In the regime of domain classifications, the protein universe unveils a discrete set of folds connected by hierarchical relationships. Instead, at sub-domain-size resolution and because of physical constraints not necessarily requiring evolution to shape polypeptide chains, networks of protein motifs depict a continuous view that lies beyond the extent of hierarchical classification schemes. A number of studies, however, suggest that universal sub-sequences could be the descendants of peptides emerged in an ancient pre-biotic world. Should this be the case, evolutionary signals retained by structurally conserved motifs, along with hierarchical features of ancient domains, could sew relationships among folds that diverged beyond the point where homology is discernable. In view of the aforementioned, this paper provides a rationale where a network with hierarchical and continuous levels of the protein space, together with sequence profiles that probe the extent of sequence similarity and contacting residues that capture the transition from pre-biotic to domain world, has been used to explore relationships between ancient folds. Statistics of detected signals have been reported. As a result, an example of an emergent sub-network that makes sense from an evolutionary perspective, where conserved signals retrieved from the assessed protein space have been co-opted, has been discussed.

中文翻译：

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对蛋白质宇宙中进化关系的微调探索

在域分类的体系中，蛋白质宇宙揭示了一组由层次关系连接的离散折叠。相反，在子域大小的分辨率下，并且由于物理限制不一定需要进化来形成多肽链，蛋白质基序网络描绘了一个超出层次分类方案范围的连续视图。然而，许多研究表明，通用子序列可能是古代前生物世界中出现的肽的后代。如果是这种情况，结构上保守的基序保留的进化信号，以及古代领域的层次特征，可以缝合折叠之间的关系，这些折叠超出了同源性可辨别的点。鉴于上述情况，本文提供了一个基本原理，其中具有蛋白质空间的分层和连续级别的网络，以及探测序列相似性程度的序列图谱和捕捉从前生物到域世界的过渡的接触残基，已被用于探索关系古老的褶皱之间。已报告检测到的信号的统计数据。因此，已经讨论了一个从进化的角度来看有意义的新兴子网络的例子，其中从评估的蛋白质空间中检索到的保守信号已被选择。已被用来探索古代褶皱之间的关系。已报告检测到的信号的统计数据。因此，已经讨论了一个从进化的角度来看有意义的新兴子网络的例子，其中从评估的蛋白质空间中检索到的保守信号已被选择。已被用来探索古代褶皱之间的关系。已报告检测到的信号的统计数据。因此，已经讨论了一个从进化的角度来看有意义的新兴子网络的例子，其中从评估的蛋白质空间中检索到的保守信号已被选择。