Kim Hyunwoo, Jeong Euna, Lee Seong-Wook, Han Kyungsook
School of Computer Science and Engineering, Inha University, 402-751 Inchon, South Korea.
FEBS Lett. 2003 Sep 25;552(2-3):231-9. doi: 10.1016/s0014-5793(03)00930-x.
Structural analysis of protein-RNA complexes is labor-intensive, yet provides insight into the interaction patterns between a protein and RNA. As the number of protein-RNA complex structures reported has increased substantially in the last few years, a systematic method is required for automatically identifying interaction patterns. This paper presents a computational analysis of the hydrogen bonds in the most representative set of protein-RNA complexes. The analysis revealed several interesting interaction patterns. (1) While residues in the beta-sheets favored unpaired nucleotides, residues in the helices showed no preference and residues in turns favored paired nucleotides. (2) The backbone hydrogen bonds were more dominant than the base hydrogen bonds in the paired nucleotides, but the reverse was observed in the unpaired nucleotides. (3) The protein-RNA complexes contained more paired nucleotides than unpaired nucleotides, but the unpaired nucleotides were observed more frequently interacting with the proteins. And (4) Arg-U, Thr-A, Lys-A, and Asn-U were the most frequently observed pairs. The interaction patterns discovered from the analysis will provide us with useful information in predicting the structure of the RNA binding protein and the structure of the protein binding RNA.
蛋白质-RNA复合物的结构分析工作强度大，但能深入了解蛋白质与RNA之间的相互作用模式。随着过去几年报道的蛋白质-RNA复合物结构数量大幅增加，需要一种系统方法来自动识别相互作用模式。本文对最具代表性的一组蛋白质-RNA复合物中的氢键进行了计算分析。分析揭示了几种有趣的相互作用模式。（1）β折叠中的残基倾向于未配对的核苷酸，而螺旋中的残基没有偏好，转角处的残基则倾向于配对的核苷酸。（2）在配对核苷酸中，主链氢键比碱基氢键更占主导，但在未配对核苷酸中则观察到相反的情况。（3）蛋白质-RNA复合物中配对核苷酸比未配对核苷酸多，但观察到未配对核苷酸与蛋白质相互作用的频率更高。并且（4）精氨酸-尿嘧啶、苏氨酸-腺嘌呤、赖氨酸-腺嘌呤和天冬酰胺-尿嘧啶是最常观察到的配对。从分析中发现的相互作用模式将为我们预测RNA结合蛋白的结构和蛋白质结合RNA的结构提供有用信息。
