Exploring the sequence patterns in the alpha-helices of proteins.

Junwen Wang, Jin-An Feng
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引用次数: 41

Abstract

This paper reports an extensive sequence analysis of the alpha-helices of proteins. alpha-Helices were extracted from the Protein Data Bank (PDB) and were divided into groups according to their sizes. It was found that some amino acids had differential propensity values for adopting helical conformation in short, medium and long alpha-helices. Pro and Trp had a significantly higher propensity for helical conformation in short helices than in medium and long helices. Trp was the strongest helix conformer in short helices. Sequence patterns favoring helical conformation were derived from a neighbor-dependent sequence analysis of proteins, which calculated the effect of neighboring amino acid type on the propensity of residues for adopting a particular secondary structure in proteins. This method produced an enhanced statistical significance scale that allowed us to explore the positional preference of amino acids for alpha-helical conformations. It was shown that the amino acid pair preference for alpha-helix had a unique pattern and this pattern was not always predictable by assuming proportional contributions from the individual propensity values of the amino acids. Our analysis also yielded a series of amino acid dyads that showed preference for alpha-helix conformation. The data presented in this study, along with our previous study on loop sequences of proteins, should prove useful for developing potential 'codes' for recognizing sequence patterns that are favorable for specific secondary structural elements in proteins.

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探索蛋白质α螺旋的序列模式。
本文报道了蛋白质α螺旋的广泛序列分析。从蛋白质数据库(PDB)中提取α -螺旋,并根据其大小进行分组。研究发现,某些氨基酸在短、中、长α -螺旋构象上具有不同的倾向值。Pro和Trp在短螺旋上的螺旋构象倾向明显高于中螺旋和长螺旋。在短螺旋中,Trp是最强的螺旋构象。有利于螺旋构象的序列模式是从蛋白质的邻接依赖序列分析中得到的,该分析计算了邻近氨基酸类型对蛋白质中残基采用特定二级结构的倾向的影响。这种方法产生了一个增强的统计显著性量表,使我们能够探索氨基酸对α -螺旋构象的位置偏好。结果表明,氨基酸对α -螺旋的偏好具有独特的模式,这种模式并不总是通过假设氨基酸个体倾向值的比例贡献来预测。我们的分析也产生了一系列的氨基酸二联体,显示出偏爱α -螺旋构象。本研究中提供的数据,以及我们之前对蛋白质环序列的研究,应该证明有助于开发潜在的“代码”,以识别有利于蛋白质中特定二级结构元件的序列模式。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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