Department of Chemistry, University of Nebraska-Lincoln, 68588-0304, United States.
Comput Biol Chem. 2011 Feb;35(1):24-33. doi: 10.1016/j.compbiolchem.2010.12.004. Epub 2011 Jan 18.
Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As expected, the analysis demonstrates a sharp structural divergence between the bacterial phyla Firmicutes and Proteobacteria. Additionally, each COG had a distinct sequence/structure relationship, indicating that different evolutionary pressures affect the degree of structural divergence. However, our analysis also shows the relative drift rate between sequence identity and structure divergence remains constant.
与蛋白质折叠空间相比，蛋白质序列空间是巨大的。这就提出了一个重要的问题，即结构如何适应蛋白质序列的进化变化。一种日益增长的趋势是将蛋白质折叠空间视为连续体，而不是离散结构的系列。从这个角度来看，同一功能分类内的同源蛋白质结构应该相对于序列变化显示出恒定的结构漂移速率。共同源群（COG）分类系统用于注释蛋白质数据库（PDB）中的同源细菌蛋白质结构。比较每个 COG 中的蛋白质结构和序列，以确定它们的相关性。正如预期的那样，该分析表明细菌门Firmicutes 和 Proteobacteria 之间存在明显的结构分歧。此外，每个 COG 都有独特的序列/结构关系，表明不同的进化压力会影响结构分歧的程度。然而，我们的分析还表明，序列同一性和结构分歧之间的相对漂移率保持不变。
