Identification of Uncharacterized Plasmodium falciparum Proteins via In-silico Analysis
Abstract
Background: Numerous types of research on malaria were done over a long period of time but there are still some unknowns. However, it is globally known that malaria is caused by the Plasmodium parasite, mainly and most lethally by Plasmodium falciparum. The purpose of this research is to understand the structure and function of three uncharacterized P. falciparum proteins (PF3D7_1468000, PF3D7_1147400, PF3D7_1351100) using bioinformatic methods in hopes to learn more about malaria. Methods: The three uncharacterized P. falciparum proteins were inserted into Phyre2 for knowing the protein homology, InterPro, and SUPERFAMILY hidden Markov models for understanding the domain annotation, scanprosite for knowing the post-translational modification, Ramachandran plot for protein validation, and Yasara for visualizing the protein. Results: According to the Phyre2 results, the third protein showed the highest confidence and coverage level of 100%, followed by the second protein, and the lowest was the first protein. Interpro and SUPERFAMILY results identified the first protein as WD40 repeat superfamily, the second protein as Cytochrome C subunit II-like, and the third protein as CXXC motif. Scanprosite revealed all sequences possessing protein domains in which the first protein has three protein domains, the second protein has one protein domain, and the third protein has two protein domains. According to the Ramachandran plot, the first and second protein generally has an α-helix structure while the third protein has an overall β-sheet structure, which differs to some extent from the protein structure visualization. The three protein visualizations exhibited secondary structures and more than 50 amino acid residues for each protein. Conclusion: This research concluded that the second and third uncharacterized proteins (PF3D7_1147400, PF3D7_1351100) could be promising antimalarial drug targets leading to the P. falciparum parasite death.
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Baum, J., Tonkin, C. J., Paul, A. S., Rug, M., Smith, B. J., Gould, S. B., ... & Cowman, A. F. (2008). A malaria parasite formin regulates actin polymerization and localizes to the parasite-erythrocyte moving junction during invasion. Cell host & microbe, 3(3), 188-198. https://doi.org/10.1016/j.chom.2008.02.006
Bayat, A. (2002). Science, medicine, and the future: Bioinformatics. BMJ: British Medical Journal, 324(7344), 1018.
Beri, D., Balan, B., Chaubey, S., Subramaniam, S., Surendra, B., & Tatu, U. (2017). A disrupted transsulphuration pathway results in accumulation of redox metabolites and induction of gametocytogenesis in malaria. Scientific Reports, 7(1). https://doi.org/10.1038/srep40213
Blum, M., Chang, H. Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., ... & Finn, R. D. (2021). The InterPro protein families and domains database: 20 years on. Nucleic acids research, 49(D1), D344-D354. doi: 10.1093/nar/gkaa977
Capaldi, R., Malatesta, F., & Darley-Usmar, V. (1983). Structure of cytochrome c oxidase. Biochimica Et Biophysica Acta (BBA) - Reviews On Bioenergetics, 726(2), 135-148. doi: 10.1016/0304-4173(83)90003-4.
Castresana, J., Lübben, M., Saraste, M., & Higgins, D. G. (1994). Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen. The EMBO journal, 13(11), 2516–2525.
Chakrabarti, D., Da Silva, T., Barger, J., Paquette, S., Patel, H., Patterson, S., & Allen, C. M. (2002). Protein Farnesyltransferase and Protein Prenylation in Plasmodium falciparum. Journal of Biological Chemistry, 277(44), 42066-42073.
Dehghani, B., Hashempour, T., Hasanshahi, Z., & Moayedi, J. (2020). Bioinformatics analysis of domain 1 of HCV-core protein: Iran. International Journal of Peptide Research and Therapeutics, 26(1), 303-320.
Eastman, R. T., White, J., Hucke, O., Bauer, K., Yokoyama, K., Nallan, L., ... & Van Voorhis, W. C. (2005). Resistance to a protein farnesyltransferase inhibitor in Plasmodium falciparum. Journal of Biological Chemistry, 280(14), 13554-13559.
Edwards, T., Wilkinson, B., Wharton, R., & Aggarwal, A. (2003). Model of the Brain Tumor–Pumilio translation repressor complex. Genes & Development, 17(20), 2508-2513. https://doi.org/10.1101/gad.1119403
Eissenberg, J. (2006). Molecular biology of the chromo domain: an ancient chromatin module comes of age. Gene, 275(1), 19-29. https://doi.org/10.1016/s0378-1119(01)00628-x
Ellis, R. D., Sagara, I., Doumbo, O., & Wu, Y. (2010). Blood stage vaccines for Plasmodium falciparum: current status and the way forward. Human vaccines, 6(8), 627-634.
Flueck, C., Bartfai, R., Volz, J., Niederwieser, I., Salcedo-Amaya, A. M., Alako, B. T., ... & Voss, T. S. (2009). Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PLoS pathogens, 5(9), e1000569. https://doi.org/10.1371/journal.ppat.1000569
Fontanesi, F., Soto, I. C., & Barrientos, A. (2008). Cytochrome c oxidase biogenesis: new levels of regulation. IUBMB life, 60(9), 557–568. https://doi.org/10.1002/iub.86
Furukawa, Y., Lim, C., Tosha, T., Yoshida, K., Hagai, T., Akiyama, S., ... & Shiro, Y. (2018). Identification of a novel zinc-binding protein, C1orf123, as an interactor with a heavy metal-associated domain. Plos one, 13(9), e0204355. doi: 10.1371/journal.pone.0204355
García-Horsman, J., Barquera, B., Rumbley, J., Ma, J., & Gennis, R. (1994). The superfamily of heme-copper respiratory oxidases. Journal Of Bacteriology, 176(18), 5587-5600. doi: 10.1128/jb.176.18.5587-5600.1994
Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., ... & Barrell, B. (2002). Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419(6906), 498-511.
Gaudet, P., Livstone, M. S., Lewis, S. E., & Thomas, P. D. (2011). Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics, 12(5), 449-462.
Gough, J., Karplus, K., Hughey, R., & Chothia, C. (2001). Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. Journal Of Molecular Biology, 313(4), 903-919. doi: 10.1006/jmbi.2001.5080
Ha, Y. R., & Lee, S. J. (2012). Effect of farnesyltransferase inhibitor on the function of mitochondria of Plasmodium falciparum. Malaria Journal, 11(1), 1-2.
Hall, N., Pain, A., Berriman, M., Churcher, C., Harris, B., Harris, D., ... & Barrell, B. G. (2002). Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13. Nature, 419(6906), 527-531.
Hamid, P. H., Prastowo, J., Ghiffari, A., Taubert, A., & Hermosilla, C. (2017). Aedes aegypti resistance development to commonly used insecticides in Jakarta, Indonesia. PLoS One, 12(12), e0189680.
Hast, M. A., & Beese, L. S. (2011). Structural Biochemistry of CaaX Protein Prenyltransferases. In The Enzymes (Vol. 29, pp. 235-257). Academic Press.
Hasyim, H., Nursafingi, A., Haque, U., Montag, D., Groneberg, D. A., Dhimal, M., ... & Müller, R. (2018). Spatial modelling of malaria cases associated with environmental factors in South Sumatra, Indonesia. Malaria journal, 17(1), 1-15.
Hollingsworth, S. A., & Karplus, P. A. (2010). A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins.
Houston, S., Lithgow, K. V., Osbak, K. K., Kenyon, C. R., & Cameron, C. E. (2018). Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis. BMC structural biology, 18(1), 1-18.
Jaimes, J. A., André, N. M., Chappie, J. S., Millet, J. K., & Whittaker, G. R. (2020). Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein reveals an evolutionary distinct and proteolytically sensitive activation loop. Journal of molecular biology, 432(10), 3309-3325.
Jain, B., & Pandey, S. (2018). WD40 Repeat Proteins: Signalling Scaffold with Diverse Functions. The Protein Journal, 37(5), 391-406. doi: 10.1007/s10930-018-9785-7
Jeong, J. K., Kwon, O., Lee, Y. M., Oh, D. B., Lee, J. M., Kim, S., Kim, E. H., Le, T. N., Rhee, D. K., & Kang, H. A. (2009). Characterization of the Streptococcus pneumoniae BgaC protein as a novel surface beta-galactosidase with specific hydrolysis activity for the Galbeta1-3GlcNAc moiety of oligosaccharides. Journal of bacteriology, 191(9), 3011–3023. https://doi.org/10.1128/JB.01601-08
Kaltashov, I., Bobst, C., Abzalimov, R., Wang, G., Baykal, B., & Wang, S. (2012). Advances and challenges in analytical characterization of biotechnology products: Mass spectrometry-based approaches to study properties and behavior of protein therapeutics. Biotechnology Advances, 30(1), 210-222. doi: 10.1016/j.biotechadv.2011.05.006
Katz, J., Dlakić, M., & Clarke, S. (2003). Automated Identification of Putative Methyltransferases from Genomic Open Reading Frames. Molecular & Cellular Proteomics, 2(8), 525-540. https://doi.org/10.1074/mcp.m300037-mcp200
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature protocols, 10(6), 845-858.
Kemenkes RI. (2020) Informasi Malaria Resmi Indonesia. Retrieved 13 August 2021, from https://www.malaria.id/en.
Kozbial, P., & Mushegian, A. (2005). Natural history of S-adenosylmethionine-binding proteins. BMC Structural Biology, 5(1). https://doi.org/10.1186/1472-6807-5-19
Langhorne, J., Ndungu, F. M., Sponaas, A. M., & Marsh, K. (2008). Immunity to malaria: more questions than answers. Nature immunology, 9(7), 725-732.
Lima, M., Sacramento, L., Quirino, G., Ferreira, M., Benevides, L., & Santana, A. (2017). Leishmania infantum Parasites Subvert the Host Inflammatory Response through the Adenosine A2A Receptor to Promote the Establishment of Infection. Frontiers In Immunology, 8. https://doi.org/10.3389/fimmu.2017.00815
Maurer-Stroh, S., Washietl, S., & Eisenhaber, F. (2003). Protein prenyltransferases. Genome Biology, 4(4). https://doi.org/10.1186/gb-2003-4-4-212
Osier, F. H., Mackinnon, M. J., Crosnier, C., Fegan, G., Kamuyu, G., Wanaguru, M., ... & Marsh, K. (2014). New antigens for a multicomponent blood-stage malaria vaccine. Science translational medicine, 6(247), 247ra102-247ra102.
Pandey, I., Quadiri, A., Wadi, I., Pillai, C. R., Singh, A. P., & Das, A. (2021). Conserved Plasmodium Protein (PF3D7_0406000) of Unknown Function: In-silico Analysis and Cellular Localization. Infection, Genetics and Evolution, 92, 104848.
Pandurangan, A., Stahlhacke, J., Oates, M., Smithers, B., & Gough, J. (2018). The SUPERFAMILY 2.0 database: A significant proteome update and a new webserver. Nucleic Acids Research, 47(D1), D490-D494. doi: 10.1093/nar/gky1130
Punta, M., Coggill, P., Eberhardt, R., Mistry, J., Tate, J., & Boursnell, C. et al. (2011). The Pfam protein families database. Nucleic Acids Research, 40(D1), D290-D301. doi: 10.1093/nar/gkr1065.
Pearson, W. R. (2013). An introduction to sequence similarity ("homology”) searching. Current protocols in bioinformatics, 42(1), 3-1.
Phyo, A. P., & Nosten, F. (2018). The artemisinin resistance in Southeast Asia: An imminent global threat to malaria elimination. Towards Malaria Elimination-A Leap Forward.
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., ... & Bateman, A. (2010). The Pfam protein families database. Nucleic acids research, 38(suppl_1), D211-D222. doi: 10.1093/nar/gkr1065
Ramachandran, G. N. T., & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Advances in protein chemistry, 23, 283-437.
Ramachandran, G. N. T., Ramakrishnan, C., and Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. J Mol Biol, 7, 95-99.
Richart, A., Brunner, C., Stott, K., Murzina, N., & Thomas, J. (2005). Characterization of Chromoshadow Domain-mediated Binding of Heterochromatin Protein 1α (HP1α) to Histone H3. Journal Of Biological Chemistry, 287(22), 18730-18737. https://doi.org/10.1074/jbc.m111.337204
Rivero, F., Muramoto, T., Meyer, A., Urushihara, H., Uyeda, T., & Kitayama, C. (2005). A comparative sequence analysis reveals a common GBD/FH3-FH1-FH2-DAD architecture in formins from Dictyostelium, fungi and metazoa. BMC Genomics, 6(1). https://doi.org/10.1186/1471-2164-6-28
Scherf, A., Lopez-Rubio, J. J., & Riviere, L. (2008). Antigenic variation in Plasmodium falciparum. Annu. Rev. Microbiol., 62, 445-470.
Sheik, S. S., Sundararajan, P., Hussain, A. S. Z., & Sekar, K. (2002). Ramachandran plot on the web. Bioinformatics, 18(11), 1548-1549.
Srinivasan, S., Spear, J., Chandran, K., Joseph, J., Kalyanaraman, B., & Avadhani, N. G. (2013). Oxidative stress induced mitochondrial protein kinase A mediates cytochrome c oxidase dysfunction. PloS one, 8(10), e77129. https://doi.org/10.1371/journal.pone.0077129
Sumarnrote, A., Overgaard, H. J., Marasri, N., Fustec, B., Thanispong, K., Chareonviriyaphap, T., & Corbel, V. (2017). Status of insecticide resistance in Anopheles mosquitoes in Ubon Ratchathani province, Northeastern Thailand. Malaria journal, 16(1), 1-13.
Tehlivets, O., Malanovic, N., Visram, M., Pavkov-Keller, T., & Keller, W. (2013). S-adenosyl-L-homocysteine hydrolase and methylation disorders: yeast as a model system. Biochimica et biophysica acta, 1832(1), 204–215. https://doi.org/10.1016/j.bbadis.2012.09.007
Thayer, K. M. (2016). Structure prediction and analysis of neuraminidase sequence variants. Biochemistry and Molecular Biology Education, 44(4), 361-376.
Venkatachalam, C. M. (1968). Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers: Original Research on Biomolecules, 6(10), 1425-1436.
Weng, A., & Jiang, C. (2004). Ramachandran Plot Server. Retrieved 10 November 2021, from https://zlab.umassmed.edu/bu/rama/
WHO. (2021a). Fact sheet about Malaria. Retrieved 25 July 2021, from https://www.who.int/news-room/fact-sheets/detail/malaria
WHO. (2021b). Malaria. Retrieved 25 July 2021, from https://www.who.int/indonesia/health-topics/malaria
Wlodarski, T., Kutner, J., Towpik, J., Knizewski, L., Rychlewski, L., Kudlicki, A., ... & Ginalski, K. (2011). Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PloS one, 6(8), e23168. https://doi.org/10.1371/journal.pone.0023168
Zekar, L., & Sharman, T. (2020). Plasmodium Falciparum Malaria.
Zhang, S., & Liu, S. (2013). Bioinformatics. Brenner's Encyclopedia Of Genetics, 338-340. https://doi.org/10.1016/b978-0-12-374984-0.00155-8.
Bayat, A. (2002). Science, medicine, and the future: Bioinformatics. BMJ: British Medical Journal, 324(7344), 1018.
Beri, D., Balan, B., Chaubey, S., Subramaniam, S., Surendra, B., & Tatu, U. (2017). A disrupted transsulphuration pathway results in accumulation of redox metabolites and induction of gametocytogenesis in malaria. Scientific Reports, 7(1). https://doi.org/10.1038/srep40213
Blum, M., Chang, H. Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., ... & Finn, R. D. (2021). The InterPro protein families and domains database: 20 years on. Nucleic acids research, 49(D1), D344-D354. doi: 10.1093/nar/gkaa977
Capaldi, R., Malatesta, F., & Darley-Usmar, V. (1983). Structure of cytochrome c oxidase. Biochimica Et Biophysica Acta (BBA) - Reviews On Bioenergetics, 726(2), 135-148. doi: 10.1016/0304-4173(83)90003-4.
Castresana, J., Lübben, M., Saraste, M., & Higgins, D. G. (1994). Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen. The EMBO journal, 13(11), 2516–2525.
Chakrabarti, D., Da Silva, T., Barger, J., Paquette, S., Patel, H., Patterson, S., & Allen, C. M. (2002). Protein Farnesyltransferase and Protein Prenylation in Plasmodium falciparum. Journal of Biological Chemistry, 277(44), 42066-42073.
Dehghani, B., Hashempour, T., Hasanshahi, Z., & Moayedi, J. (2020). Bioinformatics analysis of domain 1 of HCV-core protein: Iran. International Journal of Peptide Research and Therapeutics, 26(1), 303-320.
Eastman, R. T., White, J., Hucke, O., Bauer, K., Yokoyama, K., Nallan, L., ... & Van Voorhis, W. C. (2005). Resistance to a protein farnesyltransferase inhibitor in Plasmodium falciparum. Journal of Biological Chemistry, 280(14), 13554-13559.
Edwards, T., Wilkinson, B., Wharton, R., & Aggarwal, A. (2003). Model of the Brain Tumor–Pumilio translation repressor complex. Genes & Development, 17(20), 2508-2513. https://doi.org/10.1101/gad.1119403
Eissenberg, J. (2006). Molecular biology of the chromo domain: an ancient chromatin module comes of age. Gene, 275(1), 19-29. https://doi.org/10.1016/s0378-1119(01)00628-x
Ellis, R. D., Sagara, I., Doumbo, O., & Wu, Y. (2010). Blood stage vaccines for Plasmodium falciparum: current status and the way forward. Human vaccines, 6(8), 627-634.
Flueck, C., Bartfai, R., Volz, J., Niederwieser, I., Salcedo-Amaya, A. M., Alako, B. T., ... & Voss, T. S. (2009). Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PLoS pathogens, 5(9), e1000569. https://doi.org/10.1371/journal.ppat.1000569
Fontanesi, F., Soto, I. C., & Barrientos, A. (2008). Cytochrome c oxidase biogenesis: new levels of regulation. IUBMB life, 60(9), 557–568. https://doi.org/10.1002/iub.86
Furukawa, Y., Lim, C., Tosha, T., Yoshida, K., Hagai, T., Akiyama, S., ... & Shiro, Y. (2018). Identification of a novel zinc-binding protein, C1orf123, as an interactor with a heavy metal-associated domain. Plos one, 13(9), e0204355. doi: 10.1371/journal.pone.0204355
García-Horsman, J., Barquera, B., Rumbley, J., Ma, J., & Gennis, R. (1994). The superfamily of heme-copper respiratory oxidases. Journal Of Bacteriology, 176(18), 5587-5600. doi: 10.1128/jb.176.18.5587-5600.1994
Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., ... & Barrell, B. (2002). Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419(6906), 498-511.
Gaudet, P., Livstone, M. S., Lewis, S. E., & Thomas, P. D. (2011). Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics, 12(5), 449-462.
Gough, J., Karplus, K., Hughey, R., & Chothia, C. (2001). Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. Journal Of Molecular Biology, 313(4), 903-919. doi: 10.1006/jmbi.2001.5080
Ha, Y. R., & Lee, S. J. (2012). Effect of farnesyltransferase inhibitor on the function of mitochondria of Plasmodium falciparum. Malaria Journal, 11(1), 1-2.
Hall, N., Pain, A., Berriman, M., Churcher, C., Harris, B., Harris, D., ... & Barrell, B. G. (2002). Sequence of Plasmodium falciparum chromosomes 1, 3–9 and 13. Nature, 419(6906), 527-531.
Hamid, P. H., Prastowo, J., Ghiffari, A., Taubert, A., & Hermosilla, C. (2017). Aedes aegypti resistance development to commonly used insecticides in Jakarta, Indonesia. PLoS One, 12(12), e0189680.
Hast, M. A., & Beese, L. S. (2011). Structural Biochemistry of CaaX Protein Prenyltransferases. In The Enzymes (Vol. 29, pp. 235-257). Academic Press.
Hasyim, H., Nursafingi, A., Haque, U., Montag, D., Groneberg, D. A., Dhimal, M., ... & Müller, R. (2018). Spatial modelling of malaria cases associated with environmental factors in South Sumatra, Indonesia. Malaria journal, 17(1), 1-15.
Hollingsworth, S. A., & Karplus, P. A. (2010). A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins.
Houston, S., Lithgow, K. V., Osbak, K. K., Kenyon, C. R., & Cameron, C. E. (2018). Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis. BMC structural biology, 18(1), 1-18.
Jaimes, J. A., André, N. M., Chappie, J. S., Millet, J. K., & Whittaker, G. R. (2020). Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein reveals an evolutionary distinct and proteolytically sensitive activation loop. Journal of molecular biology, 432(10), 3309-3325.
Jain, B., & Pandey, S. (2018). WD40 Repeat Proteins: Signalling Scaffold with Diverse Functions. The Protein Journal, 37(5), 391-406. doi: 10.1007/s10930-018-9785-7
Jeong, J. K., Kwon, O., Lee, Y. M., Oh, D. B., Lee, J. M., Kim, S., Kim, E. H., Le, T. N., Rhee, D. K., & Kang, H. A. (2009). Characterization of the Streptococcus pneumoniae BgaC protein as a novel surface beta-galactosidase with specific hydrolysis activity for the Galbeta1-3GlcNAc moiety of oligosaccharides. Journal of bacteriology, 191(9), 3011–3023. https://doi.org/10.1128/JB.01601-08
Kaltashov, I., Bobst, C., Abzalimov, R., Wang, G., Baykal, B., & Wang, S. (2012). Advances and challenges in analytical characterization of biotechnology products: Mass spectrometry-based approaches to study properties and behavior of protein therapeutics. Biotechnology Advances, 30(1), 210-222. doi: 10.1016/j.biotechadv.2011.05.006
Katz, J., Dlakić, M., & Clarke, S. (2003). Automated Identification of Putative Methyltransferases from Genomic Open Reading Frames. Molecular & Cellular Proteomics, 2(8), 525-540. https://doi.org/10.1074/mcp.m300037-mcp200
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature protocols, 10(6), 845-858.
Kemenkes RI. (2020) Informasi Malaria Resmi Indonesia. Retrieved 13 August 2021, from https://www.malaria.id/en.
Kozbial, P., & Mushegian, A. (2005). Natural history of S-adenosylmethionine-binding proteins. BMC Structural Biology, 5(1). https://doi.org/10.1186/1472-6807-5-19
Langhorne, J., Ndungu, F. M., Sponaas, A. M., & Marsh, K. (2008). Immunity to malaria: more questions than answers. Nature immunology, 9(7), 725-732.
Lima, M., Sacramento, L., Quirino, G., Ferreira, M., Benevides, L., & Santana, A. (2017). Leishmania infantum Parasites Subvert the Host Inflammatory Response through the Adenosine A2A Receptor to Promote the Establishment of Infection. Frontiers In Immunology, 8. https://doi.org/10.3389/fimmu.2017.00815
Maurer-Stroh, S., Washietl, S., & Eisenhaber, F. (2003). Protein prenyltransferases. Genome Biology, 4(4). https://doi.org/10.1186/gb-2003-4-4-212
Osier, F. H., Mackinnon, M. J., Crosnier, C., Fegan, G., Kamuyu, G., Wanaguru, M., ... & Marsh, K. (2014). New antigens for a multicomponent blood-stage malaria vaccine. Science translational medicine, 6(247), 247ra102-247ra102.
Pandey, I., Quadiri, A., Wadi, I., Pillai, C. R., Singh, A. P., & Das, A. (2021). Conserved Plasmodium Protein (PF3D7_0406000) of Unknown Function: In-silico Analysis and Cellular Localization. Infection, Genetics and Evolution, 92, 104848.
Pandurangan, A., Stahlhacke, J., Oates, M., Smithers, B., & Gough, J. (2018). The SUPERFAMILY 2.0 database: A significant proteome update and a new webserver. Nucleic Acids Research, 47(D1), D490-D494. doi: 10.1093/nar/gky1130
Punta, M., Coggill, P., Eberhardt, R., Mistry, J., Tate, J., & Boursnell, C. et al. (2011). The Pfam protein families database. Nucleic Acids Research, 40(D1), D290-D301. doi: 10.1093/nar/gkr1065.
Pearson, W. R. (2013). An introduction to sequence similarity ("homology”) searching. Current protocols in bioinformatics, 42(1), 3-1.
Phyo, A. P., & Nosten, F. (2018). The artemisinin resistance in Southeast Asia: An imminent global threat to malaria elimination. Towards Malaria Elimination-A Leap Forward.
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., ... & Bateman, A. (2010). The Pfam protein families database. Nucleic acids research, 38(suppl_1), D211-D222. doi: 10.1093/nar/gkr1065
Ramachandran, G. N. T., & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Advances in protein chemistry, 23, 283-437.
Ramachandran, G. N. T., Ramakrishnan, C., and Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. J Mol Biol, 7, 95-99.
Richart, A., Brunner, C., Stott, K., Murzina, N., & Thomas, J. (2005). Characterization of Chromoshadow Domain-mediated Binding of Heterochromatin Protein 1α (HP1α) to Histone H3. Journal Of Biological Chemistry, 287(22), 18730-18737. https://doi.org/10.1074/jbc.m111.337204
Rivero, F., Muramoto, T., Meyer, A., Urushihara, H., Uyeda, T., & Kitayama, C. (2005). A comparative sequence analysis reveals a common GBD/FH3-FH1-FH2-DAD architecture in formins from Dictyostelium, fungi and metazoa. BMC Genomics, 6(1). https://doi.org/10.1186/1471-2164-6-28
Scherf, A., Lopez-Rubio, J. J., & Riviere, L. (2008). Antigenic variation in Plasmodium falciparum. Annu. Rev. Microbiol., 62, 445-470.
Sheik, S. S., Sundararajan, P., Hussain, A. S. Z., & Sekar, K. (2002). Ramachandran plot on the web. Bioinformatics, 18(11), 1548-1549.
Srinivasan, S., Spear, J., Chandran, K., Joseph, J., Kalyanaraman, B., & Avadhani, N. G. (2013). Oxidative stress induced mitochondrial protein kinase A mediates cytochrome c oxidase dysfunction. PloS one, 8(10), e77129. https://doi.org/10.1371/journal.pone.0077129
Sumarnrote, A., Overgaard, H. J., Marasri, N., Fustec, B., Thanispong, K., Chareonviriyaphap, T., & Corbel, V. (2017). Status of insecticide resistance in Anopheles mosquitoes in Ubon Ratchathani province, Northeastern Thailand. Malaria journal, 16(1), 1-13.
Tehlivets, O., Malanovic, N., Visram, M., Pavkov-Keller, T., & Keller, W. (2013). S-adenosyl-L-homocysteine hydrolase and methylation disorders: yeast as a model system. Biochimica et biophysica acta, 1832(1), 204–215. https://doi.org/10.1016/j.bbadis.2012.09.007
Thayer, K. M. (2016). Structure prediction and analysis of neuraminidase sequence variants. Biochemistry and Molecular Biology Education, 44(4), 361-376.
Venkatachalam, C. M. (1968). Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers: Original Research on Biomolecules, 6(10), 1425-1436.
Weng, A., & Jiang, C. (2004). Ramachandran Plot Server. Retrieved 10 November 2021, from https://zlab.umassmed.edu/bu/rama/
WHO. (2021a). Fact sheet about Malaria. Retrieved 25 July 2021, from https://www.who.int/news-room/fact-sheets/detail/malaria
WHO. (2021b). Malaria. Retrieved 25 July 2021, from https://www.who.int/indonesia/health-topics/malaria
Wlodarski, T., Kutner, J., Towpik, J., Knizewski, L., Rychlewski, L., Kudlicki, A., ... & Ginalski, K. (2011). Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PloS one, 6(8), e23168. https://doi.org/10.1371/journal.pone.0023168
Zekar, L., & Sharman, T. (2020). Plasmodium Falciparum Malaria.
Zhang, S., & Liu, S. (2013). Bioinformatics. Brenner's Encyclopedia Of Genetics, 338-340. https://doi.org/10.1016/b978-0-12-374984-0.00155-8.
Authors
Widjaja , V., Lim, A., Aini, B., Audrey Gandasasmita, G., Theddy Darmawan, J., & Aditya Parikesit, A. (2022). Identification of Uncharacterized Plasmodium falciparum Proteins via In-silico Analysis. BIOEDUSCIENCE, 6(2), 198–210. https://doi.org/10.22236/j.bes/628770
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