Correlation of N-glycan dynamics and interaction network with allosteric antigen binding and Fc receptor recognition

Aim: Fragment crystallizable (Fc) glycans modulate Fc conformations and functions, and glycan may also regulate antigen recognition. In the antibody drug development, glycosylation patterns affect antibody drug characteristics and quality control. In order to provide a global feature of N-glycan interactions in response to antigen and Fc receptor bindings, the interactions among Fc N-glycans and N-glycans’ interaction with Fc CH2 and CH3 domains have been studied. Methods: Molecular dynamics simulations were used to generate conformation ensembles of free antibody, antibody-antigen complex, antibody-human Fc-gamma-receptor-I (hFcγRI) and antibody-antigen-hFcγRI, the hydrogen bonds and radial distance distribution involving N-glycans carbohydrate chains have been analyzed. Results: Two important interaction patterns have been observed. The first is the strong but non-specific interactions between two carbohydrate chains in free antibody. Secondly, it has been found that N-glycans carbohydrate chains can directly interact with CH3 domain in free antibody, and that the distance distribution between carbohydrate chains and CH3 domain clearly differentiate the free antibody, antibody-antigen complex, antibody-hFcγRI complex, and final antibody-antigen-hFcγRI complex. Conclusions: N-glycans partially acts as allosteric sensor and respond to antigen and hFcγRI binding.

The mycoplasma surface proteins MIB and MIP promote the dissociation of the antibody-antigen interaction

Mycoplasma immunoglobulin binding (MIB) and mycoplasma immunoglobulin protease (MIP) are surface proteins found in the majority of mycoplasma species, acting sequentially to capture antibodies and cleave off their VH domains. Cryo–electron microscopy structures show how MIB and MIP bind to a Fab fragment in a “hug of death” mechanism. As a result, the orientation of the VL and VH domains is twisted out of alignment, disrupting the antigen binding site. We also show that MIB-MIP has the ability to promote the dissociation of the antibody-antigen complex. This system is functional in cells and protects mycoplasmas from antibody-mediated agglutination. These results highlight the key role of the MIB-MIP system in immunity evasion by mycoplasmas through an unprecedented mechanism, and open exciting perspectives to use these proteins as potential tools in the antibody field.

Сell-free pertussis vaccine from antigens of freshly isolated strain of B. pertussis serotype 1.2.3

Aim. Development of technology for the manufacture of cell-free pertussis vaccine (CPV) from a freshly isolated strain of B. pertussis No. 211 serotype 1.2.3 and the study of its protective activity and safety in comparison with the preparation of vaccine strains. Materials and methods. Following B. pertussis strains were used: freshly isolated strain No. 211, serotype 1.2.3; vaccine strains No. 305, serotype 1.2.0, and No. 475a, serotype 1.2.3. According to the original method, a CPV was obtained from the supernatant of the liquid culture medium of B. pertussis strain No. 211 and its protective and toxic properties were studied. Results. Studies have shown that the use of enriched nutrient media for the cultivation of the strain and the increase in the duration of the the detoxification period of the protective antigen complex isolated from the culture medium are needed to obtain a CPV vaccine consisting of antigens of a freshly isolated strain. CPV obtained from the freshly isolated strain had protectivity 1.7 times higher compared to those of CPV obtained from vaccine strains, was nontoxic and had a low sensitizing properties. The results indicate that the freshly isolated strain No. 211 is a promising candidate for use in the development of pertussis vaccines.

Ab-Ligity: Identifying sequence-dissimilar antibodies that bind to the same epitope

Solving the structure of an antibody-antigen complex gives atomic level information of the interactions between an antibody and its antigen, but such structures are expensive and hard to obtain. Alternative experimental sources include epitope mapping and binning experiments which can be used as a surrogate to identify key interacting residues. However, their resolution is usually not sufficient to identify if two antibodies have identical interactions. Computational approaches to this problem have so far been based on the premise that antibodies with similar sequences behave similarly. Such approaches will fail to identify sequence-distant antibodies that target the same epitope.We present Ab-Ligity, a structure-based similarity measure tailored to antibody-antigen interfaces. Using predicted paratopes on model antibody structures, we assessed its ability to identify those antibodies that target highly similar epitopes. Most antibodies adopting similar binding modes can be identified from sequence similarity alone, using methods such as clonotyping. In the challenging subset of antibodies whose sequences differ significantly, Ab-Ligity is still able to predict antibodies that would bind to highly similar epitopes (precision of 0.95 and recall of 0.69). We compared Ab-Ligity’s performance to an existing tool for comparing general protein interfaces, InterComp, and showed improved performance on antibody cases alongside a significant speed-up. These results suggest that Ab-Ligity will allow the identification of diverse (sequence-dissimilar) antibodies that bind to the same epitopes from large datasets such as immune repertoires. The tool is available at http://opig.stats.ox.ac.uk/resources.

An Assessment of Mesoporous Silica Nanoparticle Architectures as Antigen Carriers

Mesoporous silica nanoparticles (MSNPs) have the potential to be used as antigen carriers due to their high surface areas and highly ordered pore network. We investigated the adsorption and desorption of diphtheria toxoid as a proof-of-concept. Two series of nanoparticles were prepared—(i) small pores (SP) (<10 nm) and (ii) large pores (LP) (>10 nm). SBA-15 was included as a comparison since this is commercially available and has been used in a large number of studies. External diameters of the particles ranged from 138 to 1509 nm, surface area from 632 to 1110 m2/g and pore size from 2.59 to 16.48 nm. Antigen loading was assessed at a number of different ratios of silica-to-antigen and at 4 °C, 20 °C and 37 °C. Our data showed that protein adsorption by the SP series was in general consistently lower than that shown by the large pore series. Unloading was then examined at 4 °C, 20 °C and 37 °C and a pH 1.2, 4.5, 6.8 and 7.4. There was a trend amongst the LP particles towards the smallest pores showing the lowest release of antigen. The stability of the MSNP: antigen complex was tested at two different storage temperatures, and storage in solution or after lyophilization. After 6 months there was negligible release from any of the particles under any of the storage conditions. The particles were also shown not to cause hemolysis.

A class of γδ T cell receptors recognize the underside of the antigen-presenting molecule MR1

T cell receptors (TCRs) recognize antigens presented by major histocompatibility complex (MHC) and MHC class I–like molecules. We describe a diverse population of human γδ T cells isolated from peripheral blood and tissues that exhibit autoreactivity to the monomorphic MHC-related protein 1 (MR1). The crystal structure of a γδTCR–MR1–antigen complex starkly contrasts with all other TCR–MHC and TCR–MHC-I-like complex structures. Namely, the γδTCR binds underneath the MR1 antigen-binding cleft, where contacts are dominated by the MR1 α3 domain. A similar pattern of reactivity was observed for diverse MR1-restricted γδTCRs from multiple individuals. Accordingly, we simultaneously report MR1 as a ligand for human γδ T cells and redefine the parameters for TCR recognition.

Introduction to Measurement of Avidity of Anti-Coxiella burnetii IgG in Diagnosis of Q Fever

ABSTRACT Due to the atypical serological profile of some patients with primary Q fever infection who do not develop IgM against Coxiella burnetii, we developed an avidity test to distinguish recent or past infections. We tested 39 serum samples by immunofluorescence with conventional assay and after urea treatment from 26 patients at different stages of the disease. We observed a strong avidity in the 15 serum samples from patients with infections of >6 months and a low avidity for sera from patients with recent infections. A complete denaturation of the antibody-antigen complex was observed for patients for whom the time since the beginning of infection was <1 month and a mean of 2.06 ± 0.54 lowered titers when the infection was less than 3 months old. That was statistically significant compared to sera from patients with infections of greater than 6 months (mean 0.20 ± 0.41) and with infections between 3 and 6 months (mean, 1.17 ± 0.41) (P = 0.0022 and P < 0.0001, respectively). These results were visualized by Western blotting. We concluded that high avidity (≤1 lowered titer) ruled out infection during the last 6 months and that complete denaturation was related to an infection which had occurred within the previous 3 months. Between these two situations, the avidity test is inconclusive. We suggest using an avidity test for atypical Q fever serology that could be misclassified as residual antibodies (IgG against C. burnetii detected without active or recent infection) and for pregnant women risking obstetrical complications. This new test will dramatically improve the diagnosis and management of patients with Q fever.