Mariana Mariana, Saipul Abbas, Salamiah Salamiah, Yusriadi Marsuni, Samharinto Soedijo, Muslimin Sepe, Muhammad I. Pramudi, Ismed S. Budi, Dewi Fitriyanti, Elly Liestiany, Lyswiana Aphrodyanti, Noor Aidawati, Helda O. Rosa


Aspergillus spp. is a type of fungi that can contaminate and damage various types of food and agricultural products. To better understand the structure and function of proteins, in silico research was conducted using Internal Transcribed Spacer (ITS) primers and SWISS Model protein prediction tools. The objective of this study was to identify fungal species using the BLAST method and to analyze the structure and function of proteins from Aspergillus spp. The methods used included BLAST for species identification, Web Expasy to translate DNA sequences into proteins, SWISS Models to model protein structures, SAVES to validate protein structures, and STRING to analyze the function of proteins. The results of the BLAST analysis showed that the identified fungal species were Aspergillus flavus, A. tamarii, and A. nomius. Furthermore, the results of translating DNA sequences into proteins using Web Expasy showed that there were three open reading frames with the highest residual values of 119 and 83, while the lowest residual value was 4. Only two of these frames met the protein criteria. Moreover, the results of protein structure modeling using the SWISS Model method produced a fairly accurate Aspergillus spp. protein structure model with a validation value of protein structure using ERRAT (SAVES V6.0) of 100%. Additionally, the results of protein function analysis using STRING showed that the Aspergillus spp. protein has a function in producing enzymes that play a role in the metabolic process of cells.


Aspergillus flavus; in silico; ITS primer; protein structure; protein function; SWISS Model.

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Ayaz, A., Zaman, W., Saqib, S., Ullah, F., & Mahmood, T. (2020). Phylogeny and diversity of Lamiaceae based on rps14 gene in Pakistan. Genetika, 52(2), 435-452.

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002). From DNA to RNA. In Molecular Biology of the Cell. 4th edition. Garland Science.

Abrar, M., Anjum, F. M., Butt, M. S., Pasha, I., Randhawa, M. A., Saeed, F., & Waqas, K. (2013). Aflatoxins: biosynthesis, occurrence, toxicity, and remedies. Critical reviews in food science and nutrition, 53(8), 862-874.

Ayofemi Olalekan Adeyeye, S. (2020). Aflatoxigenic fungi and mycotoxins in food: a review. Critical reviews in food science and nutrition, 60(5), 709-721.

Amaike, S., & Keller, N. P. (2011). Aspergillus flavus. Annual review of phytopathology, 49, 107-133.

Bhatnagar-Mathur, P., Sunkara, S., Bhatnagar-Panwar, M., Waliyar, F., & Sharma, K. K. (2015). Biotechnological advances for combating Aspergillus flavus and aflatoxin contamination in crops. Plant science, 234, 119-132.

Bhattacharya, A., Tejero, R., & Montelione, G. T. (2007). Evaluating protein structures determined by structural genomics consortia. Proteins: Structure, Function, and Bioinformatics, 66(4), 778-795.

Blackburn, G. M. (Ed.). (2006). Nucleic acids in chemistry and biology. Royal Society of Chemistry.

Breda, A., Valadares, N. F., de Souza, O. N., & Garratt, R. C. (2007). Protein structure, modelling and applications. In Bioinformatics in tropical disease research: a practical and case-study approach [Internet]. National Center for Biotechnology Information (US).

Benkert, P., Tosatto, S. C., & Schomburg, D. (2008). QMEAN: A comprehensive scoring function for model quality assessment. Proteins: Structure, Function, and Bioinformatics, 71(1), 261-277.

Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27(3), 343-350.

Bordoli, L., & Schwede, T. (2012). Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. Homology Modeling: Methods and Protocols, 107-136.

Bose, P., Gowrie, S. U., & Chathurdevi, G. (2019). Optimization of Culture Conditions for Growth and Production of Bioactive Metabolites by Endophytic Fungus-Aspergillus tamarii. International Journal of Pharmacy and Biological Sciences, 9(2), 469-478.

Balina, A., Kebede, A., & Tamiru, Y. (2018). Review on aflatoxin and its impacts on livestock. Journal of Dairy and Veterinary Sciences, 6(2), e555685.

Bashir, S., Janiad, S., Zeeshan, A., Farah, N., Mehboob, S., Butt, H. I., & Qari, S. H. (2022). In Silico Analysis and Function Prediction of Sr22 Gene Product as Stem Rust Resistant Protein. Annals of the Romanian Society for Cell Biology, 26(01), 258-262.

Cram, D. J., & Cram, J. M. (1971). Cyclophane chemistry: bent and battered benzene rings. Accounts of Chemical Research, 4(6), 204-213.

Corley, M., Burns, M. C., & Yeo, G. W. (2020). How RNA-binding proteins interact with RNA: molecules and mechanisms. Molecular cell, 78(1), 9-29.

de la Cruz, J., Karbstein, K., & Woolford Jr, J. L. (2015). Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo. Annual review of biochemistry, 84, 93-129.

Dhanamjayulu, P., Boga, R. B., & Mehta, A. (2019). Inhibition of aflatoxin B1 biosynthesis and down regulation of aflR and aflB genes in presence of benzimidazole derivatives without impairing the growth of Aspergillus flavus. Toxicon, 170, 60-67.

Damodaran, S., & Parkin, K. L. (2017). Amino acids, peptides, and proteins. In Fennema’s food chemistry (pp. 235-356). CRC Press.

Dreyfuss, G., Kim, V. N., & Kataoka, N. (2002). Messenger-RNA-binding proteins and the messages they carry. Nature reviews Molecular cell biology, 3(3), 195-205.

Dutta, B., Banerjee, A., Chakraborty, P., & Bandopadhyay, R. (2018). In silico studies on bacterial xylanase enzyme: Structural and functional insight. Journal of Genetic Engineering and Biotechnology, 16(2), 749-756.

Elliott, D., & Ladomery, M. (2017). Molecular biology of RNA. Oxford University Press.

Frank, J., & Spahn, C. M. (2006). The ribosome and the mechanism of protein synthesis. Reports on Progress in Physics, 69(5), 1383.

Fouad, A. M., Ruan, D., El-Senousey, H. K., Chen, W., Jiang, S., & Zheng, C. (2019). Harmful effects and control strategies of aflatoxin b1 produced by Aspergillus flavus and Aspergillus parasiticus strains on poultry. Toxins, 11(3), 176.

Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., ... & Jensen, L. J. (2012). STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic acids research, 41(D1), D808-D815.

Glisovic, T., Bachorik, J. L., Yong, J., & Dreyfuss, G. (2008). RNA-binding proteins and post-transcriptional gene regulation. FEBS letters, 582(14), 1977-1986.

Gourama, H., & Bullerman, L. B. (1995). Aspergillus flavus and Aspergillus parasiticus: Aflatoxigenic fungi of concern in foods and feeds: A review. Journal of Food protection, 58(12), 1395-1404.

Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic acids research, 31(13), 3784-3788.

Hou, T., Sana, S. S., Li, H., Xing, Y., Nanda, A., Netala, V. R., & Zhang, Z. (2022). Essential oils and its antibacterial, antifungal and anti-oxidant activity applications: A review. Food Bioscience, 47, 101716.

Kirubakaran, P., Karthikeyan, M., Singh, K. D., Nagamani, S., & Premkumar, K. (2013). In silico structural and functional analysis of the human TOPK protein by structure modeling and molecular dynamics studies. Journal of molecular modeling, 19, 407-419.

Klich, M. A. (2007). Aspergillus flavus: the major producer of aflatoxin. Molecular plant pathology, 8(6), 713-722.

Laskowski, R. A., Furnham, N., & Thornton, J. M. (2013). The Ramachandran plot and protein structure validation. In Biomolecular forms and functions: a celebration of 50 years of the ramachandran map (pp. 62-75). 9789814449144_0005

Lake, J. A. (1981). The ribosome. Scientific American, 245(2), 84-97. scientificamerican0881-84

Lovell, S. C., Davis, I. W., Arendall III, W. B., De Bakker, P. I., Word, J. M., Prisant, M. G., ... & Richardson, D. C. (2003). Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437-450.

Lobo, I. (2008). Basic local alignment search tool (BLAST). Nature Education, 1(1).

Nguyen, H. N., Chaves-Lopez, C., Oliveira, R. C., Paparella, A., & Rodrigues, D. F. (2019). Cellular and metabolic approaches to investigate the effects of graphene and graphene oxide in the fungi Aspergillus flavus and Aspergillus niger. Carbon, 143, 419-429.

Ogodo, A. C., & Ugbogu, O. C. (2016). Public health significance of aflatoxin in food industry—A review. European Journal of Clinical and Biomedical Sciences, 2(5), 51-58.

Rozario, L. T., Sharker, T., & Nila, T. A. (2021). In silico analysis of deleterious SNPs of human MTUS1 gene and their impacts on subsequent protein structure and function. PloS one, 16(6), e0252932.

Ramirez, M. L., Cendoya, E., Nichea, M. J., Zachetti, V. G. L., & Chulze, S. N. (2018). Impact of toxigenic fungi and mycotoxins in chickpea: A review. Current Opinion in Food Science, 23, 32-37.

Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., & Mering, C. V. (2010). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic acids research, 39(suppl_1), D561-D568.

Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., ... & von Mering, C. (2023). The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic acids research, 51(D1), D638-D646.

Tam, E. W., Chen, J. H., Lau, E. C., Ngan, A. H., Fung, K. S., Lee, K. C., & Woo, P. C. (2014). Misidentification of Aspergillus nomius and Aspergillus tamarii as Aspergillus flavus: characterization by internal transcribed spacer, β-tubulin, and calmodulin gene sequencing, metabolic fingerprinting, and matrix-assisted laser desorption ionization–time of flight mass spectrometry. Journal of Clinical Microbiology, 52(4), 1153-1160. 10.1128/JCM.03258-13

Von Hippel, P. H., Bear, D. G., Morgan, W. D., & McSwiggen, J. A. (1984). Protein-nucleic acid interactions in transcription: a molecular analysis. Annual Review of Biochemistry, 53(1), 389-446. 10.1146/

Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., ... & Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research, 46(W1), W296-W303.

Yu, J., Cleveland, T. E., Nierman, W. C., & Bennett, J. W. (2005). Aspergillus flavus genomics: gateway to human and animal health, food safety, and crop resistance to diseases. Revista iberoamericana de micología, 22(4), 194-202.

Zain, M. E. (2011). Impact of mycotoxins on humans and animals. Journal of Saudi chemical society, 15(2), 129-144.



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