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Although multiple vaccines have been developed and widely administered, several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been reported to evade immune responses and spread diffusely. Here, 108 RNA-seq files from coronavirus disease 2019 (COVID-19) patients and healthy donors (HD) were downloaded to extract their TCR immune repertoire by MiXCR. Those extracted TCR repertoire were compared and it was found that disease progression was related negatively with diversity and positively with clonality. Specifically, greater proportions of high-abundance clonotypes were observed in active and severe COVID-19 samples, probably resulting from strong stimulation of SARS-CoV-2 epitopes and a continued immune response in host. To investigate the specific recognition between TCR CDR3 and SARS-CoV-2 epitopes, we constructed an accurate classifier CoV2-TCR with an AUC of 0.967 in an independent dataset, which outperformed several similar tools. Based on this model, we observed a huge range in the number of those TCR CDR3 recognizing those different peptides, including 28 MHC-I epitopes from SARS-CoV-2 and 22 immunogenic peptides from SARS-CoV-2 variants. Interestingly, their proportions of high-abundance, low-abundance and rare clonotypes were close for each peptide. To expand the potential application of this model, we established the webserver, CoV2-TCR, in which users can obtain those recognizing CDR3 sequences from the TCR repertoire of COVID-19 patients based on the 9-mer peptides containing mutation site(s) on the four main proteins of SARS-CoV-2 variants. Overall, this study provides preliminary screening for candidate antigen epitopes and the TCR CDR3 that recognizes them, and should be helpful for vaccine design on SARS-CoV-2 variants.

There is increasing interest in gluten-degrading enzymes for use during food and drink processing. The industrially available enzymes usually work best at low to ambient temperatures. However, food manufacturing is often conducted at higher temperatures. Therefore, thermostable gluten-degrading enzymes are of great interest. We have identified a new thermostable gluten-degrading proline-specific prolyl endoprotease from the archaea Thermococcus kodakarensis. We then cloned and expressed it in Escherichia coli. The prolyl endoprotease was found to have a size of 70.1 kDa. The synthetic dipeptide Z-Gly-Pro- p -nitroanilide was used to characterize the prolyl endoprotease and it had maximum activity at pH 7 and 77°C. The V max, K m and k cat values of the purified prolyl endoprotease were calculated to be 3.14 mM/s, 1.10 mM and 54 s−1, respectively. When the immunogenic gluten peptides PQPQLPYPQPQLPY (α-gliadin) and SQQQFPQPQQPFPQQP (γ-hordein) were used as substrates, the prolyl endoprotease was able to degrade these. Furthermore, gluten in wort was reduced when the prolyl endoprotease was used during mashing of barley malt. The discoveries open up new food processing possibilities and further the understanding of proline-specific protease diversity. [ABSTRACT FROM AUTHOR]

[Display omitted] • Glycation only occurred in the dry-heated soy protein sample. • Wet heating increased in vitro infant digestion, while dry heating decreased it. • 29 T-cell epitopes and 27 B-cell epitopes were predicted in the digests. • Cross-reactive epitopes were predicted between soy and other legume proteins. • Heating and digestion time may modulate peptide-induced immune responses. During production of soy-based infant formula, soy protein undergoes heating processes. This study investigated the differential impact of heating modes on the immunogenic potential of peptides in soy protein digests. Wet or dry heating was applied, followed by in vitro gastrointestinal infant digestion. The released peptides were analyzed by LC-MS/MS. Bioinformatics tools were utilized to predict and identify potential linear B-cell and T-cell epitopes, as well as to explore cross-reactivity with other legumes. Subsequently, the peptide intensities of the same potential epitope across different experimental conditions were compared. As a result, we confirmed the previously observed enhancing effect of wet heating on infant digestion and inhibitory effect of dry heating. A total of 8,546 peptides were detected in the digests, and 6,684 peptides were with a score over 80. Among them, 29 potential T-cell epitopes and 27 potential B-cell epitopes were predicted. Cross-reactivity between soy and other legumes, including peanut, pea, chickpea, lentil, kidney bean, and lupine, was also detected. Overall, heating and digestion time could modulate the potential to trigger peptide-induced immune responses. [ABSTRACT FROM AUTHOR]

• Five immunogenic T-cell peptides of PE_PGRS33 were identified by bioinformatics. • Immunogenic T-cell peptides of PE_PGRS33 cross-react with HLA class II molecules. • Immunogenic T-cell peptides of PE_PGRS33 show a global population coverage >50 %. • Immunogenic peptides induced IFN-γ by PBMC from household contacts of TB patients. The development of a more efficient vaccine is needed to improve tuberculosis control. One of the current approaches is to identify immunogenic T-cell peptides that can elicit a protective and specific immune response. These peptides come from immunogenic proteins of the pathogen. The PE_PGRS33 protein of Mycobacterium tuberculosis has been proved immunogenic. However, little is known about immunogenic T-cell peptides of PE_PGRS33 and their interactions with MHC-II molecules. Therefore, we used the SYFPHEITHI database to determine the immunogenic PE_PGRS33 T-cell peptides. Next, we built homology models by using MOE v2018.1 software in order to obtain information about the specific interactions between the peptides and I-Ak. The AlgPred server was employed to look for allergenic sites in PE_PGRS33. We developed a sequence alignment between PE_PGRS33 and all the human proteins by using BLAST. Three peptides were commercially synthesized, and their activity was evaluated in vitro by the stimulation of PBMC from household contacts of TB patients. Our in silico results showed five immunogenic T-cell peptides. BLAST analysis showed low homology of PE_PGRS33 with human proteins and AlgPred did not reveal allergenic sites in PE_PGRS33. The three peptides triggered the activation of CD4+ T cells from the households contacts, showed by the production of IFN-γ. We identified three immunogenic peptides of PE_PGRS33 that demonstrated activity in vitro which allows to deepen into the immune response towards mycobacterial antigens, moving forward to the identification of new vaccine candidates. [ABSTRACT FROM AUTHOR]

Celiac disease (CeD) is an autoimmune enteropathy triggered by immunogenic gluten peptides released during the gastrointestinal digestion of wheat. Our aim was to identify T cell epitope-containing peptides after ex vivo digestion of ancestral (einkorn, spelt and emmer) and common (hexaploid) wheat (Fram, Bastian, Børsum and Mirakel) using human gastrointestinal juices. Wheat porridge was digested using a static ex vivo model. Peptides released after 240 min of digestion were analyzed by liquid chromatography coupled to high-resolution mass spectrometry (HPLC-ESI MS/MS). Ex vivo digestion released fewer T cell epitope-containing peptides from the ancestral wheat varieties (einkorn (n = 38), spelt (n = 45) and emmer (n = 68)) compared to the common wheat varieties (Fram (n = 72), Børsum (n = 99), Bastian (n = 155) and Mirakel (n = 144)). Neither the immunodominant 33mer and 25mer α-gliadin peptides, nor the 26mer γ-gliadin peptide, were found in any of the digested wheat types. In conclusion, human digestive juice was able to digest the 33mer and 25mer α-gliadin, and the 26mer γ-gliadin derived peptides, while their fragments still contained naive T cell reactive epitopes. Although ancestral wheat released fewer immunogenic peptides after human digestion ex vivo, they are still highly toxic to celiac patients. More general use of these ancient wheat variants may, nevertheless, reduce CeD incidence.

Graphical abstract Highlights • The structure of the proenzyme form of Sm32 was determined by means of homology modeling and MD refinement. • The charge distribution in the core and LSAM domains in Sm32 is different when compared to the AEs of mouse and human. • The His151 of the catalytic dyad shows a hydrogen bond with Asp150 and a cation pi interaction with Arg52. • In the active site, amino acid differences were identified in the β IV strand. • IMT-26, a highly immunogenic fragment of the activation peptide, is considered for the development of diagnostic methods. Abstract Asparaginyl endopeptidase (AE) of Schistosoma mansoni (Sm32), also known as legumain, is a cysteine protease indirectly involved in the digestion of hemoglobin of Schistosoma sp. in the gastrodermis, being a vaccine candidate against this trematode and a potential drug target. This study presents a model for the three-dimensional structure of Sm32 determined by means of homology modeling and a molecular dynamics simulation with explicit solvent refinement. The structure proved to be consistent with other AEs of known crystal structures described in their proenzyme form, revealing a catalytic domain that has a caspase-like overall structure and a C -terminal prodomain that adopts a death-domain-like architecture. We identified amino acid mutations in the βIV strand, differences in the active site and in the surface electrostatic potentials between Sm32 and its homologous proteins of mouse and human. Additionally, amino acid changes in the activation peptide (AP) of the S. mansoni protein were determined. Our results strongly suggest that Sm32 can be exploited as a potential target for drug design and for the development of biomarkers used in diagnosis and in novel vaccines for the control of parasitic infection, opening the perspective of medicinal chemistry developments. [ABSTRACT FROM AUTHOR]

Abstract: The CBD1 peptide (SLEQIWNNMTWMQWDK), corresponding to the consensus caveolin-1 binding domain in HIV-1 envelope glycoprotein gp41 (CBD1), elicits the production of antibodies that inhibit infection of primary CD4+ T lymphocytes by various primary HIV-1 isolates. Here we show that HIV-neutralizing antibodies against CBD1 react with multiple conformational epitopes that overlap the highly conserved caveolin-1 binding motif (CBM) with the N-terminal conserved isoleucine residue. The CBM-based peptides IWNNMTWMQW and IWNNMTW when fused to a T helper epitope are immunogenic by inducing high titer CBM-specific antibodies capable of neutralizing HIV-1 infection in primary T lymphocyte cultures. Interestingly, neutralizing immune sera raised against a given peptide do not cross-react with related CBM-derived peptides, thus suggesting the existence of distinct neutralizing epitopes that probably reflect the dynamic conformational features of CBD1. In accord with this, the mixture of neutralizing immune sera raised against several CBM-derived peptides exerts a synergistic neutralizing activity against HIV-1 infection. Finally, the existence of several distinct overlapping epitopes in CBD1 is confirmed by murine monoclonal antibodies that we generated against the CBM-derived chimeric peptides. Our results indicate that CBD1- and CBM-based peptides mimic distinct dynamic conformations of CBD1, and thus such peptides could provide specific immunogens for an efficient vaccine preparation against HIV/AIDS infection. [Copyright &y& Elsevier]

Abstract: The potential caveolin-1 binding domain (CBD), referred to as CBD1 and CBD2, is highly conserved in the transmembrane envelope glycoprotein of various HIV-1 and HIV-2 isolates, respectively. However, HIV-1 neutralizing antibodies raised against the synthetic CBD1 peptide (SLEQIWNNMTWMQWDK) do not cross-react with the CBD2 peptide (SLTPDWNNMTWQEWER) and have no effect on HIV-2 infection. Here we show that the CBD2 peptide is not immunogenic under similar immunization conditions as the CBD1 peptide. Moreover, the CBD1 but not the CBD2 peptide has the capacity to bind caveolin-1 in crude cell extracts thus suggesting the existence of structural and/or conformational differences between CBD1 and CBD2. Accordingly, circular dichroism spectroscopy and fluorimetry analysis indicated that CBD1 but not CBD2 could adopt a defined secondary structure and form a complex with a peptide corresponding to the caveolin-1 scaffolding domain, which is the site of interaction of caveolin-1 with various proteins. In line with these observations, CBD1 but not CBD2 binds cells and forms large aggregates at the plasma membrane by colocalizing with cytofacial caveolin-1. This latter is dependent on the lipid raft integrity of the plasma membrane. Supporting that the ability to penetrate into plasma membranes is sustained by folding at the interface, CBD1 but not CBD2 has the capacity to insert into lipid monolayers, penetrate into artificial membranes and adopt a β-sheet conformation in presence of lipid vesicles. These structural determinants and membrane partitioning properties could account for the immunogenicity of the CBD1 peptide in various animals. [Copyright &y& Elsevier]

• Bread was prepared using fast fermentation and mechanical dough development (MDD). • Dough was developed using MDD at different speeds and degrees of optimal work input. • The degree of work input and MDD speed altered gluten's structure within bread. • Breads were digested in vitro and immunogenicity probed (mass spectrometry, ELISA). • MDD did not alter the in vitro peptide release profile or antigenicity of gluten. Modern high-speed mechanical dough development (MDD) alters the gluten macropolymer's (GMP) structure. Changes to both the protein and food matrix structure can influence protein digestibility and immunogenicity. This study investigated the relationship between protein structural changes imparted by MDD and gluten's digestibility plus celiac reactivity. Dough was prepared at three mixing speeds (63 rpm, 120 rpm and 200 rpm) to different degrees of development (between 10 and 180% wh.kg−1). Protein structural changes were characterised by confocal microscopy, free thiol determination and protein extractability assays. MDD altered the structure of gluten within bread, changing the protein's surface area and macrostructure. Breads were digested using the INFOGEST in vitro protocol. Gluten's antigenicity and digestibility were monitored using ELISA and mass spectrometry, by monitoring the concentration of six immunogenic peptides causative of celiac disease. The structural changes imparted by mixing did not affect bread's digestibility or celiac reactivity. [ABSTRACT FROM AUTHOR]

Celiac disease is activated by digestion-resistant gluten peptides that contain immunogenic epitopes. Sourdough fermentation is a potential strategy to reduce the concentration of these peptides within food. However, we currently know little about the effect of partial sourdough fermentation on immunogenic gluten. This study examined the effect of a single sourdough culture (representative of those that the public may consume) on the digestion of immunogenic gluten peptides. Sourdough bread was digested via the INFOGEST protocol. Throughout digestion, quantitative and discovery mass spectrometry were used to model the kinetic release profile of key immunogenic peptides and profile novel peptides, while ELISA probed the gluten's allergenicity. Macrostructural studies were also undertaken. Sourdough fermentation altered the protein structure, in vitro digestibility, and immunogenic peptide release profile. Interestingly, sourdough fermentation did not decrease the total immunogenic peptide concentration but altered the in vitro digestion profile of select immunogenic peptides. This work demonstrates that partial sourdough fermentation can alter immunogenic gluten digestion, and is the first study to examine the in vitro kinetic profile of immunogenic gluten peptides from sourdough bread. [ABSTRACT FROM AUTHOR]

• Microbial transglutaminase changes gluten protein macrostructure in dough. • The ω-gliadin protein extractability is reduced by microbial transglutaminase. • Microbial transglutaminase does not deamidate immunogenic gluten in dough. • In vitro gluten digestibility is not altered by microbial transglutaminase. Microbial transglutaminase (mTG) catalyses the formation of protein crosslinks, deamidating glutamine in a side-reaction. Gluten deamidation by human tissue transglutaminase is critical to activate celiac disease pathogenesis making the addition of mTG to wheat-based products controversial. The ability of mTG (0–2000 U.kg−1) to alter gluten's structure, digestibility and the deamidation state of six immunogenic gluten peptides within bread was investigated. Gluten's structure was altered when mTG exceeded 100 U.kg−1, determined by confocal microscopy, extractability and free sulfhydryl assays. The effect of mTG on six immunogenic peptides was investigated by in vitro digestion (INFOGEST) and mass spectrometry. The addition of mTG to bread (0–2000 U.kg−1) did not alter the deamidation state or digestibility of the immunogenic peptides investigated. Overall, this investigation indicated that the addition of mTG to bread does not create activated gluten peptides. This analysis provides evidence for risk assessments of mTG as a food processing aid. [ABSTRACT FROM AUTHOR]

Previous studies have shown that baking alters the digestibility of gluten. This study compared the structure and in vitro digestibility of gluten within dough and bread, baked at either 230 °C or 150 °C for 25, 35 or 45 min. Protein digestion was investigated using mass spectrometry, specifically by calculating the accurate concentration and defining the release profile of six immunogenic gluten peptides that are involved in celiac disease activation. The release profile of these peptides in the intestinal phase differed between dough and bread; multiple peptides, including the immunodominant 33mer, were present at higher concentrations earlier in dough digesta suggesting raw gluten may exhibit and higher-gluten load and different immunogenicity profile. • Gluten protein structure and digestibility were examined within a bread system. • Mass spectrometry was used to track the release of immunogenic celiac peptides. • Baking temperature and time increased the degree of gluten polymer aggregation. • The baking temperature and time did not alter the peptide release profile. • Peptide release differed between dough and bread suggesting altered immunogenicity. Previous work has shown that baking induces structural changes within the gluten macropolymer (GMP) that reduce gluten protein digestibility. The precise nature of these structural changes within dough/bread, and how they alter the in vitro release profile of immunogenic gluten peptides that activate celiac disease is unknown. This work examined the effect of dough baking temperature and duration on the GMP's structure and the release profile of immunogenic gluten peptides. Dough was baked at either 150 °C or 230 °C for 25, 35 or 45 min. The structure of the GMP within the resulting loaves was defined and compared using confocal microscopy, quantitative protein network analysis, gliadin protein extractability (HPLC) and determination of the free thiol content. Both bread and dough were digested in vitro (INFOGEST) and the release profile of six immunogenic gluten peptides (including the immunodominant 33mer) defined using quantitative mass spectrometry. Higher baking temperatures and longer durations increased the degree of intermolecular disulfide bonds between the sulfur-rich gliadins and GMP backbone. The thermal load did not alter the GMP macrostructure, but significant differences between bread and dough were observed. Baking altered the concentration and release profile of the immunogenic gluten peptides throughout in vitro digestion causing the digestion of immunogenic gluten peptides differed between raw and heat-treated bread. [ABSTRACT FROM AUTHOR]

Celiac disease (CeD) is an autoimmune enteropathy triggered by immunogenic gluten peptides released during the gastrointestinal digestion of wheat. Our aim was to identify T cell epitope-containing peptides after ex vivo digestion of ancestral (einkorn, spelt and emmer) and common (hexaploid) wheat (Fram, Bastian, Børsum and Mirakel) using human gastrointestinal juices. Wheat porridge was digested using a static ex vivo model. Peptides released after 240 min of digestion were analyzed by liquid chromatography coupled to high-resolution mass spectrometry (HPLC-ESI MS/MS). Ex vivo digestion released fewer T cell epitope-containing peptides from the ancestral wheat varieties (einkorn (n = 38), spelt (n = 45) and emmer (n = 68)) compared to the common wheat varieties (Fram (n = 72), Børsum (n = 99), Bastian (n = 155) and Mirakel (n = 144)). Neither the immunodominant 33mer and 25mer α-gliadin peptides, nor the 26mer γ-gliadin peptide, were found in any of the digested wheat types. In conclusion, human digestive juice was able to digest the 33mer and 25mer α-gliadin, and the 26mer γ-gliadin derived peptides, while their fragments still contained naive T cell reactive epitopes. Although ancestral wheat released fewer immunogenic peptides after human digestion ex vivo, they are still highly toxic to celiac patients. More general use of these ancient wheat variants may, nevertheless, reduce CeD incidence. [ABSTRACT FROM AUTHOR]