Abstract
Although a β-turn consists of only four amino acids, it assumes many different types in proteins. Is this basically dependent on the tetrapeptide sequence alone or is it due to a variety of interactions with the other part of a protein? To answer this question, a residue-coupled model is proposed that can reflect the sequence-coupling effect for a tetrapeptide in not only a β-turn or non-β-turn, but also different types of a β-turn. The predicted results by the model for 6022 tetrapeptides indicate that the rates of correct prediction for β-turn types I, I′, II, II′, VI, and VIII and non-β-turns are 68.54%, 93.60%, 85.19%, 97.75%, 100%, 88.75%, and 61.02%, respectively. Each of these seven rates is significantly higher than \(\frac{1}{7}\) = 14.29%, the completely randomized rate, implying that the formation of different β-turn types or non-β-turns is considerably correlated with the sequences of a tetrapeptide.
Similar content being viewed by others
REFERENCES
Bhat, U. N. (1984). In Elements of Applied Stochastic Processes, Chap. 3, John Wiley & Sons, New York.
Chou, K. C. (1997). Prediction of β-turns, J. Peptide Res. 49, 120–144.
Chou, K. C., and Zhang, C. T. (1995). Prediction of protein structural classes, Crit. Rev. Biochem. Mol. Biol. 30, 275–349.
Chou, P. Y., and Fasman, G. D. (1974). Conformational parameters for amino acids in helical, β-sheet and random coil regions calculated from proteins, Biochemistry, 13, 211–223.
Chou, P. Y., and Fasman, G. D. (1979). Prediction of β-turns, Biophys. J. 26, 367–384.
Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., and Fletterick, R. J. (1986). The prediction in proteins using a pattern-matching approach, Biochemistry, 25, 266–275.
Dyson, H. J., Rance, M., Houghten, R. A., Lerner, R. A., and Wright, P. E. (1988). Folding of immunogenic peptide fragments of proteins in water solution: I. Sequence requirements for the formation of a reverse turn, J. Mol. Biol. 201, 161–200.
Garnier, J., Osguthorpe, D. J., and Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins, J. Mol. Biol. 120, 97–120.
Herriott, J. R., Sieker, L. C., Jensen, L. H., and Lovenberg. W. (1970). Structure or rubredoxin. An x-ray study to 2.5 angstroms resolution, J. Mol. Biol. 50, 391–406.
Hutchinson, E. G., and Thornton, J. M. (1994). A revised set of potentials for β-turn formation in proteins, Protein Sci. 3, 2207–2216.
Kabsch, W., and Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577–2637.
Klein, P. (1986). Prediction of protein structural class by discriminant analysis, Biochem. Biophys. Acta 874, 205–215.
Lewis, P. N., Momany, F. A., and Scheraga, H. A. (1973). Chain reversals in proteins, Biochim. Biophys. Acta 303, 211–229.
Mardia, K. V., Kent, J. T., and Bibby, J. M. (1979). Multivariate Analysis, Academic Press, London, pp. 322, 381.
McGregor, M. J., Flores, T. P., and Sternberg, M. J. E. (1989). Prediction of β-turns in proteins using neural networks, Protein Eng 2, 521–526.
Richardson, J. S. (1981). The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34, 167–339.
Rose, G. D., Gierasch, L. M., and Smith, J. A. (1985). Turns in peptides and proteins, Adv. Protein Chem., 37, 1–109.
Venkatachalam, C. M. (1968). Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units, Biopolymers 6, 1425–1436.
Wilmot, C. M., and Thornton, J. M. (1988). Analysis and prediction of the different types of β-turn in proteins, J. Mol. Biol. 203, 221–232.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Chou, KC., Blinn, J.R. Classification and Prediction of β-Turn Types. J Protein Chem 16, 575–595 (1997). https://doi.org/10.1023/A:1026366706677
Published:
Issue Date:
DOI: https://doi.org/10.1023/A:1026366706677