Type I and II [beta]-turns prediction using NMR chemical shifts

• Published in: Journal of biomolecular NMR Vol. 59; no. 3; p. 175
• Main Authors: Wang, Ching-cheng, Lai, Wen-chung, Chuang, Woei-jer
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Nature B.V 01.07.2014
• Subjects: Correlation coefficient; NMR; Nuclear magnetic resonance; Statistical analysis
• ISSN: 0925-2738; 1573-5001
• DOI: 10.1007/s10858-014-9837-z

A method for predicting type I and II [beta]-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated [beta]-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes [beta]-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (i + 3). Considering the central two residues of type I [beta]-turns, the mean values of C^sub [omicron]^, C^sub [alpha]^, H^sub N^, and N^sub H^ chemical shifts were generally (i + 1) > (i + 2). The mean values of C^sub [beta]^ and H^sub [alpha]^ chemical shifts were (i + 1) < (i + 2). The distributions of the central two residues in type II and VIII [beta]-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 [beta]-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 [beta]-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 [beta]-turn types in proteins. The proposed method can be incorporated into other chemical-shift based protein secondary structure prediction methods.[PUBLICATION ABSTRACT]