Massey Steven E
Biology Department, University of South Florida, Tampa, FL, USA.
In Silico Biol. 2006;6(4):259-73.
Three aminoacyl-tRNA synthetases from yeast, one from plants and one from mammals possess unusual structures at their N termini, namely alpha helices with basic residues distributed asymmetrically, on a single face of the helix. It is unknown if these 'basic faced' alpha helices (BFAHs) are unique to the aminoacyl-tRNA synthetases. Analysis of the amino acid sequences of these five aminoacyl-tRNA synthetases using the hydrophobic moment algorithm failed to accurately identify the BFAHs. A new algorithm was therefore developed, called the 'basic moment'. This is a Fourier analysis procedure that predicts the distribution of basic residues within protein secondary structure. The basic moment identifies with a high degree of accuracy the five known BFAHs and also identifies further potential BFAHs at evolutionarily conserved positions in the peptide extensions of aspartyl-, lysyl- and valyl- tRNA synthetases from a range of eukaryotic species. In addition, the algorithm identifies the two-helix pair tRNA binding domain of alanyl-tRNA synthetase, implying that the domain includes a BFAH. The functional and evolutionary aspects of these structural features are discussed.
来自酵母的三种氨酰 - tRNA合成酶、来自植物的一种氨酰 - tRNA合成酶以及来自哺乳动物的一种氨酰 - tRNA合成酶在其N端具有不同寻常的结构，即α螺旋，其碱性残基在螺旋的单面上不对称分布。尚不清楚这些“碱性面”α螺旋（BFAH）是否为氨酰 - tRNA合成酶所特有。使用疏水矩算法对这五种氨酰 - tRNA合成酶的氨基酸序列进行分析，未能准确识别出BFAH。因此开发了一种新算法，称为“碱性矩”。这是一种傅里叶分析程序，可预测蛋白质二级结构内碱性残基的分布。碱性矩能高度准确地识别出五个已知的BFAH，还能识别出一系列真核生物中天冬氨酰 - 、赖氨酰 - 和缬氨酰 - tRNA合成酶肽段延伸中进化保守位置上的其他潜在BFAH。此外，该算法还识别出丙氨酰 - tRNA合成酶的双螺旋对tRNA结合结构域，这意味着该结构域包含一个BFAH。本文讨论了这些结构特征的功能和进化方面。
