Evolution of protein structural classes and protein sequence families
Evolution of protein structural classes and protein sequence families
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DOI：
10.1073/pnas.0606239103
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发表时间：
2006-09-19
影响因子：
11.1
通讯作者：
Kim, Sung-Hou
中科院分区：
文献类型：
--
作者：
Choi, In-Geol;Kim, Sung-Hou
在蛋白质结构空间中，当仅基于3D结构之间的相似性进行映射时，蛋白质结构聚集成四个拉长区域。这四个区域对应于由二级结构类型的含量及其拓扑排列定义的四大类现代蛋白质。这四种类型的进化和限制表明，在大多数情况下，基因的进化可能被限制或选择为那些导致结构稳定的蛋白质占据蛋白质结构空间四个“允许”区域之一的遗传变化，即“结构选择”，这是基因进化中自然选择的重要组成部分。我们对每个已知结构的蛋白质序列家族的“共同结构祖先”的追踪研究表明：(I)最近出现的蛋白质主要属于三类；(Ii)较早出现的蛋白质进化成一个新的类；(Iii)最早出现的蛋白质进化成为四大类中的现代蛋白质，第四类蛋白质成为最主要的种群。此外，我们的研究还表明，并不是所有的现代蛋白质都是从最后一个共同祖先有机体中的一组蛋白质进化而来的，而是新的共同祖先蛋白质是在不同的进化时间“诞生”的，不能追溯到一两个祖先蛋白质：蛋白质序列家族进化的“多胎模式”。
In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, the evolution of genes may have been constrained or selected to those genetic changes that results in structurally stable proteins occupying one of the four "allowed" regions of the protein structure space, "structural selection," an important component of natural selection in gene evolution. Our studies on tracing the "common structural ancestor" for each protein sequence family of known structure suggest that: (i) recently emerged proteins belong mostly to three classes; (ii) the proteins that emerged earlier evolved to gain a new class; and (iii) the proteins that emerged earliest evolved to become the present-day proteins in the four major classes, with the fourth-class proteins becoming the most dominant population. Furthermore, our studies also show that not all present-day proteins evolved from one single set of proteins in the last common ancestral organism, but new common ancestral proteins were "born" at different evolutionary times, not traceable to one or two ancestral proteins: "the multiple birth model" for the evolution of protein sequence families.