Comprehensive Analysis of Sequence-Structure Relationships in the Loop Regions of Proteins

Shugo Nakamura (
Kentaro Shimizu (

Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi,Bunkyo-ku, Tokyo 113-8657, Japan


Local sequence-structure relationships in the loop regions of proteins were comprehensively estimated using simple prediction tools based on support vector regression (SVR). End-to-end distance was selected as a rough structural property of fragments, and the end-to-end distances of an enormous number of loop fragments from a wide variety of protein folds were directly predicted from sequence information by using SVR. We found that our method was more accurate than random prediction for predicting the structure of fragments comprising 5, 9, and 17 amino acids; moreover, the extended loop fragments could be successfully distinguished from turn structures on the basis of their sequences, which implies that the sequence-structure relationships were significant for loop fragments with a wide range of end-to-end distances. These results suggest that many loop regions as well as helices and strands restrict the conformational space of the entire tertiary structure of proteins to some extent; moreover, our findings throw light on the mechanism of protein folding and prediction of the tertiary structure of proteins without using structural templates.

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Japanese Society for Bioinformatics