Abstract
The conformational parametersP k for each amino acid species (j=1–20) of sequential peptides in proteins are presented as the product ofP i,k, wherei is the number of the sequential residues in thekth conformational state (k=α-helix,Β-sheet,Β-turn, or unordered structure). Since the average parameter for ann-residue segment is related to the average probability of finding the segment in the kth state, it becomes a geometric mean of (P k)av=π(P i,k)1/n with amino acid residuei increasing from 1 ton. We then used ln(Pk)av to convert a multiplicative process to a summation, i.e., ln(P k)av=(1/n)⌆P i,k (i=1 ton) for ease of operation. However, this is unlike the popular Chou-Fasman algorithm, which has the flaw of using the arithmetic mean for relative probabilities. The Chou-Fasman algorithm happens to be close to our calculations in many cases mainly because the difference between theirP k and our InP k is nearly constant for about one-half of the 20 amino acids. When stronger conformation formers and breakers exist, the difference become larger and the prediction at the N- and C-terminalα-helix orΒ-sheet could differ. If the average conformational parameters of the overlapping segments of any two states are too close for a unique solution, our calculations could lead to a different prediction.
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Chou, P. Y. (1979). New approaches to protein structural analysis and conformational prediction, inRapport d'Activité Scientifique du CECAM, Orsay, pp. 149–216.
Chou, P. Y. (1989). Prediction of protein structural classes from amino acid compositions, inPrediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), Plenum Press, New York, pp. 549–586.
Chou, P. Y., and Fasman, G. D. (1974a). Conformational parameters for amino acids in helical,Β-σηεεΤ, and random coil regions calculated from proteins.Biochemistry 13, 211–222.
Chou, P. Y., and Fasman, G. D., (1974a). Prediction of protein conformation,Biochemistry 13, 222–245.
Chou, P. Y., and Fasman, G. D. (1977).Β-turns in proteins,J. Mol. Biol. 115, 135–175.
Chou, P. Y., and Fasman, G. D. (1978a). Prediction of the secondary structure of proteins from their amino acid sequence,Adv. Enzymol. 47, 45–148.
Chou, P. Y., and Fasman, G. D. (1978b). Empirical prediction of protein conformation,Annu. Rev. Biochem. 47, 251–276.
Fasman, G. D., ed. (1989a).Prediction of Protein Structure and the Principles of Protein Conformation, Plenum Press, New York.
Fasman, G. D. (1989b). The development of the prediction of protein structure, inPrediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), Plenum Press, New York, pp. 193–316.
Garnier, J., and Robson, B. (1989). The GOR method for predicting secondary structures in proteins, inPrediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), Plenum Press, New York, pp. 417–465.
Garnier, J., Osguthorpe, D. J., and Robson, B. (1978). Analysis of the accuracy and implication of simple methods for predicting the secondary structure of globular proteins,J. Mol. Biol. 120, 97–120.
Lim, V. I. (1974a). Structural principles of the globular organization of protein chains: A stereochemical theory of globular protein secondary structure,J. Mol. Biol. 88, 857–872.
Lim, V. I. (1974b). Algorithms for prediction ofα-helices andΒ-structure in globular proteins,J. Mol. Biol. 88, 873–894.
Mathews, C. K., and van Holde, K. E., (1990).Biochemistry, Benjamin/Cummings, Redwood City, California.
Prevelige, P., Jr., and Fasman, G. D., (1989). Chou-Fasman prediction of the secondary structure of proteins. The Chou-Fasman-Prevelige algorithm, inPrediction of Protein Structure and the Principles of Protein Conformation (Fasman, G. D., ed.), Plenum Press, New York, pp. 391–416.
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Yang, J.T. Prediction of protein secondary structure from amino acid sequence. J Protein Chem 15, 185–191 (1996). https://doi.org/10.1007/BF01887399
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DOI: https://doi.org/10.1007/BF01887399