isolated ligands.

Antibody catalysis based on functional mimicry

Approaches aiming at eliciting antibodies (Abs) that catalyze specific chemical transformations are numerous. Most of the developed methods are based on the chemical steps of the reaction catalyzed rather than on the structure of known enzyme active sites. The authors have developed an approach that rests on the mimicry properties of the idiotypic network of immune regulation. Recent results, together with the existence of natural catalytic Abs in autoimmune diseases, indicate the need to better understand the regulation properties of immune response, in order to improve the efficiency of tailor-made catalytic Abs.

Hepatitis B virus capsid: localization of the putative immunodominant loop (residues 78 to 83) on the capsid surface, and implications for the distinction between c and e-antigens

Hepatitis B virus capsid protein comprises a 149 residue "assembly" domain that polymerizes into icosahedral particles, and a 34 residue RNA-binding "protamine" domain. Recently, the capsid structure has been studied to resolutions below 10 A by cryo-electron microscopy, revealing much of its alpha-helical substructure and that it appears to have a novel fold for a capsid protein; however, the resolution is still too low for chain-tracing by conventional criteria. Aiming to establish a fiducial marker to aid in the process of chain-tracing, we have used cryo-microscopy to pinpoint the binding site of a monoclonal antibody that recognizes the peptide from residues 78 to 83. This epitope resides on the outer rim of the 30 A long spikes that protrude from the capsid shell. These spikes are four-helix bundles formed by the pairing of helix-turn-helix motifs from two subunits; by means of a tilting experiment, we have determined that this bundle is right-handed. Variants of the same protein present two clinically important and non-crossreactive antigens: core antigen (HBcAg), which appears early in infection as assembled capsids; and the sentinel e-antigen (HBeAg), a non-particulate form. Knowledge of the binding site of our anti-HBcAg antibody bears on the molecular basis of the distinction between the two antigens, which appears to reflect conformational differences between the assembled and unassembled states of the capsid protein dimer, in addition to epitope masking in capsids.

Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation

The diversity in the lengths and the amino acid sequences of the third complementarity determining region of the antibody heavy chain (CDR-H3) has made it difficult to establish a relationship between the sequences and the tertiary structures, in contrast to the other CDRs, which are classified by their canonical structures. Enhanced conformational sampling of two different CDR-H3s was performed by multicanonical molecular dynamics (multicanonical MD) simulation while restricting the base structures, with and without the other surrounding CDR segments. The results showed that the multicanonical MD sampled a much larger conformational space than the conventional MD, independent of the initial conformations of the simulations. When the other CDRs surrounding the CDR-H3 segments were included in the calculations, the predominant conformations at 300 K corresponded to the X-ray crystal structures. When only the single CDR-H3 loops were considered with the restricted base structures, a greater number of different conformations were sampled as putative loops, but only a small number of stable conformations appeared at 300 K. Analyses of the resultant conformations revealed a structural role for the glycine, when it is located at position three residues before the last residue of CDR-H3 (Gly-X-X-last residue), coincident with the statistical tendencies of many antibody crystal structures. This reflects the general consistency between the energetically stable conformations and the empirically observed conformations. The current method is expected to be applicable to the structural modeling and the design of antibodies, especially for the inherently flexible loops.

Harmful somatic mutations: lessons from the dark side

The ability of somatic mutation to modify the course of an immune response is well documented. However, emphasis has been placed almost exclusively on the ability of somatic mutation to improve the functional characteristics of representative antibodies. The harmful effects of somatic mutation, its dark side, have been far less well characterized. Yet evidence suggests that the number of B cells directed to wastage pathways as a result of harmful somatic mutation probably far exceeds the number of cells whose antibodies have been improved. Here we review our recent findings in understanding the structural and functional consequences of V-region mutation.

Atypical phosphorylcholine-reactive protein from Atlantic salmon, Salmo salar L

A phosphorylcholine-reactive protein was isolated from serum of Atlantic salmon (Salmo salar L.) by affinity chromatography on a phosphorylcholine-conjugated Sepharose column followed by elution with phosphorylcholine. Based on the method used we describe the isolated protein as salmon phosphorylcholine-reactive protein (salmon PRP). Salmon PRP has calcium-independent binding to phosphorylcholine. The protein exists in a monomeric and dimeric form with molecular weight of approximately 80 and 160 kD, respectively. Separation of the protein preparation on SDS-PAGE under reducing conditions resulted in disappearance of the 80 and 160 kD bands and appearance of a major protein band of approximately 100 kD. The N-terminal amino acid sequences of the non-reduced 80 and 160 kD bands and the reduced 100 kD band were identical. Apart from the dimeric form, the molecular weight of salmon PRP and its appearance on SDS-PAGE is similar to human plasminogen. Comparison of the sequence in a protein database resulted in approximately 50% identity with human and bovine plasminogen. In addition, cross-reactivity between antibodies to human plasminogen and salmon PRP was demonstrated. Thus, salmon PRP appears to be different from other phosphorylcholine-reactive proteins which are mostly reported to be CRP-like proteins with calcium-dependent binding to phosphorylcholine, pentameric ring-structure and sequence homology between species. Whether salmon PRP is a new type of phosphorylcholine-binding protein with an unknown function or a plasminogen-like protein with binding specificity for phosphorylcholine calls for further investigation.

Structural characterization of mouse monoclonal antibody 13-1 against a porphyrin derivative: identification of a disulfide bond in CDR-H3 of Mab 13-1

The amino acid sequence of a mouse monoclonal antibody Mab13-1, a catalytic antibody against TCPP (meso-tetrakis(4-carboxyphenyl)porphyrin), was confirmed by mass spectrometric (MS) peptide mapping. The amino-terminal sequence of the heavy chain was established by MS/MS analysis of the isolated N-terminal peptide. The presence of a unique disulfide bond between Cys93H and Cys102H was identified by MS peptide mapping and sequence analysis of an S-S containing peptide. Positions of other disulfide bonds were identified to be conserved. The non-conserved disulfide bridge was found to be resistant as other intra-chain disulfide bonds against reduction under non-denaturing condition, and to be buried inside the molecule. This extra disulfide bond is expected to support antigen-binding by restricting the flexibility of CDR-H3 loop, and it might be favorable for the recognition of a plane antigen, a porphyrin derivative.

The rate-limiting steps for the folding of an antibody scFv fragment

The refolding kinetics of a single-chain Fv (scFv) fragment, derived from the phosphorylcholine binding antibody McPC603, was investigated. Both prolyl-peptide bonds which are cis in the native state affect the refolding kinetics of long-term denatured protein. The rate-limiting step is the trans --> cis isomerization at the ProL95-peptide bond, which is catalyzed by peptidyl-prolyl-cis/trans-isomerase (PPIase), and is the prerequisite for correct V(H)/V(L) domain association. Refolding of short-term denatured protein resulted in complex refolding kinetics, too. This kinetic heterogeneity could be ascribed to cis --> trans re-isomerization at the ProL95-peptide bond to the wrong conformation in a folding intermediate. PPIase was shown to increase the fraction of slowly folding species, thereby competing with the fast folding of short-term denatured scFv, having native proline conformations. A trapped intermediate is rapidly populated, and the return from this state becomes rate-limiting.