Antigen Binding Site Of Antibody Research Articles

Comparison of lateral flow immunoassays based on oriented and nonoriented immobilization of antibodies for the detection of aflatoxin B1

In recent years, some studies have found that oriented immobilization of antibodies to microspheres can fully expose the antigen binding sites of antibodies, which can improve the sensitivity of sandwich immunoassays for the detection of proteins. Can this antibody immobilization strategy also improve the sensitivity of competitive immunoassays for the detection of small molecules? To answer this question, the conjugate MS-SPG-Ab (oriented immobilization of aflatoxin B1 antibody to time-resolved fluorescent microspheres via streptococcal protein G) and the conjugate MS-Ab (nonoriented immobilization of aflatoxin B1 antibody to time-resolved fluorescent microspheres) were prepared, and a lateral flow immunoassay (LFIA) for the detection of aflatoxin B1 (AFB1) was established. The detection performance of the two methods was compared. The results showed that under the condition that the number of “effective” antibodies immobilized on TRF-MS was similar, compared with the nonoriented immobilization strategy (IC50 = 0.21 ng mL−1), the LFIA method established by the oriented immobilization strategy reduced the sensitivity of AFB1 detection (IC50 = 0.37 ng mL−1). However, this method can obtain higher detection precision for AFB1, the CV values were all below 8%. And it has stronger tolerance to the matrix of maize and peanut samples. The bias of LFIAs based on oriented immobilization technology (−14.93%–7.92%) was lower than nonoriented immobilization technology (28.16%–34.19%) for AFB1 detection in the two sample extracts. This study suggests that the LFIA method based on the oriented immobilization of antibodies can improve the accuracy of the detection results when performing rapid screening of small molecules.

The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage.

Understanding affinity maturation of antibodies that can target many variants of HIV-1 is important for vaccine development. While the antigen-binding site of antibodies is known to mutate throughout the co-evolution of antibodies and viruses in infected individuals, the roles of the mutations in the antibody framework region are not well understood. Throughout affinity maturation, the CH103 broadly neutralizing antibody lineage, from an individual designated CH505, altered the orientation of one of its antibody variable domains. The change in orientation was a response to insertions in the variable loop 5 (V5) of the HIV envelope. In this study, we generated CH103 lineage antibody variants in which residues in the variable domain interface were mutated, and measured the binding to both autologous and heterologous HIV-1 envelopes. Our data show that very few mutations in an early intermediate antibody of the lineage can improve binding toward both autologous and heterologous HIV-1 envelopes. We also crystallized an antibody mutant to show that framework mutations alone can result in a shift in relative orientations of the variable domains. Taken together, our results demonstrate the functional importance of residues located outside the antigen-binding site in affinity maturation.

In Vitro Evolution of Antibodies Inspired by In Vivo Evolution.

In vitro generation of antibodies often requires variable domain sequence evolution to adapt the protein in terms of affinity, specificity, or developability. Such antibodies, including those that are of interest for clinical development, may have their origins in a diversity of immunoglobulin germline genes. Others and we have previously shown that antibodies of different origins tend to evolve along different, preferred trajectories. Apart from substitutions within the complementary determining regions, evolution may also, in a germline gene-origin-defined manner, be focused to residues in the framework regions, and even to residues within the protein core, in many instances at a substantial distance from the antibody’s antigen-binding site. Examples of such germline origin-defined patterns of evolution are described. We propose that germline gene-preferred substitution patterns offer attractive alternatives that should be considered in efforts to evolve antibodies intended for therapeutic use with respect to appropriate affinity, specificity, and product developability. We also hypothesize that such germline gene-origin-defined in vitro evolution hold potential to result in products with limited immunogenicity, as similarly evolved antibodies will be parts of conventional, in vivo-generated antibody responses and thus are likely to have been seen by the immune system in the past.

Cysteine Proteases Inhibitors with Immunoglobulin-Like Fold in Protozoan Parasites and their Role in Pathogenesis.

The number of protein folds in nature is limited, thus is not surprising that proteins with the same fold are able to exert different functions. The cysteine protease inhibitors that adopt an immunoglobulin- like fold (Ig-ICPs) are inhibitors encoded in bacteria and protozoan parasites. Structural studies indicate that these inhibitors resemble the structure of archetypical proteins with an Ig fold, like antibodies, cadherins or cell receptors. The structure of Ig-ICPs from four different protozoan parasites clearly shows the presence of three loops that form part of a protein-ligand interaction surface that resembles the antigen binding sites of antibodies. Thus, Ig-ICPs bind to different cysteine proteases using a tripartite mechanism in which their BC, DE and FG loops are responsible for the main interactions with the target cysteine protease. Ig-ICPs from different protozoan parasites regulate the enzymatic activity of host or parasite's proteases and thus regulate virulence and pathogenesis.

Revisiting antibody modeling assessment for CDR-H3 loop.

The antigen-binding site of antibodies, also known as complementarity-determining region (CDR), has hypervariable sequence properties. In particular, the third CDR loop of the heavy chain, CDR-H3, has such variability in its sequence, length, and conformation that ordinary modeling techniques cannot build a high-quality structure. At Stage 2 of the Second Antibody Modeling Assessment (AMA-II) held in 2013, the model structures of the CDR-H3 loops were submitted by the seven modelers and were critically assessed. After our participation in AMA-II, we rebuilt one of the long CDR-H3 loops with 13 residues (A52 antibody) by a more precise method, using enhanced conformational sampling with the explicit water model, as compared to our previous method employed at AMA-II. The current stable models obtained from the free energy landscape at 300 K include structures similar to the X-ray crystal structures. Those models were not built in our previous work at AMA-II. The current free energy landscape suggested that the CDR-H3 loop structures in the crystal are not stable in solution, but they are stabilized by the crystal packing effect.

Antigen-Induced Activation of Antibody Measured by Fluorescence Enhancement of FITC Label at Fc.

Three anti-carbohydrate antibodies of defined specificity isolated from plasma were used to demonstrate that macromolecular antigen binding caused considerable enhancement of fluorescence of FITC-labeled antibody. Mono and disaccharide antigens which could compete with the large antigens in antibody binding could not however produce any increase in fluorescence. Fluorescence enhancement in a given antibody sample increased with the size of the occupying macromolecular antigen. Conversely in antibody samples of same ligand specificity isolated from plasma of different individuals, fluorescence enhancement produced by the same antigen correlated with specific activity of the antibody sample. Removal of Fc part of antibody, confirmed by electrophoresis and Fc-specific antibody binding, caused abolition of most of the antigen-driven fluorescence increase. Since antigen binding sites of antibodies were protected during FITC labeling, the above results suggest that conformational shift in Fc produced by occupation of binding sites by large antigens resulted in the enhancement of fluorescence of FITC tags on Fc. Data provides a tool for detection and measurement of specific ligands using fluorolabeled whole antibodies.

Abstract 2664: An anti-Jagged-1/-2 Probody demonstrates inhibition of Jagged-dependent Notch signaling and is activated in multiple types of tumors

Abstract Probodies represent a unique class of antibody therapeutics that specifically target therapeutic activity to diseased tissues, such as cancer. A Probody is a fully recombinant protein that contains a masking peptide that blocks the antibody's antigen-binding site and is linked to the light chain of the antibody by a protease-cleavable peptide substrate. Probodies are designed to be inactive in circulation and in healthy tissues but activated within the tumor microenvironment. The Probody™ approach is designed to widen the therapeutic index of antibodies to promising therapeutic targets that may be limited by significant toxicity. One such promising set of targets are components of the Notch pathway, which is involved in both oncogenic and healthy tissue signaling. We have developed a fully human IgG1 monoclonal antibody that binds and inhibits the activity of both human and mouse Jagged-1 and Jagged-2, two key ligands in the Notch signaling pathway. A Probody produced from this antibody induced dose-dependent inhibition of Notch signaling, resulting in anti-tumor activity in in vivo tumor models without significant toxicity. To further explore the clinical relevance of the anti-Jagged Probody for the treatment of cancer, we evaluated (i) the heterogeneity of Jagged expression in multiple tumor types, (ii) the activation of the Jagged Probody in tumor biopsies, and (iii) the blockade of Notch signaling using an intracellular pharmacodynamic biomarker. Patient tumor tissues were screened for Jagged-1/-2 IHC across lung, pancreatic and breast cancer_ indications where activation of the Notch pathway is implicated. Overall, more than 75% of patient tumors demonstrated moderate to high Jagged-1/-2 expression. We also developed and validated a technique termed IHZ™ analysis that enables the measurement of proteolytic Probody activation and binding to Jagged ligands ex vivo in human tumor sections. We evaluated 120 patients across the three tumor types and observed ∼99% of samples that were positive for antibody binding were also positive by IHZ analysis, signifying sufficient proteolytic activity to activate the Probody. Finally, we evaluated the accumulation of the Notch Intracellular Domain (NICD), a biomarker of Notch signaling, in the nucleus of tumor cells in animals treated with antibody. Notably, our data showed that Notch signaling blockade as indicated by a decrease in the accumulation of NICD correlated with dose-response in in vivo models. Taken together, our data suggest that the anti-Jagged-1/-2 Probody may have wide therapeutic utility as a tumor-specific inhibitor of Jagged-dependent Notch signaling in oncology. Citation Format: Olga Vasiljeva, Elizabeth Menendez, Jason Sagert, James W. West, Jennifer Richardson, Luc Desnoyers, Shouchun Liu, Judi Ford, Krishna Plou, Henry Lowman. An anti-Jagged-1/-2 Probody demonstrates inhibition of Jagged-dependent Notch signaling and is activated in multiple types of tumors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2664. doi:10.1158/1538-7445.AM2014-2664

A Structurally Distinct Human Mycoplasma Protein that Generically Blocks Antigen-Antibody Union

We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known protein structures, as does its mechanism of antibody binding. Protein M binds with high affinity to all types of human and nonhuman immunoglobulin G, predominantly through attachment to the conserved portions of the variable region of the κ and λ light chains. Protein M blocks antibody-antigen union, likely because of its large C-terminal domain extending over the antibody-combining site, blocking entry to large antigens. Similar to the other immunoglobulin-binding proteins such as Protein A, Protein M as well as its orthologs in other Mycoplasma species could become invaluable reagents in the antibody field.

Covalent Inactivation of Factor VIII Antibodies from Hemophilia A Patients by an Electrophilic FVIII Analog

The antigen-binding sites of antibodies (Abs) can express enzyme-like nucleophiles that react covalently with electrophilic compounds. We examined the irreversible and specific inactivation of antibodies (Abs) to Factor VIII (FVIII) responsible for failure of FVIII replacement therapy in hemophilia A (HA) patients. Electrophilic analogs of FVIII (E-FVIII) and its C2 domain (E-C2) were prepared by placing the strongly electrophilic phosphonate groups at surface-exposed Lys side chains of diverse antigenic epitopes. IgG Abs to FVIII from HA patients formed stable immune complexes with E-FVIII and E-C2 that were refractory to dissociation by SDS treatment and boiling, procedures that dissociate noncovalent Ab-antigen complexes. The rate-limiting step in the reaction was formation of the initial noncovalent complexes. Conversion of the initial complexes to the irreversible state occurred rapidly. The antigenic epitopes of E-FVIII were largely intact, and most of the Abs were consumed covalently. E-FVIII expressed poor FVIII cofactor activity in clotting factor assays. Nonspecific interference by E-FVIII in clotting factor function was not evident. Treatment with E-FVIII, and to a lesser extent E-C2, irreversibly relieved the FVIII inhibitory effect of HA IgG in clotting factor assays. Small FVIII peptides did not display useful reactivity, highlighting the diverse epitope specificities of the Abs and the conformational character of FVIII epitopes. E-FVIII is a prototype reagent able to attain irreversible and specific inactivation of pathogenic Abs.

Structural Consequences of Mutations in Interfacial Tyr Residues of a Protein Antigen-Antibody Complex: THE CASE OF HyHEL-10-HEL

Tyrosine is an important amino acid in protein-protein interaction hot spots. In particular, many Tyr residues are located in the antigen-binding sites of antibodies and endow high affinity and high specificity to these antibodies. To investigate the role of interfacial Tyr residues in protein-protein interactions, we performed crystallographic studies and thermodynamic analyses of the interaction between hen egg lysozyme (HEL) and the anti-HEL antibody HyHEL-10 Fv fragment. HyHEL-10 has six Tyr residues in its antigen-binding site, which were systematically mutated to Phe and Ala using site-directed mutagenesis. The crystal structures revealed several critical roles for these Tyr residues in the interaction between HEL and HyHEL-10 as follows: 1) the aromatic ring of Tyr-50 in the light chain (LTyr-50) was important for the correct ternary structure of variable regions of the immunoglobulin light chain and heavy chain and of HEL; 2) deletion of the hydroxyl group of Tyr-50 in the heavy chain (HTyr-50) resulted in structural changes in the antigen-antibody interface; and 3) the side chains of HTyr-33 and HTyr-53 may help induce fitting of the antibody to the antigen. Hot spot Tyr residues may contribute to the high affinity and high specificity of the antigen-antibody interaction through a diverse set of structural and thermodynamic interactions.

Cross-reactivity of mimotopes with a monoclonal antibody against the high molecular weight melanoma-associated antigen (HMW-MAA) does not predict cross-reactive immunogenicity

The high molecular weight melanoma-associated antigen (HMW-MAA) is highly expressed in advanced primary and metastatic melanoma. An epitope of the core protein of HMW-MAA is recognized by the murine monoclonal antibody (mAb) 225.28S. In this study, we aimed to characterize peptides that antigenically mimicked this epitope and to determine their efficacy as components of an HMW-MAA-based anti-melanoma vaccine. Therefore, we screened a constrained 10 mer phage display peptide library against mAb 225.28S. Selected phage-displayed peptides were then tested for their specificity for the antibody's antigen-binding site. DNA sequences coding for specific peptide ligands were determined. Binding of mAb 225.28S to HMW-MAA was inhibited in a dose-dependent manner by phage-displayed peptides from 51 to 83% and by synthetic peptides from 38 to 87%. Subsequently, the immunogenicity of the five mimotopes with the highest inhibition capacity was examined in rabbits. Immunizations with synthetic mimotopes conjugated to tetanus toxoid resulted in peptide-specific antibodies, but none of the highly antigenic mimotopes induced HMW-MAA cross-reactive antibodies. This report describes an example of disparity between antigenicity and cross-reactive immunogenicity, complicating the selection of potential vaccine candidates.

Crystal Structure of HEL4, a Soluble, Refoldable Human VH Single Domain with a Germ-line Scaffold

The antigen binding site of antibodies usually comprises associated heavy (VH) and light (VL) chain variable domains, but in camels and llamas, the binding site frequently comprises the heavy chain variable domain only (referred to as VHH). In contrast to reported human VH domains, VHH domains are well expressed from bacteria and yeast, are readily purified in soluble form and refold reversibly after heat-denaturation. These desirable properties have been attributed to highly conserved substitutions of the hydrophobic residues of VH domains, which normally interact with complementary VL domains. Here, we describe the discovery and characterisation of an isolated human VH domain (HEL4) with properties similar to those of VHH domains. HEL4 is highly soluble at concentrations of ≥3 mM, essentially monomeric and resistant to aggregation upon thermodenaturation at concentrations as high as 56 μM. However, in contrast to VHH domains, the hydrophobic framework residues of the VH:VL interface are maintained and the only sequence changes from the corresponding human germ-line segment (V3-23/DP-47) are located in the loops comprising the complementarity determining regions (CDRs). The crystallographic structure of HEL4 reveals an unusual feature; the side-chain of a framework residue (Trp47) is flipped into a cavity formed by Gly35 of CDR1, thereby increasing the hydrophilicity of the VH:VL interface. To evaluate the specific contribution of Gly35 to domain properties, Gly35 was introduced into a VH domain with poor solution properties. This greatly enhanced the recovery of the mutant from a gel filtration matrix, but had little effect on its ability to refold reversibly after heat denaturation. Our results confirm the importance of a hydrophilic VH:VL interface for purification of isolated VH domains, and constitute a step towards the design of isolated human VH domains with practical properties for immunotherapy.

The generation of antibody diversity through somatic hypermutation and class switch recombination.

Antibody-mediated immunity is critical to the resistance of vertebrate species to pathogenic organisms. Although low-affinity immunoglobin (Ig) M antibodies circulate in the blood prior to encountering pathogens, high-affinity IgG and IgA antibodies are required to inactivate toxins, neutralize viruses, and promote the clearance of microorganisms. Individuals, such as those with hyper-IgM syndrome (HIGM), who lack the ability to make such high-affinity IgG and IgA antibodies, are unable to combat bacterial and viral infections and usually die at a young age (Revy et al. 2000; Imai et al. 2003). Prior to exposure to antigen, the initial generation of a diverse antibody repertoire is achieved early in B-lymphocyte development by the successful rearrangement of the V, D, and J gene segments to produce B cells, each of which makes a unique Ig heavyand light-chain variable (V) region (Fig. 1A; Tonegawa 1983). These V regions encode the antigen binding sites of antibodies that are then expressed on the surface of a B lymphocyte and its clonal progeny. Following specific antigen recognition by its cognate B lymphocyte and costimulation by helper T lymphocytes, the B lymphocyte enters the germinal center of peripheral lymphoid organs to become a centroblast B cell. There, a second wave of antibody diversification occurs through somatic hypermutation (SHM) and/or gene conversion (GC) of the V region to generate high-affinity antigen binding sites (Fig. 1B; MacLennan 1994). SHM is the predominant mechanism in mice and humans, whereas GC occurs in chickens and some other species (Weill and Reynaud 1996). In the same centroblast B cell, the heavy-chain V regions encoding the antigen binding sites are rearranged down the chromosome through class switch recombination (CSR) so that they can be expressed with one of the constant (C) region genes to carry out many different effector functions and be distributed throughout the body (Fig. 1B; Manis et al. 2002b). SHM and CSR are largely targeted to the Ig genes, but their targeting to other genes causes many of the B-cell lymphomas in mice and humans (Pasqualucci et al. 2001). The biochemical mechanism and regulation of SHM and CSR are the topic of this review.

Selection of Mimotopes of the Cell Surface Adhesion Molecule Mel-CAM from a Random pVIII-28aa Phage Peptide Library

The cell surface adhesion molecule Mel-CAM is highly expressed in advanced primary and metastatic melanoma. Mel-CAM was first described as an integral membrane glycoprotein of malignant melanoma cells. The murine monoclonal antibody MAd18-5D7 recognizes an epitope of the extracellular domain of Mel-CAM and is able to enhance Mel-CAM mediated adhesion of melanoma cells in aggregation assays. For the characterization of peptides that antigenically mimic surface-exposed areas of Mel-CAM we screened a newly constructed random pVIII-28aa bacteriophage peptide library against MAd18-5D7. After three panning rounds a population of phages binding to MAd18-5D7 was enriched. Peptides expressed on the surface of these phages were then tested for their specificity for the antibody's antigen binding site. DNA sequences coding for two specific peptide ligands were determined. One of the deduced amino acid sequences showed similarity to a portion of the sequence of the third immunoglobulin-like extracellular domain of Mel-CAM. Both peptides blocked the interaction of MAd18-5D7 with Mel-CAM present in a MelJuSo melanoma cell line lysate. Phage displayed as well as synthetic peptides inhibited in a dose-dependent manner the binding of MAd18-5D7 to recombinant Mel-CAM in enzyme-linked immunosorbent assay experiments. No such inhibition was observed using a panel of other anti-Mel-CAM antibodies. Our results clearly indicate that these 28mer peptides are structural equivalents of the MAd18-5D7 epitope of Mel-CAM and that they will be useful tools for further in vitro and in vivo studies of Mel-CAM mediated cell-cell interaction.

Modifications to canonical structure sequence patterns: analysis for L1 and L3.

The conformation of five of the six hypervariable loops that form the antigen-binding site of antibodies is limited to a small set of structures designated as canonical structures. The canonical structure model has been constituted as a fundamental tool for the modeling of antibodies. The detailed study of tens of crystallographic structures of antibodies has shown the validity of this model in the great majority of cases. The robustness of the forecast capacity of this model depends fundamentally on the precision with which the sequence patterns that characterize each canonical structure form can be defined. Nevertheless, due to the enormous quantity of structural information about antibodies generated during the last decade, it is difficult to avoid mistakes or confusion in the model. In the present work, we propose some corrections to the model for loops L1 and L3 that permit defining sequence patterns that avoid confusion and make better forecasting of the canonical structure model possible.

VIR.II: a new interface with the antibody sequences in the Kabat database

The Kabat database is the source of information par excellence on antibody sequences. In 1995, we developed an interface with the Kabat database, called VIR. VIR has been very useful in conducting studies aiming to find structure-function relationships in antibodies. Here we report a new version adapted to the World Wide Web, called VIR.II. VIR.II allows searches by type of chain (V H or V L), by species, and by specificity. The species are selected using a pulldown menu, whereas the specificities can be selected from a list containing the unique specificities reported in the Kabat database. These facilities avoid mistakes and redundancies in the searches. Another feature, and probably the most important one, is that VIR.II introduces a classification of specificities in terms of the chemical and biochemical nature of the antigen, like anti-protein, anti-peptide, anti-hapten, etc. This classification has been useful in discovering patterns in the antigen-binding site of antibodies that correlate with the type of antigen the antibody interacts with. To illustrate this, while showing the capabilities of VIR.II, we analyze all the murine anti-peptide and anti-protein antibody sequences compiled as of July, 2000 in the Kabat database.

Identification of protein functions from a molecular surface database, eF-site.

A bioinformatics method was developed to identify the protein surface around the functional site and to estimate the biochemical function, using a newly constructed molecular surface database named the eF-site (electrostatic surface of Functional site. Molecular surfaces of protein molecules were computed based on the atom coordinates, and the eF-site database was prepared by adding the physical properties on the constructed molecular surfaces. The electrostatic potential on each molecular surface was individually calculated solving the Poisson-Boltzmann equation numerically for the precise continuum model, and the hydrophobicity information of each residue was also included. The eF-site database is accessed by the internet (http://pi.protein.osaka-u.ac.jp/eF-site/). We have prepared four different databases, eF-site/antibody, eF-site/prosite, eF-site/P-site, and eF-site/ActiveSite, corresponding to the antigen binding sites of antibodies with the same orientations, the molecular surfaces for the individual motifs in PROSITE database, the phosphate binding sites, and the active site surfaces for the representatives of the individual protein family, respectively. An algorithm using the clique detection method as an applied graph theory was developed to search of the eF-site database, so as to recognize and discriminate the characteristic molecular surfaces of the proteins. The method identifies the active site having the similar function to those of the known proteins.