Exposure Of Epitopes Research Articles

Biophysical Correlates of Enhanced Immunogenicity of a Stabilized Variant of the Receptor Binding Domain of SARS-CoV-2.

The receptor binding domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We have previously reported the design and characterization of a mammalian cell expressed RBD derivative, mRBD1-3.2, that has higher thermal stability and greatly enhanced immunogenicity relative to the wild type mRBD. The protein is highly thermotolerant and immunogenic and is being explored for use in room temperature stable Covid-19 vaccine formulations. In the current study, we have investigated the folding pathway of both WT and stabilized RBD. It was found that chemical denaturation of RBD proceeds through a stable equilibrium intermediate. Thermal and chemical denaturation is reversible, as assayed by binding to the receptor ACE2. Unusually, in its native state, RBD binds to the hydrophobic probe ANS, and enhanced ANS binding is observed for the equilibrium intermediate state. Further characterization of the folding of mRBD1-3.2, both in solution and after reconstitution of lyophilized protein stored for a month at 37 °C, revealed a higher stability represented by higher Cm, faster refolding, slower unfolding, and enhanced resistance to proteolytic cleavage relative to WT. In contrast to WT RBD, the mutant showed decreased interaction with the hydrophobic moiety linoleic acid. Collectively, these data suggest that the enhanced immunogenicity results from reduced conformational fluctuations that likely enhance in vivo half-life as well as reduce the exposure of irrelevant non-neutralizing epitopes to the immune system.

An integrative and multiscale approach to study dengue virus-like particle dynamics.

Dengue virus is an enveloped virus which infects millions of people worldwide. The only available vaccine has low efficacy and is recommended only for individuals with prior dengue infection. Virus-like particles (VLPs) are promising platforms as vaccine candidates due to their non-infectious and highly immunogenic nature. These particles lack a genomic core and are highly unstable and heterogeneous in size. This motivates the characterization of the biophysical and structural properties of VLPs to facilitate the rational production of stable and homogenous particles. Dengue VLPs elicits neutralizing antibodies similar to infectious virions. Dengue VLPs are enveloped particles in which sixty envelope (E) and membrane (M) proteins are embedded in a lipid vesicle. Similarly, to the dengue virus, the VLPs undergo a maturation process, involving large conformational changes, leading to exposure of epitopes that subsequently determine the immune response. In this work, the structure and intrinsic dynamics of VLPs and their conformational transitions were investigated using integrative modeling and molecular simulations. To gain atomistic insights into the maturation process and to facilitate the development of stable enveloped VLPs, we employed an integrative approach combining multiscale modeling and simulations with experimental data from cryo-electron microscopy, lipidomics, and secretion assays. Coarse-grained simulations of mature and immature VLPs revealed the effective number of lipids that result in optimally stable and spherical particles. Furthermore, these models were used as a platform to simulate the transition between conformational states in order to understand the maturation process in unprecedented detail. Finally, atomistic MD simulations performed on native dengue and dengue-Japanese encephalitis virus chimeric E/M proteins and their mutants highlighted the role of protein-lipid interactions in governing VLP stability. This integrative approach aims towards the future development of stable and immunogenic next-generation vaccines.

Uncovering the conformational dynamics of dengue virus and its virus-like particles as novel vaccine candidates.

Dengue virus (DENV) is an enveloped virus that infects millions of people worldwide. The only commercially available vaccine has low efficacy and safety issues. DENV is ∼50 nm in diameter, and contains 90 envelope (E) and membrane (M) protein dimers embedded within a lipid envelope, encapsulating an RNA genome. There are four closely related DENV serotypes, which hamper broad neutralization by host antibodies and can result in antibody dependent enhancement worsening the clinical symptoms of dengue infections. During its life cycle, DENV adopts numerous conformations in response to environmental factors such as pH and temperature changes, which result in varying degrees of exposure of its accessible epitopes. These factors make vaccine development challenging both from the immunological and structural points of view. Virus-like particles (VLPs) represent promising platforms as novel vaccine alternatives because they are non-infectious and highly immunogenic. DENV VLPs are ∼30 nm in diameter, containing 30 E/M protein dimers on their surface, likely leading to significant differences in their conformational dynamics compared to the virus itself. Notably, these VLPs exhibit a significant “groove” at the E protein dimeric interface, yielding more exposed epitopes than those present on the typical DENV particle. This factor is likely to be critical to the efficacy of resultant vaccines. Here, we employed an integrative modeling and multiscale simulation approach supported by various experimental measurements to understand the differences in conformational dynamics between both mature and immature DENV and its VLPs, to assess epitope exposure and particle stability. Similar tools were also used to guide several site-directed mutations that may guide the improvement of such VLPs, and hence represents a platform for novel vaccine development strategies.

SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact.

The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer's receptor binding domain (RBD) switching from a “down” (closed) to an “up” (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally, we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody's epitope is continuously exposed, explaining its high efficacy.

From closed to open: Omicron mutations increase interdomain interactions and reduce epitope exposure.

Omicron BA.1 is a highly infectious variant of SARS-CoV-2 that carries more than thirty mutations on the spike protein in comparison to the Wuhan wild type (WT). Some of the Omicron mutations, located on the receptor binding domain (RBD), are exposed to the surrounding solvent and are known to help evade immunity. However, the impact of buried mutations on the RBD conformations and on the mechanics of the spike opening is less evident. Here, we use all-atom molecular dynamics (MD) simulations with metadynamics to characterize the thermodynamic RBD-opening ensemble, identifying significant differences between WT and Omicron. Specifically, the Omicron mutations S371L, S373P, and S375F make more RBD interdomain contacts during the spike's opening. Moreover, Omicron takes longer to reach the transition state than WT. It stabilizes up-state conformations with fewer RBD epitopes exposed to the solvent, potentially favoring immune or antibody evasion.

Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike

Omicron BA.1 is a highly infectious variant of SARS-CoV-2 that carries more than thirty mutations on the spike protein in comparison to the Wuhan wild type (WT). Some of the Omicron mutations, located on the receptor-binding domain (RBD), are exposed to the surrounding solvent and are known to help evade immunity. However, the impact of buried mutations on the RBD conformations and on the mechanics of the spike opening is less evident. Here, we use all-atom molecular dynamics (MD) simulations with metadynamics to characterize the thermodynamic RBD-opening ensemble, identifying significant differences between WT and Omicron. Specifically, the Omicron mutations S371L, S373P, and S375F make more RBD interdomain contacts during the spike's opening. Moreover, Omicron takes longer to reach the transition state than WT. It stabilizes up-state conformations with fewer RBD epitopes exposed to the solvent, potentially favoring immune or antibody evasion.

Non-phosphorylatable mutants of Ser184 lead to incomplete activation of Bax.

The S184 residue of Bax is the target of several protein kinases regulating cell fate, including AKT. It is well-established that, in cellulo, the substitution of S184 by a non-phosphorylatable residue stimulates both the mitochondrial localization of Bax, cytochrome c release, and apoptosis. However, in in vitro experiments, substituted mutants did not exhibit any increase in their binding capacity to isolated mitochondria or liposomes. Despite exhibiting a significant increase of the 6A7 epitope exposure, substituted mutants remain limited in their ability to form large oligomers, suggesting that they high capacity to promote apoptosis in cells was more related to a high content than to an increased ability to form large pores in the outer mitochondrial membranes.

Cysteine-Dependent Conformational Heterogeneity of Shigella flexneri Autotransporter IcsA and Implications of Its Function.

Shigella IcsA is a versatile surface virulence factor required for early and late pathogenesis stages extracellularly and intracellularly. Despite IcsA serving as a model Type V secretion system (T5SS) autotransporter to study host-pathogen interactions, its detailed molecular architecture is poorly understood. Recently, IcsA was found to switch to a different conformation for its adhesin activity upon sensing the host stimuli by Shigella Type III secretion system (T3SS). Here, we reported that the single cysteine residue (C130) near the N terminus of the IcsA passenger had a role in IcsA adhesin activity. We also showed that the IcsA passenger (IcsAp) existed in multiple conformations, and the conformation populations were influenced by a central pair of cysteine residues (C375 and C379), which was not previously reported for any Type V autotransporter passengers. Disruption of either or both central cysteine residues altered the exposure of IcsA epitopes to polyclonal anti-IcsA antibodies previously shown to block Shigella adherence, yet without loss of IcsA intracellular functions in actin-based motility (ABM). Anti-IcsA antibody reactivity was restored when the IcsA-paired cysteine substitution mutants were expressed in an ΔipaD background with a constitutively active T3SS, highlighting an interplay between T3SS and T5SS. The work here uncovered a novel molecular switch empowered by a centrally localized, short-spaced cysteine pair in the Type V autotransporter IcsA that ensured conformational heterogeneity to aid IcsA evasion of host immunity. IMPORTANCE Shigella species are the leading cause of diarrheal-related death globally by causing bacillary dysentery. The surface virulence factor IcsA, which is essential for Shigella pathogenesis, is a unique multifunctional autotransporter that is responsible for cell adhesion, and actin-based motility, yet detailed mechanistic understanding is lacking. Here, we showed that the three cysteine residues in IcsA contributed to the protein's distinct functions. The N-terminal cysteine residue within the IcsA passenger domain played a role in adhesin function, while a centrally localized cysteine pair provided conformational heterogeneity that resulted in IcsA molecules with different reactivity to adhesion-blocking anti-IcsA antibodies. In synergy with the Type III secretion system, this molecular switch preserved biological function in distinct IcsA conformations for cell adhesion, actin-based motility, and autophagy escape, providing a potential strategy by which Shigella evades host immunity and targets this essential virulence factor.

Heat-induced changes in epitopes and IgE binding capacity of soybean protein isolate

The effects of heating temperature on epitopes, IgE-binding capacity, and conformation of soybean protein isolate (SPI) were investigated in this study. Indirect ELISA demonstrated that the IgE binding capacity of SPI was increased by 13.1 %−31.6 % after being heated at 60–100 °C for 20 min. SDS-PAGE demonstrated no changes in protein profiles, and native PAGE revealed the formation of aggregates. Structural analyses demonstrated the protein unfolding, appearing temperature-dependent, thus exposing conformational epitopes. Peptide mapping analysis revealed the changes in peptide profiles of major allergens (Gly m 4, Gly m 5, Gly m 6, P28, and Kunitz trypsin inhibitor). LC/MS-MS demonstrated that heating caused the masking or exposure of linear epitopes in Gly m 4 − Gly m 6 and P28. Therefore, heating caused structural changes to expose epitopes to increase IgE binding capacity in SPI. Patients with soybean allergy should avoid the heated SPI until the results of clinical trials are confirmed.

SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact

The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomer’s receptor binding domain (RBD) switching from a "down” (closed) to an "up” (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 μs of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally, we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibody’s epitope is continuously exposed, explaining its high efficacy.

Examination of Abnormal Alpha-synuclein Aggregates in the Enteric Neural Plexus in Patients with Ulcerative Colitis.

Parkinson's disease (PD) is the second most neurodegenerative disease after Alzheimer's disease. Accumulating knowledge points to the notion that abnormal aggregation of alpha-synuclein (αSyn) starts in the gut and ascends to the substantia nigra via the vagus nerve in about a half of PD patients. Epidemiological studies revealed that ulcerative colitis (UC) increases a risk for PD 1.3 to 1.8-folds. However, it remains unknown whether αSyn is abnormally aggregated in the enteric neurons in UC patients. We first inspected and optimized the immunostaining protocols with an anti-phosphorylated αSyn antibody, pSyn#64, using the brain and the gut of eight autopsied cases (five with PD and three without PD). Then, we examined abnormal αSyn aggregation in the enteric neurons in 23 and 18 colectomized patients with and without UC, respectively. Five or more sections were stained for αSyn in each of 87 and 25 paraffin- embedded blocks in patients with and without UC, respectively. Ten different protocols of epitope exposure appropriately stained aggregated αSyn in the brain, but only complete lack of epitope exposure stained aggregated αSyn in the colon with low background. Abnormal αSyn aggregates, which was confirmed by co-localization of p62, in the enteric neurons were detected in a single patient with UC but not in any patients without UC. Omission of epitope exposure enabled us to immunostain aggregated αSyn in the colon by pSyn#64 with low nonspecific staining, but the number of 23 UC patients was not high enough to discern whether abnormal αSyn aggregation in the colonic neural plexus was increased in UC or not.

Gastrointestinal digestion products of shrimp (Penaeus vannamei) proteins retain an allergenic potential

The allergenic potential of shrimp (Penaeus vannamei) proteins during gastrointestinal (GI) digestion is currently unclear. In this study, the role of gastric, intestinal, and GI digestion on the sensitizing and eliciting capacity of shrimp proteins was investigated using a BALB/c mice model. Gastric digestion products of shrimp proteins produced lower specific IgE/IgG1, histamine and mMCP-1 levels and significantly reduced the proportion of degranulated mast cells as compared to the shrimp protein extract; furthermore, no histopathological changes were observed in the lung, spleen and jejunum. Conversely, their GI digestion products caused high specific IgE/IgG1 levels, mast cells degranulation and severe allergic symptoms in the mice, similar to those in the shrimp protein extract group. These results may be due to the masking or exposure of shrimp epitopes during digestion. Consequently, the GI digestion products of shrimp proteins retained an allergenic potential, although gastric digestion products showed a lowering effect.

Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules.

Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).

Inactivated genotype 1a, 2a and 3a HCV vaccine candidates induced broadly neutralising antibodies in mice

ObjectiveA prophylactic vaccine is needed to control the HCV epidemic, with genotypes 1–3 causing >80% of worldwide infections. Vaccine development is hampered by HCV heterogeneity, viral escape including protection of...

Comparing methods for immobilizing HIV-1 SOSIPs in ELISAs that evaluate antibody binding

Enzyme-linked immunosorbent assays (ELISAs) are used to evaluate binding of broadly neutralizing antibodies (bNAbs) and polyclonal sera to native-like HIV-1 Env SOSIPs. Methods for immobilizing SOSIPs on plates differ, which can lead to variable or, in some cases, misleading results. Three methods used to immobilize SOSIPs were compared to determine how antigen immobilization methods affect Env conformation and ELISA results. HIV-1 SOSIPs were directly coated on polystyrene plates, captured by a monoclonal antibody against a C-terminal affinity tag, or randomly biotinylated and coated on a streptavidin plate. Binding of bNAbs with known epitopes were compared for each immobilization method. Binding of bNAbs targeting the V1V2, V3, CD4 binding site, and gp120/gp41 interface was comparable for all antigen immobilization methods. However, directly coated HIV-1 SOSIP ELISAs showed detectable binding of 17b, a CD4-induced antibody that binds a V3 epitope that is concealed on closed prefusion Env trimers in the absence of added CD4, whereas antibody-immobilized and randomly biotinylated Env-coated ELISAs did not show detectable binding of 17b in the absence of CD4. We conclude direct coating of HIV-1 SOSIPs on ELISA plates can result in exposure of CD4-induced antibody epitopes, suggesting disruption of Env structure and exposure of epitopes that are hidden in the closed, prefusion trimer.

Rational Design and Evaluation of the Recombinant Multiepitope Protein for Serodiagnosis of Rubella.

Rubella is an infection caused by rubella virus (RV) and is generally regarded as a mild childhood disease. The disease continues to be of public health importance mainly because when the infection is acquired during early pregnancy, it often results in fetal abnormalities, which are classified as congenital rubella syndrome (CRS). An accurate diagnosis of rubella is thus of pivotal importance for proper treatment. The aim of the study was to produce a recombinant multiepitope protein (rMERUB) for the diagnosis of rubella, based on conserved immunodominant epitopes of glycoprotein E1 and E2. A synthetic gene was designed and cloned into vector pET21a with a 6xHis tag at the Cterminal for affinity purification and overexpressed in Escherichia coli cells. Biophysical analysis of rMERUB was performed by circular dichroism. Biological activity was assessed using an in-house ELISA assay. Expression in Escherichia coli showed a ~22 kDa protein that was purified and used to perform structural assays and an IgG ELISA. Structural analyses reveal that rMERUB has a β leaf pattern that promotes the exposure of epitopes, thus allowing antibody recognition. Evaluation of 33 samples (22=positive; 11=negative) was performed using in-house ELISA and this was compared with a commercial kit. The sensitivity was 100% (95% CI: 85-100) and specificity 90.91% (95% CI: 62-99). Excellent agreement (Kappa index = 0.9) was obtained between ELISA assays. The careful choice of epitopes and the high epitope density, coupled with simple-step purification, pinpoints rMERUB as a promising alternative for rubella diagnosis, with potential for the development of a diagnostic kit.

Gastrointestinal fate of food allergens and its relationship with allergenicity.

Food allergens are closely related to their gastrointestinal digestion fate, but the changes in food allergens during digestion and related mechanisms are quite complicated. This review presents in detail digestion models for predicting allergenicity, the fates of food allergens in oral, gastric and duodenal digestion, and the applications of digestomics in mapping IgE-binding epitopes of digestion-resistant peptides. Moreover, this review highlights the structure-activity relationships of food allergens during gastrointestinal digestion. Digestion-labile allergens may share common structural characteristics, such as high flexibility, rendering them easier to be hydrolyzed into small fragments with decreased or eliminated allergenicity. In contrast, the presence of disulfide bonds, tightly wound α-helical structures, or hydrophobic domains in food allergens helps them resist gastrointestinal digestion, stabilizing IgE-binding epitopes, thus maintaining their sensitization. In rare cases, digestion leads to increased allergenicity due to exposure of new epitopes. Finally, the action of the food matrix and processing on the digestion and allergenicity of food allergens as well as the underlying mechanisms was overviewed. The food matrix can directly act on the allergen by forming complexes or new epitopes to affect its gastrointestinal digestibility and thereby alter its allergenicity or indirectly affect the allergenicity by competing for enzymatic cleavage or influencing gastrointestinal pH and microbial flora. Several processing techniques attenuate the allergenicity of food proteins by altering their conformation to improve susceptibility to degradation by digestive enzymes. Given the complexity of food components, the food itself rather than a single allergen should be used to obtain more accurate data for allergenicity assessment. PRACTICAL APPLICATION: The review article will help to understand the relationship between food protein digestion and allergenicity, and may provide fundamental information for evaluating and reducing the allergenicity of food proteins.

First Data on Ornithodoros moubata Aquaporins: Structural, Phylogenetic and Immunogenic Characterisation as Vaccine Targets.

Ornithodoros moubata transmits African swine fever and human relapsing fever in Africa. The elimination of O. moubata populations from anthropic environments is expected to improve the prevention and control of these diseases. Tick vaccines have emerged as a sustainable method for tick control, and tick aquaporins (AQPs) are promising targets for tick vaccines due to their vital functions, immunogenicity and ease of access by neutralising host antibodies. This study aimed at the systematic identification of the AQPs expressed by O. moubata (OmAQPs) and their characterisation as vaccine targets. Therefore, AQP coding sequences were recovered from available transcriptomic datasets, followed by PCR amplification, cloning, sequence verification and the analysis of the AQP protein structure and epitope exposure. Seven OmAQPs were identified and characterised: six were aquaglyceroporins, and one was a water-specific aquaporin. All of these were expressed in the salivary glands and midgut and only three in the coxal glands. Epitope exposure analysis identified three extracellular domains in each AQP, which concentrate overlapping B and T cell epitopes, making them interesting vaccine targets. Based on these domain sequences, a set of ten antigenic peptides was designed, which showed adequate properties to be produced and tested in pilot vaccine trials.

Regulation of epitope exposure in the gp41 membrane-proximal external region through interactions at the apex of HIV-1 Env.

Glycoprotein Env of human immunodeficiency virus type 1 (HIV-1) mediates viral entry through membrane fusion. Composed of gp120 and gp41 subunits arranged as a trimer-of-heterodimers, Env adopts a metastable, highly dynamic conformation on the virion surface. This structural plasticity limits the temporospatial exposure of many highly conserved, neutralizing epitopes, contributing to the difficulty in developing effective HIV-1 vaccines. Here, we employed antibody neutralization of HIV-1 infectivity to investigate how inter- and intra-gp120 interactions mediated by variable loops V1/V2 and V3 at the Env apex regulate accessibility of the gp41 membrane-proximal external region (MPER) at the Env base. Swapping the V3 loop from EnvSF162 into the EnvHXB2 background shifted MPER exposure from the prefusogenic state to a functional intermediate conformation that was distinct from the prehairpin-intermediate state sensitive to gp41-targeted fusion inhibitors. The V3-loop swap had a profound impact on global protein dynamics, biasing the equilibrium to a closed conformation resistant to most anti-gp120 antibodies, stabilizing the protein to both cold- and soluble CD4-induced Env inactivation, and increasing the CD4 requirements for viral entry. Further dissection of the EnvHXB2 V3 loop revealed that residue 306 uniquely modulated epitope exposure and trimer stability. The R306S substitution substantially decreased sensitivity to antibodies targeting the gp41 MPER and, surprisingly, the gp120 V3-loop crown (residues 312–315), but had only modest effects on exposure of intervening gp120 epitopes. Furthermore, the point mutation reduced soluble CD4-induced inactivation, but had no impact on cold inactivation. The residue appeared to exert its effects by electrostatically modifying the strength of intra-subunit interactions between the V1/V2 and V3 loops. The distinct patterns of neutralization and stability pointed to a novel prefusogenic Env conformation along the receptor activation pathway and suggested that apical Env-regulation of gp41 MPER exposure can be decoupled from much of the dynamics of gp120 subunits.

From the Editor’s Desk...

From the Editor’s Desk...