Abstract
Majority of proteins undergo important post-translational modifications (PTM) that may alter physical and chemical properties of the protein and mainly their functions. Laboratory processes of determining PTM sites in proteins are laborious and expensive. On the contrary, computational approaches are far swifter and economical; and the models for prediction of PTMs can be quite accurate too. Among the PTMs, Protein N- terminal N-myristoylation by myristoyl-CoA protein N-myristoyltransferase (NMT) is an important lipid anchor modification of eukaryotic and viral proteins; occurring in about 0.5% encoded NMT substrates. Reliable recognition of myristoylation capability from the substrate amino acid sequence is useful for proteomic functional annotation projects as also in building therapeutics targeting the NMT. Using computational techniques, prediction-based models can be developed and new functions of protein substrates can be identified.
In this study, we employ Biogeography based Optimization (BBO) for feature selection along with Support Vector Machines (SVM) and Random Forest for classification of N-myristoylation sequences. The simulations indicate that N-myristoylation sites can be identified with high accuracy using hybrid BBO wrappers in combination with weighted filter methods.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Chou, P.Y., Fasman, G.D.: Empirical predictions of protein conformations. Annu. Rev. Biochem. 47, 251–276 (1978)
Frank, E., Birgit, E., Werner, K., Sebastian, M.-S., Georg, N., Georg, S., Michael, W.: Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Π, NMT and PTS1. Nucleic Acids Research 31, 3631–3634 (2003)
Gordon, J.I., Duronio, R.J., Rudnick, D.A., Adams, S.P., Gokel, G.W.: Protein N-Myristoylation. J. Biol. Chem. 266(14), 8647–8650 (1991)
Hayashi, N., Titani, K.: N-myristoylated proteins, key components in in-tracellular signal transduction systems enabling rapid and flexible cell responses. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 86(5), 494–508 (2010)
Patwardhan, P., Resh, M.D.: Myristoylation and Membrane Binding Regulate c-Src Stability and Kinase Activity. J. Mol. Biol. 30(17), 4094–4107 (2010)
Kumar, S., Singh, B., Dimmock, J.R., Sharma, R.K.: N-myristoyltransferase in the leukocytic development processes. Cell Tissue Res. 345(2), 203–211 (2011)
Wright, M.H., Heal, W.P., Mann, D.J., Tate, E.W.: Protein myristoylation in health and disease. J. Chem. Biol. 3(1), 19–35 (2010)
Sebastian, M.-S., Birgit, E., Frank, E.: N-terminal N-Myristoylation of Proteins: Refinement of the Sequence Motif and its Taxon-specific Differences. J. Mol. Biol. 317, 523–540 (2002)
Lee, T.-Y., Huang, H.-D., Hung, J.-H., Huang, H.-Y., Yang, Y.-S., Wang, T.-H.: dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 34 (Database issue), D622–D627 (2006)
Khoury, G.A., Baliban, R.C., Floudas, C.A.: Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Sci. Rep. 1, 90 (2011)
Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., Kanehisa, M.: AAindex: amino acid index database. Nucleic Acids Res. 36 (Database issue), D202–D205 (2008)
Simon, D.: Biogeography-Based Optimization. IEEE Transactions on Evolutionary Computation 12, 702–713 (2008)
Ma, H., Simon, D.: Blended biogeography-based optimization for constrained optimization. Engineering Applications of Artificial Intelligence 24(3), 517–525 (2011)
Mo, H., Xu, L.: Biogeography based optimization for traveling salesman problem. In: Sixth International Conference of Natural Computation, vol. 6, pp. 3143–3147 (2010)
Song, Y., Liu, M., Wang, Z.: Biogeography-based optimization for the traveling alesman problems. In: Third International Joint Conference on Computational Science and Optimization (CSO), vol. 1, pp. 295–299 (2010)
Panchal, V.K., Singh, P., Kaur, N., Harish, K.: Biogeography based satellite image classification. International Journal of Computer Science and Information Security 6, 269–274 (2009)
Nikumbh S., Ghosh S., Jayaraman V. K.: Biogeography-Based Informative Gene Selection and Cancer Classification Using SVM and Random Forests. In: IEEE World Congress on Computational Intelligence (IEEE WCCI 2012), Australia. In Press (2012)
Han, J., Kamber, M., Pei, J.: Data Mining: Concepts and Techniques - Information Gain. TheKaufmann Series in Data Management Systems. Morgan Kaufmann (2011)
Hall, M., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., Witten, I.H.: The weka data mining software: An update. SIGKDD Explor. 11, 130–133 (2009)
Boser, B.E., Guyon, I.M., Vapnik, V.N.: Training algorithm for optimal margin classifiers. In: 5th Annual ACM Workshop on COLT, pp. 144–152. ACM Press, Pittsburgh (1992)
Cortes, C., Vapnik, V.N.: Support-Vector Networks. Machine Learning 20 (1995)
Chang, C.-C., Lin, C.-J.: LIBSVM: A library for support vector machines. ACM Transactions on Intelligent Systems and Technology 2, 27:1–27:27 (2011)
Breiman, L.: Random forests. Machine Learning 45, 5–32 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Ghosh, S., Ramachandran, N., Venkateshwari, C., Jayaraman, V.K. (2012). Hybrid Biogeography Based Simultaneous Feature Selection and Prediction of N-Myristoylation Substrate Proteins Using Support Vector Machines and Random Forest Classifiers. In: Panigrahi, B.K., Das, S., Suganthan, P.N., Nanda, P.K. (eds) Swarm, Evolutionary, and Memetic Computing. SEMCCO 2012. Lecture Notes in Computer Science, vol 7677. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35380-2_43
Download citation
DOI: https://doi.org/10.1007/978-3-642-35380-2_43
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-35379-6
Online ISBN: 978-3-642-35380-2
eBook Packages: Computer ScienceComputer Science (R0)