Abstract
A new algorithm to predict the types of membrane proteins is proposed. Besides the amino acid composition of the query protein, the information within the amino acid sequence is taken into account. A formulation of the autocorrelation functions based on the hydrophobicity index of the 20 amino acids is adopted. The overall predictive accuracy is remarkably increased for the database of 2054 membrane proteins studied here. An improvement of about 13% in the resubstitution test and 8% in the jackknife test is achieved compared with those of algorithms based merely on the amino acid composition. Consequently, overall predictive accuracy is as high as 94% and 82% for the resubstitution and jackknife tests, respectively, for the prediction of the five types. Since the proposed algorithm is based on more parameters than those in the amino acid composition approach, the predictive accuracy would be further increased for a larger and more class-balanced database. The present algorithm should be useful in the determination of the types and functions of new membrane proteins. The computer program is available on request.
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REFERENCES
Bairoch, A., and Apweiler, R. (1997). Nucleic. Acids Res. 25, 31–36.
Brain, L. S. (1985). The Physical Chemistry of Membranes, Solomon Press, New York, pp. 209–230.
Casey, P. J. (1995). Science 268, 221–225.
Cedano, J., Aloy, P., Perez-pons, J. A., and Querol, E. (1997). J. Mol. Biol. 266, 594–600.
Chou, K. C. (1995). Proteins Struct. Funct. Genet. 21, 319–344.
Chou, K. C., and Elrod, D. W. (1998). Biochem. Biophys. Res. Commun. 252, 63–68.
Chou, K. C., and Elrod, D. W. (1999a). Proteins Struct. Funct. Genet. 34, 137–153.
Chou, K. C., and Elrod, D. W. (1999b). Protein Eng. 12, 107–118.
Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A., and DeLisi, C. (1987). J. Mol. Biol. 195, 659–685.
Duda, R. O., and Hart, P. E. (1973). Pattern Classification and Scene Analysis, Wiley, New York, Chapter 2.
Hopp, T. P., and Woods, K. R. (1981). Proc. Natl. Acad. Sci. USA 78, 3824–3828.
Jacobson, G. R., and Saier, Jr., M. H. (1983). Lipids and membrane, in Biochemistry (Zubay, G. R., ed.), Addison-Wesley, Reading, Massachusetts.
Lifson, S., and Sander, C. (1979). Nature 282, 109–111.
Liu, W., and Chou, K. C. (1998). J. Protein Chem. 17, 209–217.
Ponnuswamy, P. K., Prabhakaran, M., and Manavalan, P. (1980). Biochim. Biophys. Acta. 623, 301–316.
Reinhardt, A., and Hubbard, T. (1998). Nucleic Acids Res. 26, 2230–2236.
Resh, M. D. (1994). Cell 76, 411–413.
Rost, B., Casadio, R., Fariselli, P., and Sander, C. (1995). Protein Sci. 4, 521–533.
Stryer, L. (1988) Biochemistry, Freeman, New York, pp. 283–312.
Thomas, D. D., and Hidalgo, C. (1978). Proc. Natl. Acad. Sci. USA 75, 5488–5492.
Tomii, K., and Kanehisa, M. (1996). Protein Eng. 9, 27–36.
Zhang, C. T., Lin, Z. S., Zhang, Z., and Yan, M. (1998). Protein Eng. 11, 971–979.
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Feng, ZP., Zhang, CT. Prediction of Membrane Protein Types Based on the Hydrophobic Index of Amino Acids. J Protein Chem 19, 269–275 (2000). https://doi.org/10.1023/A:1007091128394
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DOI: https://doi.org/10.1023/A:1007091128394