蛋白质-核酸复合物界面氨基酸与核苷酸偏好性分析

蛋白质-核酸相互作用机制到目前还不是很清楚，尤其是蛋白质与RNA的相互作用。目前，可得到的蛋白质-核酸复合物结构数据不断增多，作者收集了Protein Data Bank数据库中所有的蛋白质-核酸复合物结构数据，对复合物中结合残基和结合核苷酸的偏好性进行了统计分析。发现：1）不同功能的蛋白质-核酸复合物间的结合残基数量存在显著差异；2）在蛋白 质-DNA和蛋白质-RNA复合物界面，碱性氨基酸都是最受欢迎的；3）氨基酸的极性大小及方向在决定它是否与RNA分子进行结合时起到重要的作用，同时发现氨基酸侧链形成的空间位阻会影响氨基酸残基与RNA分子的相互作用；4）随着定义结合残基距离阈值的增大，其氨基酸使用的特异性降低，而受欢迎与不受欢迎的氨基酸种类均没有变化。

Comprehensive Analysis of Propensities of Amino Acids and Nucleotides Usage at Protein-Nucleic Acid Interfaces

The mechanism of protein-nucleic acid interaction is still not very clear, especially that of protein-RNA interaction. Therefore, with the increase of available protein-nucleic acid complex structures in the protein data bank database, the authors have collected all the structures and then analyzed the rules controlling the recognition of residues by nucleotides using classical statistical methods. The results show that: 1) The number of nucleotide-binding residues presents significant differences among each kind of protein-nucleic acid complex structures with different functions; 2) The basic amino acids are the most popular in both protein-DNA and protein-RNA interactions; 3) The size and orientation of the polarity of amino acids play important roles in determining whether they are combined with RNA molecules, and the steric hindrances formed by the side chain of amino acids appear to influence the course of recognizing residues by nucleotides; 4) Specificity of amino acid usage for binding residues reduces while the threshold in defining of nucleotide-binding residues increases, however, there is no change in types of amino acid regardless of popular or unpopular ones.