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Bioinformatics Analysis of Linear B-cell Viscumin Toxin Epitope With Potential Use in Molecularly Imprinted Polymer Biosensors

Sasan Nasirahmadi, Jamil Zargan




Background: There are many diseases around the world that threaten human health and its related hygienic issues. Cancer is among the conditions mentioned above that cause many problems for health sectors worldwide.
Methods: The present research analyzed the linear B-cell epitope of viscumin from European mistletoe using bioinformatics tools. We also provided references for the fast detection of biological agents. Several important tools, such as Protparam, NCBI, PDB, T-coffee, BCpred, Bptope, Ellipro, and Cn3D were used to predict the viscumin linear epitope and its physical and chemical properties.
Results: The 9-mer epitope found as QQTTGEEYF embedded in the A-chain of protein by the least sequence homology with other homologous rivals. Its molecular weight, theoretical isoelectric point, and the total number of negatively charged residues were 1102.1, 3.79, and 2, respectively.
Conclusion: Using different databases and establishing the accuracy level of ˃50% for linear B-cell epitope prediction, the selected epitope passed the related criteria and was introduced as a new linear epitope as a potential biological element in biosensors for cancer (viscumin) fast therapeutic detection.


Bioinformatics, Biosensors, Viscumin, Mistletoe lectin 1


Aftabi Y, Colagar AH, Mehrnejad F. An in silico approach to investigate the source of the controversial interpretations about the phenotypic results of the human AhR-gene G1661A polymorphism. Journal of Theoretical Biology. 2016; 393:1-5. [DOI:10.1016/j.jtbi.2016.01.001] [PMID]

Arinaminpathy N, Ratmann O, Koelle K, Epstein SL, Price GE, Viboud C, et al. Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza. Proceedings of the National Academy of Sciences. 2012; 109(8):3173-7. [DOI:10.1073/pnas.1113342109] [PMID] [PMCID]

Beztsinna N, de Matos MB, Walther J, Heyder C, Hildebrandt E, Leneweit G, et al. Quantitative analysis of receptor-mediated uptake and pro-apoptotic activity of mistletoe lectin-1 by high content imaging. Scientific Reports. 2018; 8:2768. [DOI:10.1038/s41598-018-20915-y] [PMID] [PMCID]

Bhakta S, Seraji MS, Suib SL, Rusling JF. Antibody-like biorecognition sites for proteins from surface imprinting on nanoparticles. ACS Applied Materials & Interfaces. 2015; 7(51):28197-206. [DOI:10.1021/acsami.5b11650] [PMID] [PMCID]

Bogdanos DP, Choudhuri K, Vergani D. Molecular mimicry and autoimmune liver disease: Virtuous intentions, malign consequences. Liver. 2001; 21(4):225-32. [DOI:10.1034/j.1600-0676.2001.021004225.x]

Bossi AM, Sharma PS, Montana L, Zoccatelli G, Laub O, Levi R. Fingerprint-imprinted polymer: Rational selection of peptide epitope templates for the determination of proteins by molecularly imprinted polymers. Analytical Chemistry. 2012; 84(9):4036-41. [DOI:10.1021/ac203422r] [PMID]

Cumbo A, Lorber B, Corvini PF, Meier W, Shahgaldian P. A synthetic nanomaterial for virus recognition produced by surface imprinting. Nature Communications. 2013; 4:1503. [DOI:10.1038/ncomms2529] [PMID]

EL-Sharif HF, Aizawa H, Reddy SM. Spectroscopic and Quartz Crystal Microbalance (QCM) characterisation of protein-based MIPs. Sensors and Actuators B. 2015; 206:239-45. [DOI:10.1016/j.snb.2014.09.053]

Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, et al. Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools. Journal of Molecular Recognition. 2007; 20(2):75-82. [DOI:10.1002/jmr.815] [PMID]

Haupt K. Biomaterials: Plastic antibodies. Nature Materials. 2010; 9(8):612-4. [DOI:10.1038/nmat2818] [PMID]

Jarząb A, Skowicki M, Witkowska D. [Subunit vaccines--antigens, carriers, conjugation methods and the role of adjuvants (Polish)]. Postepy higieny i medycyny doswiadczalnej. 2013; 67:1128-43. [DOI:10.5604/17322693.1077807] [PMID]

Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI. FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis. Genomics. 2017; 109(3-4):312-9. [DOI:10.1016/j.ygeno.2017.05.005] [PMID]

Karfa P, Roy E, Patra S, Kumar D, Madhuri R, Sharma PK. 2016. RETRACTED: A fluorescent molecularly-imprinted polymer gate with temperature and pH as inputs for detection of alpha-fetoprotein. Biosens Bioelectron. 2016; 78:454-63. [DOI:10.1016/j.bios.2015.11.092] [PMID]

Singh KP, Verma N, Akhoon BA, Bhatt V, Gupta SK, Gupta SK, et al. Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains. 3 Biotech. 2016; 6(1):39. [DOI:10.1007/s13205-015-0352-z] [PMID] [PMCID]

Larsen JE, Lund O, Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Research. 2006; 2:2. [DOI:10.1186/1745-7580-2-2] [PMID] [PMCID]

Lesk AM. Introduction to bioinformatics. New York: Oxford University Press; 2002.

Lin CY, Tai DF, Wu TZ. Discrimination of peptides by using a molecularly imprinted piezoelectric biosensor. Chemistry. 2003; 9(20):5107-10. [DOI:10.1002/chem.200304952] [PMID]

Yasser EM, Dobbs D, Honavar VG. In silico prediction of linear B-cell epitopes on proteins. In: Zhou Y, Kloczkowski A, Faraggi E, Yang Y, editors. Prediction of Protein Secondary Structure. New York: Humana Press; 2017. [DOI:10.1007/978-1-4939-6406-2_17] [PMID]

Moreira FT, Ferreira MJ, Puga JR, Sales MG. Screen-printed electrode produced by printed-circuit board technology. Application to cancer biomarker detection by means of plastic antibody as sensing material. Sensors and Actuators B: Chemical. 2016; 223:927-35. [DOI:10.1016/j.snb.2015.09.157] [PMID] [PMCID]

Olson JK, Croxford JL, Calenoff MA, Dal Canto MC, Miller SD. A virus-induced molecular mimicry model of multiple sclerosis. The Journal of Clinical Investigation. 2001; 108(2):311-8. [DOI:10.1172/JCI13032] [PMID] [PMCID]

Saha S, Raghava GP. Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network. Proteins: Structure, Function, and Bioinformatics. 2006; 65(1):40-8. [DOI:10.1002/prot.21078] [PMID]

Singh SP, Srivastava D, Mishra BN. Genome-wide identification of novel vaccine candidates for Plasmodium falciparum malaria using integrative bioinformatics approaches. 3 Biotech. 2017; 7(5):318. [DOI:10.1007/s13205-017-0947-7] [PMID] [PMCID]

Song J, He QF. Bioinformatics analysis of the structure and linear B-cell epitopes of aquaporin-3 from Schistosoma japonicum. Asian Pacific Journal of Tropical Medicine. 2012; 5(2):107-9. [DOI:10.1016/S1995-7645(12)60005-4]

Soria-Guerra RE, Nieto-Gomez R, Govea-Alonso DO, Rosales-Mendoza S. An overview of bioinformatics tools for epitope prediction: Implications on vaccine development. Journal of Biomedical Informatics. 2015; 53:405-14. [DOI:10.1016/j.jbi.2014.11.003] [PMID]

Sun P, Ju H, Liu Z, Ning Q, Zhang J, Zhao X, et al. Bioinformatics resources and tools for conformational B-cell epitope prediction. Computational and Mathematical Methods in Medicine. 2013; 2013(943636):1-11. [DOI:10.1155/2013/943636] [PMID] [PMCID]

Tai DF, Lin CY, Wu TZ, Chen LK. Recognition of dengue virus protein using epitope-mediated molecularly imprinted film. Analytical Chemistry. 2005; 77(16):5140-3. [DOI:10.1021/ac0504060] [PMID]

Tonevitsky A, Agapov I, Chelnokova O, Moisenovich M, Marx U. Comparison between the mechanisms of action of plant toxins ricin and viscumin on the stage of intracellular dissociation. Arzneimittelforschung. 2002; 52(06):500-5. [DOI:10.1055/s-0031-1299922] [PMID]

World Health Organization. World Bank. State of the world’s vaccines and immunization, Geneva: World Health Organization; 2009.

Yao B, Zheng D, Liang S, Zhang C. Conformational B-cell epitope prediction on antigen protein structures: A review of current algorithms and comparison with common binding site prediction methods. PLOS One. 2013; 8(4):e62249. [DOI:10.1371/journal.pone.0062249] [PMID] [PMCID]

Zhao XL, Li DY, He XW, Li WY, Zhang YK. An epitope imprinting method on the surface of magnetic nanoparticles for specific recognition of bovine serum album. Journal of Materials Chemistry B. 2014; 2(43):7575-82. [DOI:10.1039/C4TB01381F]

DOI: https://doi.org/10.32598/ijmtfm.v9i4.26172