On the Prediction of Transmembrane Helical Segments in Membrane Proteins
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.
[1] 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.
[2] J. Kyte, R. F. Doolittle, "A simple method for displaying the hydrophathic
character of a protein," J. Mol. Biol., 1982, 157: 105-132.
[3] 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.
[4] T. Hirokawa, S. Boon-Chieng, S. Mitaku, "SOSUI: classification and
secondary structure prediction system for membrane proteins,"
Bioinformatics, vol. 14, 1998, pp. 378-379.
[5] 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.
[6] 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.
[7] 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.
[8] B. Persson, P. Argos, "Prediction of transmembrane segments in proteins
utilizing multiple sequence alignments," J. Mol. Biol., vol. 237, 1994, pp.
182-192.
[9] B. Rost, R. Casadio, P. Fariselli, "Topology prediction for helical
transmembrane segments at 86% accuracy," Protein Sci., vol. 5, 1996, pp.
1704-1718.
[10] 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.
[11] Altaiski, M. Mornev, O. Polozov, "Wavelet analysis of DNA sequence,"
Genet. Anal.´╝î vol. 12, 1996, pp. 165-168.
[12] 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.
[13] P. Li├▓, "Wavelets in bioinformatics and computational biology: state of
art and perspectives," Bioinformatics, vol. 19(1) 2003, pp. 2-9.
[14] 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.
[15] H. Hirakawa, S. Muta, S. Kuhara, "The hydrophobic cores of proteins
predicted by wavelet analysis," Bioinformatics, vol. 15, 1999, pp.
141-148.
[16] F. S. Cordes, J. N. Bright, M. S. Sansom, "Proline-induced distortions of
transmembrane helices," J. Mol. Biol., vol. 323, 2002, pp. 951-960.
[17] D. Eisenberg, A. D. Mclachlan, "Solvation energy in protein folding and
binding," Nature, vol. 319, 1986, pp. 199-203.
[18] S. Mallat, "A theory for multiresolution signal decomposition: the
wavelet representation," IEEE Trans. Pattern Anal. Math.Intell, vol. 11,
1989, pp. 674-693.
[19] K. Palczewski, T. Kumasaka, T. Hori, "Crystal structure of rhodopsin: A
G protein-coupled receptor," Science, vol. 289, 2000, pp. 739-745.
[1] 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.
[2] J. Kyte, R. F. Doolittle, "A simple method for displaying the hydrophathic
character of a protein," J. Mol. Biol., 1982, 157: 105-132.
[3] 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.
[4] T. Hirokawa, S. Boon-Chieng, S. Mitaku, "SOSUI: classification and
secondary structure prediction system for membrane proteins,"
Bioinformatics, vol. 14, 1998, pp. 378-379.
[5] 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.
[6] 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.
[7] 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.
[8] B. Persson, P. Argos, "Prediction of transmembrane segments in proteins
utilizing multiple sequence alignments," J. Mol. Biol., vol. 237, 1994, pp.
182-192.
[9] B. Rost, R. Casadio, P. Fariselli, "Topology prediction for helical
transmembrane segments at 86% accuracy," Protein Sci., vol. 5, 1996, pp.
1704-1718.
[10] 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.
[11] Altaiski, M. Mornev, O. Polozov, "Wavelet analysis of DNA sequence,"
Genet. Anal.´╝î vol. 12, 1996, pp. 165-168.
[12] 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.
[13] P. Li├▓, "Wavelets in bioinformatics and computational biology: state of
art and perspectives," Bioinformatics, vol. 19(1) 2003, pp. 2-9.
[14] 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.
[15] H. Hirakawa, S. Muta, S. Kuhara, "The hydrophobic cores of proteins
predicted by wavelet analysis," Bioinformatics, vol. 15, 1999, pp.
141-148.
[16] F. S. Cordes, J. N. Bright, M. S. Sansom, "Proline-induced distortions of
transmembrane helices," J. Mol. Biol., vol. 323, 2002, pp. 951-960.
[17] D. Eisenberg, A. D. Mclachlan, "Solvation energy in protein folding and
binding," Nature, vol. 319, 1986, pp. 199-203.
[18] S. Mallat, "A theory for multiresolution signal decomposition: the
wavelet representation," IEEE Trans. Pattern Anal. Math.Intell, vol. 11,
1989, pp. 674-693.
[19] K. Palczewski, T. Kumasaka, T. Hori, "Crystal structure of rhodopsin: A
G protein-coupled receptor," Science, vol. 289, 2000, pp. 739-745.
@article{"International Journal of Engineering, Mathematical and Physical Sciences:61490", author = "Yu Bin and Zhang Yan", title = "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.", keywords = "hydrophobicity, membrane protein, transmembranehelical segments, wavelet transform", volume = "4", number = "1", pages = "138-4", }
