Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
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DOI：
10.1093/bioinformatics/bth297
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发表时间：
2004-11-01
期刊：
影响因子：
5.8
通讯作者：
Nishikawa, K
中科院分区：
文献类型：
--
作者：
Kinjo, AR;Nishikawa, K
氨基酸取代和序列保守的模式在许多基于结构的蛋白质序列比对分析作为百分比序列同一性的函数。将氨基酸取代的统计量转换成对数优势氨基酸取代矩阵的形式，并对其应用特征值分解。结果发现，取代矩阵的最重要的组分在30- 35%的序列同一性处表现出急剧的转变，这与过渡区相一致。在过渡点以上，最主要的组分与氨基酸的可变性有关，并且其作用不利于任何取代，而在过渡点以下，最主要的组分与氨基酸的疏水性有关，并且具有相似疏水特性的残基之间的取代是积极有利的。蛋白质进化和序列分析的影响进行了讨论。
The pattern of amino acid substitutions and sequence conservation over many structure-based alignments of protein sequences was analyzed as a function of percentage sequence identity. The statistics of the amino acid substitutions were converted into the form of log-odds amino acid substitution matrices to which eigenvalue decomposition was applied. It was found that the most important component of the substitution matrices exhibited a sharp transition at the sequence identity of 30-35%, which coincides with the twilight zone. Above the transition point, the most dominant component is related to the mutability of amino acids and it acts to disfavor any substitutions, whereas below the transition point, the most dominant component is related to the hydrophobicity of amino acids and substitutions between residues of similar hydrophobic character are positively favored. Implications for protein evolution and sequence analysis are discussed.