The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching history of the two aminoacyl-tRNA synthetase (aaRS) superfamilies. The evolutionary expansion of the genetic code is described by a simple parameterization of the aaSM, in which (i) the number of distinguishable amino acid types, (ii) the matrix dimension and (iii) the number of parameters, each increases by one for each bifurcation in an aaRS phylogeny. Parameterized matrices corresponding to trees in which the size of an amino acid sidechain is the only discernible property behind its categorization as a substrate, exclusively for a Class I or II aaRS, provide a significantly better fit to empirically determined aaSM than trees with random bifurcation patterns. A second split between polar and nonpolar amino acids in each Class effects a vastly greater further improvement. The earliest Class-separated epochs in the phylogenies of the aaRS reflect these enzymes' capability to distinguish tRNAs through the recognition of acceptor stem identity elements via the minor (Class I) and major (Class II) helical grooves, which is how the ancient operational code functioned. The advent of tRNA recognition using the anticodon loop supports the evolution of the optimal map of amino acid chemistry found in the later genetic code, an essentially digital categorization, in which polarity is the major functional property, compensating for the unrefined, haphazard differentiation of amino acids achieved by the operational code.

中文翻译：

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古代操作代码嵌入在氨基酸替代矩阵和aaRS系统发生中。

通过考虑在两个氨基酰基-tRNA合成酶（aaRS）超家族的分支历史过程中，根据氨基酸的化学特性逐步改善氨基酸的差异识别，来研究规范氨基酸替换矩阵（aaSM）的基础结构。遗传密码的进化扩展是通过aaSM的简单参数化来描述的，其中（i）可区分的氨基酸类型的数量，（ii）基质尺寸和（iii）参数的数量，对于aaRS系统发育中的每个分叉。对应于树木的参数化矩阵，其中氨基酸侧链的大小是其仅作为I或II类aaRS归类为底物后唯一可识别的特性，与具有随机分叉模式的树相比，根据经验确定的aaSM可以提供更好的拟合度。每个类别中极性和非极性氨基酸之间的第二次拆分产生了更大的进一步改进。在aaRS的系统发育中最早的以类分隔的时期反映了这些酶通过通过次要（I类）和主要（II类）螺旋凹槽识别受体茎身份元素来区分tRNA的能力，这就是古代的操作方式。代码起作用。使用反密码子环的tRNA识别技术的出现支持了后来的遗传密码（基本上是数字分类）中氨基酸化学的最佳图谱的进化，其中极性是主要的功能特性，弥补了未精制的，