蛋白质环区序列结构关系的综合分析。

Shugo Nakamura, K. Shimizu
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引用次数: 0

摘要

利用基于支持向量回归(SVR)的简单预测工具,对蛋白质环区局部序列结构关系进行综合估计。选取端到端距离作为片段的粗略结构属性,利用支持向量回归算法从序列信息中直接预测大量来自多种蛋白质折叠的环状片段的端到端距离。我们发现我们的方法在预测包含5、9和17个氨基酸的片段的结构时比随机预测更准确;此外,从序列上可以很好地区分出延伸的环状片段与转弯结构,这表明对于端到端距离较大的环状片段,序列-结构关系是显著的。这些结果表明,许多环区以及螺旋和链在一定程度上限制了蛋白质整个三级结构的构象空间;此外,我们的研究结果揭示了蛋白质折叠的机制和蛋白质三级结构的预测,而不使用结构模板。
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Comprehensive analysis of sequence-structure relationships in the loop regions of proteins.
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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