同义密码子使用的网络分析
Network analysis of synonymous codon usage
摘要：
大多数氨基酸由多个同义密码子编码。对于一个氨基酸，它的一些同义密码子比其他密码子使用得更少。对这些稀有密码子在蛋白质序列中的位置分析表明，稀有密码子可以影响共翻译蛋白质折叠，并且一些稀有密码子的位置是进化保守的。蛋白质三维结构中稀有密码子的位置比单独的序列具有更丰富的生物化学信息，分析稀有密码子在蛋白质三维结构中的位置可能进一步解释稀有密码子在蛋白质折叠中的作用。我们分析了一组最近注释密码子使用信息的蛋白质，考虑到非冗余蛋白质有足够的结构信息。我们将蛋白质的结构建模为网络，并研究由进化保守的稀有、进化非保守的稀有和常用密码子编码的氨基酸的网络位置之间的潜在差异。在84%的蛋白质中，三种密码子类别中的至少一种比其他密码子类别占据更多或更少的网络中心位置。显示不同密码子中心性趋势的不同蛋白质组（即，三种密码子类别的网络位置之间的不同类型的关系）在不同的生物学功能中富集，这意味着密码子使用、蛋白质折叠和蛋白质功能之间存在联系。
英文摘要：
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionary conserved. Analyses of positions of rare codons in proteins' 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. We analyze a protein set recently annotated with codon usage information, considering non-redundant proteins with sufficient structural information. We model the proteins' structures as networks and study potential differences between network positions of amino acids encoded by evolutionary conserved rare, evolutionary non-conserved rare, and commonly used codons. In 84% of the proteins, at least one of the three codon categories occupies significantly more or less network-central positions than the other codon categories. Different protein groups showing different codon centrality trends (i.e., different types of relationships between network positions of the three codon categories) are enriched in different biological functions, implying the existence of a link between codon usage, protein folding, and protein function.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
