Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity

Negi, Surendra S.; Braun, Werner

doi:10.1093/bioinformatics/btw767

Cited by 35 publications

(33 citation statements)

References 73 publications

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“…The high sequence homology leads to the formation of similar folds, thus conserving the IgE binding epitopes across species. This causes a significant level of cross-reactivity with other phylogenetically related or unrelated species (29). Der f 25 caused wide cross-reactivity due to its conserved structural features with different species (30).…”

Section: Discussionmentioning

confidence: 99%

Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus

Karmakar

Saha

Jana

et al. 2020

Journal of Biological Chemistry

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Aspergillus terreus is an allergenic fungus in addition to causing infections in both humans and plants. However, the allergens in this fungus are still unknown, limiting the development of diagnostic and therapeutic strategies. We used a proteomic approach to search for allergens, identifying sixteen allergens based on two-dimensional immunoblotting with A. terreus susceptible patient sera. We further characterized triosephosphate isomerase (Asp t 36), one of the dominant immunoglobulin E (IgE)-reactive proteins. The gene was cloned and expressed in E. coli. Phylogenetic analysis showed Asp t 36 to be highly conserved with close similarity to the triosephosphate isomerase protein sequence from Dermatophagoides farinae, an allergenic dust mite. We identified four immuno-dominant epitopes using synthetic peptides, and mapped them on a homology-based model of the tertiary structure of Asp t 36. Among these, two were found to create a continuous surface patch on the 3D structure, rendering it an IgE binding hotspot. Biophysical analysis indicated that Asp t 36 shows similar secondary structure content and temperature sensitivity with other reported triosephosphate isomerase allergens. In vivo studies using a murine model displayed that the recombinant Asp t 36 was able to stimulate airway inflammation, as demonstrated by an influx of eosinophils, goblet cell hyperplasia, elevated serum immunoglobulins and induction of Th2 cytokines. Collectively, our results reveal the immunogenic property of Asp t 36, a major allergen from A. terreus, and define a new fungal allergen more broadly. This allergen could serve as a potent candidate for investigating component resolved diagnosis and immunotherapy.

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Section: Discussionmentioning

confidence: 99%

Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus

Karmakar

Saha

Jana

et al. 2020

Journal of Biological Chemistry

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“…Identification of potential cross-reactive Cor a 2, was predicted by Cross-React server ( ), a tool that uses the epitope location and the three-dimensional structure of protein allergens [ 40 ]. A patch size (A) of 10, an area cutoff (A

) of 10, and the correlation cutoff of 0.10, were applied.…”

Section: Methodsmentioning

confidence: 99%

Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis

et al. 2020

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Heat treatment can modify the allergenic potential, reducing allergenicity in specific proteins. Profilins are one of the important hazelnut allergens; these proteins are considered panallergens due to their high capacity for cross-reactivity with other allergens. In the present work, we evaluated the thermostability of hazelnut profilin, combining molecular dynamics simulation and immunoinformatic techniques. This approach helped us to have reliable results in immunogenicity studies. We modeled Cor a 2 profilin and applied annealing simulation, equilibrium, and production simulation at constant temperatures ranging from 300 to 500 K using Gromacs software. Despite the hazelnut profilins being able to withstand temperatures of up to 400 K, this does not seem to reduce its allergenicity. We have found that profilin subjected to temperatures of 450 and 500 K could generate cross-reactivity with other food allergens. In conclusion, we note a remarkable thermostability of Cor a 2 at 400 K which avoids its structural unfolding.

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“…Data from previous studies have shown that epitopes with a high degree of similarity in amino acid sequences and three-dimensional structures could be recognized by cross-reaction antibodies [36]. Structural bioinformatics analysis showed cross-reactivity between allergenic proteins available with sequence identity >60% [37]. Therefore, only epitopes that showed a similarity of <60% with all other flaviviruses were considered to be specific for ZIKV and used for downstream analysis.…”

Section: Methodsmentioning

confidence: 99%

Identification of relevant regions on structural and nonstructural proteins of Zika virus for vaccine and diagnostic test development: an in silico approach

Salvador

Souza

Malaquias

et al. 2019

New Microbes and New Infections

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Zika virus (ZIKV) is an arbovirus belonging to the Flaviviridae family and the genus Flavivirus. Infection with ZIKV causes a mild, self-limiting febrile illness called Zika fever. However, ZIKV infection has been recently associated with microcephaly and Guillain-Barré syndrome. Vaccines for the disease are a high priority of World Health Organization. Several studies are currently being conducted to develop a vaccine against ZIKV, but until now there is no licensed ZIKV vaccine. This study used a novel immunoinformatics approach to identify potential T-cell immunogenic epitopes present in the structural and nonstructural proteins of ZIKV. Fourteen T-cell candidate epitopes were identified on ZIKV structural and nonstructural proteins: pr 36−50 ; C 61−75 ; C 103−117 ; E 374−382 ; E 477−491 ; NS2a 90−104 ; NS2a 174−188 ; NS2a 179−193 ; NS2a 190−204 ; NS2a 195−209 ; NS2a 200−214 ; NS3 175−189 ; and NS4a 82−96 ; NS4a 99−113 . Among these epitopes, only E 374−382 is a human leukocyte antigen (HLA) type I restricted epitope. All identified epitopes showed a low similarity with other important flaviviruses but had a high conservation rate among the ZIKV strains and a high population coverage rate. Therefore, these predicted T-cell epitopes are potential candidates targets for development of vaccines to prevent ZIKV infection.

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Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity

Abstract: ssnegi@utmb.edu.

Cited by 35 publications

References 73 publications

Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus

Identification and biochemical characterization of Asp t 36, a new fungal allergen from Aspergillus terreus

Heat-Stable Hazelnut Profilin: Molecular Dynamics Simulations and Immunoinformatics Analysis

Identification of relevant regions on structural and nonstructural proteins of Zika virus for vaccine and diagnostic test development: an in silico approach

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