Type i and II β-turns prediction using NMR chemical shifts

Ching Cheng Wang, Wen Chung Lai, Woei-Jer Chuang

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

A method for predicting type I and II β-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated β-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes β-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (i + 3). Considering the central two residues of type I β-turns, the mean values of Cο, Cα, HN, and NH chemical shifts were generally (i + 1) > (i + 2). The mean values of C β and Hα chemical shifts were (i + 1) < (i + 2). The distributions of the central two residues in type II and VIII β-turns were also distinguishable by trends of chemical shift values. Two-dimensional cluster analyses on chemical-shift data show positional distributions more clearly. Based on these propensities of chemical shift classified as a function of position, rules were derived using scoring matrices for four consecutive residues to predict type I and II β-turns. The proposed method achieves an overall prediction accuracy of 83.2 and 84.2 % with the Matthews correlation coefficient values of 0.317 and 0.632 for type I and II β-turns, indicating that its higher accuracy for type II turn prediction. The results show that it is feasible to use NMR chemical shifts to predict the β-turn types in proteins. The proposed method can be incorporated into other chemical-shift based protein secondary structure prediction methods.

Original languageEnglish
Pages (from-to)175-184
Number of pages10
JournalJournal of Biomolecular NMR
Volume59
Issue number3
DOIs
Publication statusPublished - 2014 Jan 1

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Chemical shift
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Secondary Protein Structure
Cluster Analysis
Proteins

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

Cite this

Wang, Ching Cheng ; Lai, Wen Chung ; Chuang, Woei-Jer. / Type i and II β-turns prediction using NMR chemical shifts. In: Journal of Biomolecular NMR. 2014 ; Vol. 59, No. 3. pp. 175-184.
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Type i and II β-turns prediction using NMR chemical shifts. / Wang, Ching Cheng; Lai, Wen Chung; Chuang, Woei-Jer.

In: Journal of Biomolecular NMR, Vol. 59, No. 3, 01.01.2014, p. 175-184.

Research output: Contribution to journalArticle

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