摘要
本文对来自PDB (Protein Data Bank)数据库的蛋白质-RNA复合物结构构建了非冗余非核糖体数据库(694个结构),并对此数据库统计了蛋白质和RNA序列及二级结构的界面偏好性.结果发现,蛋白质β折叠、310-helix和RNA未配对核苷酸,尤其是未配对中空间排列不规整的核苷酸,具有显著的界面偏好性.据此,对二级结构进行归类,建立了考虑序列和二级结构信息的60×12氨基酸-核苷酸成对偏好势,并将其作为打分函数用于蛋白质-RNA对接中近天然结构的筛选.结果表明,该60×12统计势的打分成功率为65.77%,优于考虑蛋白质或RNA二级结构信息的统计势,及我们小组之前在251个结构上构建的60×8*统计势.该工作有助于加深对蛋白质-RNA特异性识别的理解,可推动复合物结构预测的进展.
We constructed a non-redundant non-ribosomal protein-RNA interface dataset(including 694 structures) from the Protein Data Bank(PDB). The interface preferences of amino acids, nucleotides and the secondary structure elements of protein and RNA were computed based on the dataset. The results show that β-ladder, β-bridge and 310-helix of proteins and the unpaired nucleotides of RNA, especially those irregularly arranged nucleotides have remarkably high interface propensities. Based on these, we classified the secondary structure elements, constructed the 60×12 amino acid-nucleotide pairwise potential, and used it as a scoring function in protein-RNA docking to select the near native structures. The results show the 60×12 pairwise potential has a scoring success rate of 65.77%, better than those of the pairwise potentials with secondary structure information of protein or RNA considered, as well as better than that of our previously constructed 60×8* potential based on the 251 protein-RNA complex structures. This work is helpful for strengthening the understanding of protein-RNA specific interactions and can advance the progress of protein-RNA complex structure prediction.
作者
陆林
刘洋
李春华
LU Lin;LIU Yang;LI Chun-Hua(Faculty of Environmental and Life Sciences,Beijing University of Technology,Beijing 100124,China)
出处
《生物化学与生物物理进展》
SCIE
CAS
CSCD
北大核心
2020年第7期634-644,共11页
Progress In Biochemistry and Biophysics
基金
国家自然科学基金(31971180,11474013)
北京市自然科学基金(4152011)资助项目~~。
