Abstract
Over five thousand types of protein are produced by the malaria parasite Plasmodium falciparum. Each protein contains the address of a specific destination to which it will be trafficked by various cellular translocation mechanisms. This address may be encoded in a secretory signal, physically represented as an amino acid subsequence forming a motif or pattern. The different signal sequences are classified according to where they occur with respect to the entire amino acid sequence. Biologists are interested in computational techniques that can automatically classify the large amount of data in the Plasmodium falciparum genome, since they have inferred from ongoing experimentation that a correlation exists between particular signals and significant cellular locations. We describe the development of a web-accessible fuzzy classifier of secretory signals in proteins. The application of this classifier to the entire P. falciparum genome immediately produced some biologically-interesting predictions that are briefly discussed.
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References
Wirth, D.F.: The parasite genome: Biological revelations. Nature 419, 495–496 (2002)
Greenwood, B., Mutabingwa, T.: Malaria in 2002. Nature 415, 670–672 (2002)
Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., Paulsen, I.T., James, K., Eisen, J.A., Rutherford, K., Salzberg, S.L., Craig, A., Kyes, S., Chan, M.S., Nene, V., Shallom, S.J., Suh, B., Peterson, J., Angiuoli, S., Pertea, M., Allen, J., Selengut, J., Haft, D., Mather, M.W., Vaidya, A.B., Martin, D.M., Fairlamb, A.H., Fraunholz, M.J., Roos, D.S., Ralph, S.A., McFadden, G.I., Cummings, L.M., Subramanian, G.M., Mungall, C., Venter, J.C., Carucci, D.J., Hoffman, S.L., Newbold, C., Davis, R.W., Fraser, C.M., Barrell, B.: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511 (2002)
Baruch, D.I., Rogerson, S.J., Cooke, B.M.: Asexual blood stages of malaria antigens: cytoadherence. Chem. Immunol. 80, 144–162 (2002)
Kyte, J., Doolittle, R.F.: A Simple Method for Displaying the Hydropathic Character of a Protein. Journal of Molecular Biology 57, 105–132 (1982)
Martoglio, B., Dobberstein, B.: Signal sequences: more than just greasy peptides. Trends in Cell Biology 8, 410–415 (1998)
von Heijne, G.: A new method for predicting signal sequence cleavage sites. Nucleic Acids Research 14, 4683–4690 (1986)
von Heijne, G.: Signal sequences. The limits of variation. J. Mol. Biol. 184, 99–105 (1985)
Albano, F.R., Foley, M., Tilley, L.: Export of parasite proteins to the erythrocyte cytoplasm: secretory machinery and traffic signals. In: Transport and trafficking in the malaria-infected erythrocyte. Novartis Foundation Symposium, vol. 226, pp. 157–175. Wiley, Chichester (1999)
Lingelbach, K.R.: Plasmodium falciparum: A molecular view of protein transport from the parasite into the host erythrocyte. Experimental parasitology 76, 318–327 (1993)
Wickham, M.E., Rug, M., Ralph, S.A., Klonis, N., McFadden, G.I., Tilley, L., Cowman, A.F.: Trafficking and assembly of the cytoadherence complex in Plasmodium falciparum-infected human erythrocytes. Embo Journal 20, 5636–5649 (2001)
Nakai, K., Horton, P.: PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24, 34–36 (1999)
Nielsen, H., Engelbrecht, J., Brunak, S.: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 10, 1–6 (1997)
Nielsen, H., Krogh, A.: Prediction of signal peptides and signal anchors by a hidden Markov model. In: Glasgow, J., et al. (eds.) Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pp. 122–130 (1998)
Anders, R.F., Saul, A.: Malaria vaccines. Parasitol Today 16, 444–447 (2000)
Zhang, C.T., Chou, K.C., Maggiora, G.M.: Predicting protein structural classes from amino acid composition: application of fuzzy clustering. Protein Engineering 8, 425–435 (1995)
Schlosshauer, M., Ohlsson, M.: A novel approach to local reliability of sequence alignments. Bioinformatics 18, 847–854 (2002)
Chang, B.C., Halgamuge, S.K.: Protein motif extraction with neuro-fuzzy optimization. Bioinformatics 18, 1084–1090 (2002)
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Logan, E., Hall, R., Klonis, N., Herd, S., Tilley, L. (2004). Fuzzy Classification of Secretory Signals in Proteins Encoded by the Plasmodium falciparum Genome. In: Negoita, M.G., Howlett, R.J., Jain, L.C. (eds) Knowledge-Based Intelligent Information and Engineering Systems. KES 2004. Lecture Notes in Computer Science(), vol 3213. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30132-5_138
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DOI: https://doi.org/10.1007/978-3-540-30132-5_138
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