Commenced in January 2007
Paper Count: 30184
On the Prediction of Transmembrane Helical Segments in Membrane Proteins Based on Wavelet Transform
Abstract:The prediction of transmembrane helical segments (TMHs) in membrane proteins is an important field in the bioinformatics research. In this paper, a new method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1KQG was chosen as an example to describe the prediction of the number and location of TMHs in membrane proteins by using this method. To access the effect of the method, 80 proteins with known 3D-structure from Mptopo database are chosen at random as the test objects (including 325 TMHs), 308 of which can be predicted accurately, the average predicted accuracy is 96.3%. In addition, the above 80 membrane proteins are divided into 13 groups according to their function and type. In particular, the results of the prediction of TMHs of the 13 groups are satisfying.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1079250Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1109
 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.
 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.
 K. B. Li, P. Issac, A. Krishnan, "Predicting allergenic proteins using wavelet transform," Bioinformatics, vol. 20, 2004, pp. 2572-2578.
 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.
 S. Jayasinghe, K. Hristova, S. H. White, "MPtopo: A database of membrane protein topology," Protein Sci., vol. 10, 2001, pp. 455-458.
 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.
 M. Jormakka, S. Tornroth, B. Byrne, S. Iwata, "Molecular basis of proton motive force generation: Structure of formate dehydrogenase-N," Science, vol. 295, 2002, pp. 1863-1868.