A comprehensive immunoinformatics study to explore and characterize potential vaccine constructs against Ole e 9 allergen of Olea europaea

References

• Al Qaraghuli, M. M., Kubiak-Ossowska, K., Ferro, V. A., & Mulheran, P. A. (2020). Antibody-protein binding and conformational changes: Identifying allosteric signalling pathways to engineer a better effector response. Scientific Reports, 10(1), 13696. https://doi.org/10.1038/s41598-020-70680-0
   PubMed Web of Science ®Google Scholar
• Alsulimani, A., Bhardwaj, T., Janahi, E. M., Almalki, A. H., Tewari, B. N., Wahid, M., Mustfa, F., Somvanshi, P., & Haque, S. (2022). Systematic structure guided clustering of chemical lead compounds targeting RdRp of SARS-CoV-2. Minerva Biotechnology and Biomolecular Research, 34, 114–121.
   Google Scholar
• Ansotegui, I. J., Melioli, G., Canonica, G. W., Caraballo, L., Villa, E., Ebisawa, M., Passalacqua, G., Savi, E., Ebo, D., Gómez, R. M., Luengo Sánchez, O., Oppenheimer, J. J., Jensen-Jarolim, E., Fischer, D. A., Haahtela, T., Antila, M., Bousquet, J. J., Cardona, V., Chiang, W. C., Demoly, P. M., DuBuske, L. M., & Zuberbier, T. (2020 February 25). IgE allergy diagnostics and other relevant tests in allergy, a World Allergy Organization position paper. The World Allergy Organization Journal, 13(2), 100080. Erratum in: World Allergy Organ J. 2021 Jun 17;14(7):100557. PMID: 32128023; PMCID: PMC7044795. https://doi.org/10.1016/j.waojou.2019.100080
   PubMed Web of Science ®Google Scholar
• Balmeh, N., Mahmoudi, S., Pourhoseyni, H., & Allahyari Fard, N. (2022). An in-silico approach of allergenicity reduction in PR10 and profilin families of pan allergens using allergen-IgE docking analysis. Revue Française D'Allergologie, 62(6), 521–528. https://doi.org/10.1016/j.reval.2022.01.019
   Google Scholar
• Bartolini, G., & Petruccelli, R. (2002). Classification, origin, diffusion and history of the olive. Food and Agriculture Organization of the United Nations.
   Google Scholar
• Bastiaan-Net, S., Pina-Pérez, M. C., Dekkers, B. J. W., Westphal, A. H., America, A. H. P., Ariëns, R. M. C., de Jong, N. W., Wichers, H. J., & Mes, J. J. (2020). Identification and in silico bioinformatics analysis of PR10 proteins in cashew nut. Protein Science, 29(7), 1581–1595. https://doi.org/10.1002/pro.3856
   PubMed Web of Science ®Google Scholar
• Bhardwaj, T., Ahmad, I., & Somvanshi, P. (2023). Systematic analysis to identify novel disease indications and plausible potential chemical leads of glutamate ionotropic receptor NMDA type subunit 1, GRIN1. Journal of Molecular Recognition, 36(1), e2997.
   PubMed Web of Science ®Google Scholar
• Bhardwaj, T., Haque, S., & Somvanshi, P. (2019). Comparative assessment of the therapeutic drug targets of C. botulinum ATCC 3502 and C. difficile str. 630 using in silico subtractive proteomics approach. Journal of Cellular Biochemistry, 120(9), 16160–16184. https://doi.org/10.1002/jcb.28897
   PubMed Web of Science ®Google Scholar
• Bokka, C. S., Veeramachaneni, G. K., Thunuguntla, V. B. S. C., Bobbillapati, J., & Bondili, J. S. (2019 May 21). Peptide mapping, in silico and in vivo analysis of allergenic sorghum profilin peptides. Medicina (Kaunas), 55(5), 178. https://doi.org/10.3390/medicina55050178
   PubMed Web of Science ®Google Scholar
• Brito, F. F., Gimeno, P. M., Carnés, J., Martín, R., Fernández-Caldas, E., Lara, P., López-Fidalgo, J., & Guerra, F. (2011). Olea europaea pollen counts and aeroallergen levels predict clinical symptoms in patients allergic to olive pollen. Annals of Allergy, Asthma & Immunology, 106(2), 146–152. https://doi.org/10.1016/j.anai.2010.11.003
   PubMed Web of Science ®Google Scholar
• Budin, N., Majeux, N., & Caflisch, A. (2001). Fragment-based flexible ligand docking by evolutionary optimization. Biological Chemistry, 382(9), 1365–1372. https://doi.org/10.1515/BC.2001.168
   PubMed Web of Science ®Google Scholar
• Calzada, D., Cremades-Jimeno, L., López-Ramos, M., & Cárdaba, B. (2021). Peptide allergen immunotherapy: A new perspective in olive-pollen allergy. Pharmaceutics, 13(7), 1007. https://doi.org/10.3390/pharmaceutics13071007
   PubMed Web of Science ®Google Scholar
• de Dios Alché, J., M'rani-Alaoui, M., Castro, A. J., & Rodríguez-García, M. I. (2004). Ole e 1, the major allergen from olive (Olea europaea L.) pollen, increases its expression and is released to the culture medium during in vitro germination. Plant & Cell Physiology, 45(9), 1149–1157. https://doi.org/10.1093/pcp/pch127
   PubMed Web of Science ®Google Scholar
• Dondelinger, M., Filée, P., Sauvage, E., Quinting, B., Muyldermans, S., Galleni, M., & Vandevenne, M. S. (2018). Understanding the significance and implications of antibody numbering and antigen-binding surface/residue definition. Frontiers in Immunology, 9, 2278. https://doi.org/10.3389/fimmu.2018.02278
   PubMed Web of Science ®Google Scholar
• Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797. https://doi.org/10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Fernández-González, M., González-Fernández, E., Fernández-González, D., & Rodríguez-Rajo, F. J. (2020). Secondary outcomes of the Ole e 1 proteins involved in pollen tube development: Impact on allergies. Frontiers in Plant Science, 11(974), 974. https://doi.org/10.3389/fpls.2020.00974
   PubMedGoogle Scholar
• Florido Lopez, J. F., Quiralte Enriquez, J., Arias de Saavedra Alías, J. M., Saenz de San Pedro, B., & Martin Casañez, E. (2002). An allergen from Olea europaea pollen (Ole e 7) is associated with plant-derived food anaphylaxis. Allergy, 57(Suppl 71), 53–59. https://doi.org/10.1034/j.1398-9995.2002.057s71053.x
   PubMedGoogle Scholar
• Galli, S. J., & Tsai, M. (2012). IgE and mast cells in allergic disease. Nature Medicine, 18(5), 693–704. https://doi.org/10.1038/nm.2755
   PubMed Web of Science ®Google Scholar
• Galli, S. J., Tsai, M., & Piliponsky, A. M. (2008). The development of allergic inflammation. Nature, 454(7203), 445–454. https://doi.org/10.1038/nature07204
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In JM Walker (Ed.), The proteomics protocols handbook (pp. 571–607). Humana Press.
   Google Scholar
• Geourjon, C., & Deléage, G. (1995). SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Computer Applications in the Biosciences : CABIOS, 11(6), 681–684. https://doi.org/10.1093/bioinformatics/11.6.681
   PubMedGoogle Scholar
• Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor-Shental, D., Martz, E., & Ben-Tal, N. (2003). ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (Oxford, England), 19(1), 163–164. https://doi.org/10.1093/bioinformatics/19.1.163
   PubMed Web of Science ®Google Scholar
• Hashmi, M. A., Khan, A., Hanif, M., Farooq, U., & Perveen, S. (2015). Traditional uses, phytochemistry, and pharmacology of Olea europaea (olive). Evidence-Based Complementary and Alternative Medicine : ECAM, 2015, 541591. https://doi.org/10.1155/2015/541591
   PubMed Web of Science ®Google Scholar
• Hauser, M., Roulias, A., Ferreira, F., & Egger, M. (2010). Panallergens and their impact on the allergic patient. Allergy, Asthma & Clinical Immunology, 6(1), 1.
   PubMedGoogle Scholar
• Hetényi, C., & van der Spoel, D. (2002). Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Science, 11(7), 1729–1737. https://doi.org/10.1110/ps.0202302
   PubMed Web of Science ®Google Scholar
• Hirokawa, T., Boon-Chieng, S., & Mitaku, S. (1998). SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics (Oxford, England), 14(4), 378–379. https://doi.org/10.1093/bioinformatics/14.4.378
   PubMed Web of Science ®Google Scholar
• Huecas, S., Villalba, M., & Rodríguez, R. (2001). Ole e 9, a major olive pollen allergen is a 1,3-beta-glucanase. Isolation, characterization, amino acid sequence, and tissue specificity. The Journal of Biological Chemistry, 276(30), 27959–27966. https://doi.org/10.1074/jbc.M103041200
   PubMed Web of Science ®Google Scholar
• Jamakhani, M., Lele, S. S., & Rekadwad, B. (2018). In silico assessment data of allergenicity and cross-reactivity of NP24 epitopes from Solanum lycopersicum (Tomato) fruit. Data in Brief, 21, 660–674. https://doi.org/10.1016/j.dib.2018.09.074
   PubMed Web of Science ®Google Scholar
• Kausar, M. A., Bhardwaj, T., Anwar, S., Alenazi, F., Ali, A., Alshammari, K. F., AboElnaga, S. M. H., Singh, R., & Najm, M. Z. (2022). In silico comparative exploration of allergens of Periplaneta americana, Blattella germanica and Phoenix dactylifera for the diagnosis of patients suffering from IgE-mediated allergic respiratory diseases. Molecules, 27(24), 8740. https://doi.org/10.3390/molecules27248740
   PubMed Web of Science ®Google Scholar
• Kausar, M. A., Rabie, A. M., Azam, F., Anwar, S., Alenazi, F., Alshammari, K. F., Kar, S., Ali, A., AboElnaga, S. M. H., Jamal, A., Singh, G., Thakur, L., Najm, M. Z., & Saeed, M. (2023). The role of Aedes aegypti in inducing/aggravating IgE-mediated allergic airway disease: extensive computational studies for identification of allergenic proteins. Journal of Biomolecular Structure and Dynamics, 16, 1–8. https://doi.org/10.1080/07391102.2023.2212305
   Google Scholar
• Khan, S., Bhardwaj, T., Somvanshi, P., Mandal, R. K., Dar, S. A., Jawed, A., Wahid, M., Akhter, N., Lohani, M., Alouffi, S., & Haque, S. (2018). Inhibition of C298S mutant of human aldose reductase for antidiabetic applications: Evidence from in silico elementary mode analysis of biological network model. Journal of Cellular Biochemistry, 119(8), 6961–6973. https://doi.org/10.1002/jcb.26904
   PubMed Web of Science ®Google Scholar
• Khan, S., Somvanshi, P., Bhardwaj, T., Mandal, R. K., Dar, S. A., Wahid, M., Jawed, A., Lohani, M., Khan, M., Areeshi, M. Y., & Haque, S. (2018). Aspartate-β-semialdeyhyde dehydrogenase as a potential therapeutic target of Mycobacterium tuberculosis H37Rv: Evidence from in silico elementary mode analysis of biological network model. Journal of Cellular Biochemistry, 119(3), 2832–2842. https://doi.org/10.1002/jcb.26458
   PubMed Web of Science ®Google Scholar
• Kushwaha, P., Singh, V., Somvanshi, P., Bhardwaj, T., Barreto, G. E., Ashraf, G. M., Mishra, B. N., Chundawat, R. S., & Haque, S. (2021). Identification of new BACE1 inhibitors for treating Alzheimer’s disease. Journal of Molecular Modeling, 27(2), 58. https://doi.org/10.1007/s00894-021-04679-3
   PubMed Web of Science ®Google Scholar
• Kwok, S. C., Mant, C. T., & Hodges, R. S. (2002). Importance of secondary structural specificity determinants in protein folding: Insertion of a native beta-sheet sequence into an alpha-helical coiled-coil. Protein Science, 11(6), 1519–1531. https://doi.org/10.1110/ps.4170102
   PubMed Web of Science ®Google Scholar
• Li, L., Chen, S., Miao, Z., Liu, Y., Liu, X., Xiao, Z. X., & Cao, Y. (2019). AbRSA: A robust tool for antibody numbering. Protein Science, 28(8), 1524–1531. https://doi.org/10.1002/pro.3633
   PubMed Web of Science ®Google Scholar
• Lu, H., Zhou, Q., He, J., Jiang, Z., Peng, C., Tong, R., & Shi, J. (2020). Recent advances in the development of protein-protein interactions modulators: Mechanisms and clinical trials. Signal Transduction and Targeted Therapy, 5(1), 213.
   PubMed Web of Science ®Google Scholar
• Maurer-Stroh, S., Krutz, N. L., Kern, P. S., Gunalan, V., Nguyen, M. N., Limviphuvadh, V., Eisenhaber, F., & Gerberick, G. F. (2019). AllerCatPro-prediction of protein allergenicity potential from the protein sequence. Bioinformatics (Oxford, England), 35(17), 3020–3027. https://doi.org/10.1093/bioinformatics/btz029
   PubMed Web of Science ®Google Scholar
• Mohamad Sobri, M. F., Abd-Aziz, S., Abu Bakar, F. D., & Ramli, N. (2020). In-silico characterization of glycosyl hydrolase family 1 β-glucosidase from Trichoderma asperellum UPM1. International Journal of Molecular Sciences, 21(11), 4035. https://doi.org/10.3390/ijms21114035
   PubMed Web of Science ®Google Scholar
• Popescu, F. D. (2015). Cross-reactivity between aeroallergens and food allergens. World Journal of Methodology, 5(2), 31–50. https://doi.org/10.5662/wjm.v5.i2.31
   PubMedGoogle Scholar
• Ramaraj, T., Angel, T., Dratz, E. A., Jesaitis, A. J., & Mumey, B. (2012). Antigen-antibody interface properties: Composition, residue interactions, and features of 53 non-redundant structures. Biochimica et Biophysica Acta, 1824(3), 520–532. https://doi.org/10.1016/j.bbapap.2011.12.007
   PubMed Web of Science ®Google Scholar
• Ravachol, J., Borne, R., Tardif, C., de Philip, P., & Fierobe, H. P. (2014). Characterization of all family-9 glycoside hydrolases synthesized by the cellulosome-producing bacterium Clostridium cellulolyticum. The Journal of Biological Chemistry, 289(11), 7335–7348. https://doi.org/10.1074/jbc.M113.545046
   PubMed Web of Science ®Google Scholar
• Reis, P. B. P. S., Barletta, G. P., Gagliardi, L., Fortuna, S., Soler, M. A., & Rocchia, W. (2022). Antibody-antigen binding interface analysis in the big data era. Frontiers in Molecular Biosciences, 9, 945808. https://doi.org/10.3389/fmolb.2022.945808
   PubMed Web of Science ®Google Scholar
• Reno, A. L., Brooks, E. G., & Ameredes, B. T. (2015). Mechanisms of heightened airway sensitivity and responses to inhaled SO2 in asthmatics. Environ Health Insights, 9(Suppl 1), 13–25.
   PubMedGoogle Scholar
• Rigsby, R. E., & Parker, A. B. (2016). Using the PyMOL application to reinforce visual understanding of protein structure. Biochemistry and Molecular Biology Education, 44(5), 433–437. https://doi.org/10.1002/bmb.20966
   PubMed Web of Science ®Google Scholar
• Saetang, J., Tipmanee, V., & Benjakul, S. (2022 April 21). In silico prediction of cross-reactive epitopes of tropomyosin from shrimp and other arthropods involved in allergy. Molecules, 27(9), 2667. https://doi.org/10.3390/molecules27092667
   PubMed Web of Science ®Google Scholar
• Saha, S., & Raghava, G. P. (2006). AlgPred: Prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Research, 34(Web Server issue), W202–W209. https://doi.org/10.1093/nar/gkl343
   PubMed Web of Science ®Google Scholar
• Saponaro, A., Maione, V., Bonvin, A. M. J. J., & Cantini, F. (2020). Understanding docking complexes of macromolecules using HADDOCK: The synergy between experimental data and computations. Bio-Protocol, 10(20), e3793.
   PubMed Web of Science ®Google Scholar
• Satyam, R., Bhardwaj, T., Jha, N. K., Jha, S. K., & Nand, P. (2020). Toward a chimeric vaccine against multiple isolates of Mycobacteroides – An integrative approach. Life Sciences, 250, 117541. https://doi.org/10.1016/j.lfs.2020.117541
   PubMed Web of Science ®Google Scholar
• Satyam, R., Janahi, E. M., Bhardwaj, T., Somvanshi, P., Haque, S., & Najm, M. Z. (2018). In silico identification of immunodominant B-cell and T-cell epitopes of non-structural proteins of Usutu Virus. Microbial Pathogenesis, 125, 129–143. https://doi.org/10.1016/j.micpath.2018.09.019
   PubMed Web of Science ®Google Scholar
• Skoner, D. P. (2001). Allergic rhinitis: Definition, epidemiology, pathophysiology, detection, and diagnosis. The Journal of Allergy and Clinical Immunology, 108(1 Suppl), S2–S8. https://doi.org/10.1067/mai.2001.115569
   PubMed Web of Science ®Google Scholar
• Stepanenko, O. V., Stepanenko, O. V., Kuznetsova, I. M., Verkhusha, V. V., & Turoverov, K. K. (2013). Beta-barrel scaffold of fluorescent proteins: Folding, stability and role in chromophore formation. International Review of Cell and Molecular Biology, 302, 221–278. https://doi.org/10.1016/B978-0-12-407699-0.00004-2
   PubMed Web of Science ®Google Scholar
• Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
   PubMed Web of Science ®Google Scholar
• UniProt Consortium. (2021). UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489.
   PubMed Web of Science ®Google Scholar
• Wallander, E., & Albert, V. A. (2000). Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data. American Journal of Botany, 87(12), 1827–1841.
   PubMed Web of Science ®Google Scholar
• Wang, L., Wang, N., Zhang, W., Cheng, X., Yan, Z., Shao, G., Wang, X., Wang, R., & Fu, C. (2022). Therapeutic peptides: Current applications and future directions. Signal Transduction and Targeted Therapy, 7(1), 48.
   PubMed Web of Science ®Google Scholar
• Woodfolk, J. A., Commins, S. P., Schuyler, A. J., Erwin, E. A., & Platts-Mills, T. A. (2015). Allergens, sources, particles, and molecules: Why do we make IgE responses? Allergology International, 64(4), 295–303. https://doi.org/10.1016/j.alit.2015.06.001
   PubMed Web of Science ®Google Scholar