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On the Prediction of Transmembrane Helical Segments in Membrane Proteins
Abstract:The prediction of transmembrane helical segments (TMHs) in membrane proteins is an important field in the bioinformatics research. In this paper, a method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1F88 was chosen as an example to describe the prediction of the number and location of TMHs in membrane proteins by using this method. One group of test data sets that contain total 19 protein sequences was utilized to access the effect of this method. Compared with the prediction results of DAS, PRED-TMR2, SOSUI, HMMTOP2.0 and TMHMM2.0, the obtained results indicate that the presented method has higher prediction accuracy.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1334820Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1415
 A. Krogh, B. Larsson, G. von Heijne, E. Sonnhamme, "Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes,"J. Mol. Biol., vol. 305, 2001, pp. 567-580.
 J. Kyte, R. F. Doolittle, "A simple method for displaying the hydrophathic character of a protein," J. Mol. Biol., 1982, 157: 105-132.
 G. Heijne, "The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology," EMBO J, vol. 5, 1986, pp. 3021-3027.
 T. Hirokawa, S. Boon-Chieng, S. Mitaku, "SOSUI: classification and secondary structure prediction system for membrane proteins," Bioinformatics, vol. 14, 1998, pp. 378-379.
 C. Pasquier, V. J. Promponas, G. A. Palaios, J. S. Hamodrakas, S. J. Hamodrakas, "A novel method for predicting trsnsmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm," Protein Eng., vol. 12, 1999, pp. 381-385.
 M. Cserzö, E. Wallin, I. Simon, G. von Heijne, A. Elofsson, "Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method," Protein Eng., vol. 10, 1997, pp. 673-676.
 D. T. Jones, W. R. Taylor, J. M. Thornton, "A model recognition approach to the prediction of all-helical membrane protein structure and topology," Biochemistry, vol. 33, 1994, pp. 3038-3049.
 B. Persson, P. Argos, "Prediction of transmembrane segments in proteins utilizing multiple sequence alignments," J. Mol. Biol., vol. 237, 1994, pp. 182-192.
 B. Rost, R. Casadio, P. Fariselli, "Topology prediction for helical transmembrane segments at 86% accuracy," Protein Sci., vol. 5, 1996, pp. 1704-1718.
 G. E. Tusnady, I. Simon, "Principles governing amino acid composition of integral membrane proteins: application to topology prediction," J. Mol. Biol., vol. 283, 1998, pp. 489-506.
 Altaiski, M. Mornev, O. Polozov, "Wavelet analysis of DNA sequence," Genet. Anal.´╝î vol. 12, 1996, pp. 165-168.
 B. Yu, X. H. Meng, H. J. Liu, et al, "Prediction of transmembrane helical segments in transmembrane proteins based on wavelet transform," Journal of Shanghai University (English Edition), vol. 10, 2006, pp. 308-318.
 P. Li├▓, "Wavelets in bioinformatics and computational biology: state of art and perspectives," Bioinformatics, vol. 19(1) 2003, pp. 2-9.
 J. P. Mena-Chalco, Y. Zana, and R. M. Cesar, "Identification of protein coding regions using the modified Gabor-wavelet transform," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, 2008, pp. 198-207.
 H. Hirakawa, S. Muta, S. Kuhara, "The hydrophobic cores of proteins predicted by wavelet analysis," Bioinformatics, vol. 15, 1999, pp. 141-148.
 F. S. Cordes, J. N. Bright, M. S. Sansom, "Proline-induced distortions of transmembrane helices," J. Mol. Biol., vol. 323, 2002, pp. 951-960.
 D. Eisenberg, A. D. Mclachlan, "Solvation energy in protein folding and binding," Nature, vol. 319, 1986, pp. 199-203.
 S. Mallat, "A theory for multiresolution signal decomposition: the wavelet representation," IEEE Trans. Pattern Anal. Math.Intell, vol. 11, 1989, pp. 674-693.
 K. Palczewski, T. Kumasaka, T. Hori, "Crystal structure of rhodopsin: A G protein-coupled receptor," Science, vol. 289, 2000, pp. 739-745.