Oresic M, Shalloway D
Section of Biochemistry Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA.
J Mol Biol. 1998 Aug 7;281(1):31-48. doi: 10.1006/jmbi.1998.1921.
We found significant species-specific correlations between the use of two synonymous codons and protein secondary structure units by comparing the three-dimensional structures of human and Escherichia coli proteins with their mRNA sequences. The correlations are not explained by codon-context, expression level, GC/AU content, or positional effects. The E. coli correlation is between Asn AAC and the C-terminal regions of beta-sheet segments; it may result from selection for translational accuracy, suggesting the hypothesis that downstream Asn residues are important for beta-sheet formation. The correlation in human proteins is between Asp GAU and the N termini of alpha-helices; it may be important for eukaryote-specific sequential, cotranslational folding. The kingdom-specific correlations may reflect kingdom-specific differences in translational mechanisms. The correlations may help identify residues that are important for secondary structure formation, be useful in secondary structure prediction algorithms, and have implications for recombinant gene expression.
通过比较人类和大肠杆菌蛋白质的三维结构及其mRNA序列，我们发现两种同义密码子的使用与蛋白质二级结构单元之间存在显著的物种特异性相关性。这些相关性无法用密码子上下文、表达水平、GC/AU含量或位置效应来解释。大肠杆菌中的相关性存在于Asn AAC与β-折叠片段的C末端区域之间；这可能是由于对翻译准确性的选择导致的，这表明了一个假设，即下游的Asn残基对β-折叠的形成很重要。人类蛋白质中的相关性存在于Asp GAU与α-螺旋的N末端之间；这可能对真核生物特有的顺序共翻译折叠很重要。特定王国的相关性可能反映了翻译机制中特定王国的差异。这些相关性可能有助于识别对二级结构形成重要的残基，在二级结构预测算法中有用，并对重组基因表达有影响。
