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Classification and Prediction of β-Turn Types (1997)

Chou, Kou-Chen ; Blinn, James R.

Springer

The protein journal 16 (1997), S. 575-595

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ISSN: 1573-4943

Keywords: Residue-coupled model ; resubstitution ; jackknife

Source: Springer Online Journal Archives 1860-2000

Topics: Chemistry and Pharmacology

Notes: 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.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1026366706677

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Prediction of β-turns in proteins by 1-4 and 2-3 correlation model (1997)

Zhang, Chun-Ting ; Chou, Kou-Chen

New York : Wiley-Blackwell

Biopolymers 41 (1997), S. 673-702

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ISSN: 0006-3525

Keywords: protein folding ; coupling effect ; Chemistry ; Polymer and Materials Science

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology

Notes: A 1-4 and 2-3 residue-correlation model is proposed to predict the β-turns in proteins. The average rate of correct prediction for the 455 β-turn tetrapeptides and 4018 non-β-turn tetrapeptides in the training data base is 80.1%, and that for the 223 β-turn tetrapeptides and 12562 non-β-turn tetrapeptides in the testing data base is 80.9%. Compared with the rates of correct prediction based on the residue-independent model reported previously, the quality of prediction is significantly improved by the new model, implying that the correlation effect between the 1st and the 4th residues and that between the 2nd and 3rd residues along a tetrapeptide are important for forming a β-turn in a protein during the process of its folding. © 1997 John Wiley & Sons, Inc. Biopoly 41: 673-702, 1997

Additional Material: 4 Tab.

Type of Medium: Electronic Resource

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Prediction and classification of α-turn types (1997)

Chou, Kou-Chen

New York : Wiley-Blackwell

Biopolymers 42 (1997), S. 837-853

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ISSN: 0006-3525

Keywords: residue-coupled model ; resubstitution ; jackknife ; Chemistry ; Polymer and Materials Science

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology

Notes: Tight turns play an important role in globular proteins from both the structural and functional points of view. Of tight turns, β-turns and γ-turns have been extensively studied, but α-turns were little investigated. Recently, a systematic search for α-turns was conducted by V. Pavone et al. [(1996) Biopolymers, Vol. 38, pp. 705-721] from 190 proteins (221 protein chains). They found 356 α-turns that were classified into nine different types according to their backbone trajectory features. In view of this new discovery, a sequence-coupled model based on Markov chain theory is proposed for predicting the α-turn types in proteins. The high rates of correct prediction by resubstitution test and jackknife test imply that that the formation of different α-turn types is evidently correlated with the sequence of a pentapeptide, and hence can be approximately predicted based on the sequence information of the pentapeptide alone, although the role of its interaction with the other part of a protein cannot be completely ignored. The algorithm presented here can also be used to conduct the prediction in which a distinction between α-turns and non-α-turns is also required. © 1997 John Wiley & Sons, Inc. Biopoly 42: 837-853, 1997

Additional Material: 6 Ill.

Type of Medium: Electronic Resource

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