麻疯树核糖体失活蛋白Curcin和Curcin C与腺苷及腺嘌呤的互作方式分析

Analysis of the interaction modes of Jatropha curcas ribosome inactivating proteins Curcin and Curcin C with adenosine and adenine

摘要:

麻疯树核糖体失活蛋白Curcin和Curcin C均具N-糖苷酶活性，然而两者的体外翻译抑制能力却具有明显差异，这暗示着两者的N-糖苷酶活性也存在差异.为了探究造成这一差异的结构基础，本研究使用trRosetta对两种蛋白进行了三级结构的预测，通过PROCHECK和Qmean对预测得到的三级结构模型进行了质量评估，利用Chem3D对小分子配体腺嘌呤和腺苷进行了结构优化,借助UCSF Chimera对Curcin及Curcin C活性位点的氨基酸组成进行了预测.最终使用分子对接软件AutoDock将预测得到的模型与小分子腺嘌呤及腺苷进行分子对接.对接结果显示，两种蛋白与腺嘌呤的相互作用模式具有较高的相似性，但Curcin的关键氨基酸Arg并未参与到与配体的相互作用.此外Curcin C与腺嘌呤和腺苷之间的结合能都低于Curcin，且其和腺苷与腺嘌呤之间结合能的差值也要高于Curcin. 这一结果暗示着Curcin和Curcin C之间的活性差异与其活性位点处的结构特征有关，Curcin C中的关键氨基酸Arg与腺嘌呤及腺苷的结合位点更为靠近，从而导致Curcin C与底物之间的结合能更低，更有利于催化反应的进行.

Abstract:

Jatropha curcas ribosome-inactivating proteins Curcin and Curcin C have N-glycosidase activity, but their in vitro translation inhibition ability is significantly different, which implies that there are also differences in the N-glycosidase activity of the two proteins. In order to explore the structural basis for this difference, this study used trRosetta to predict the tertiary structure of the two proteins, and evaluates the quality of the predicted tertiary structure model through PROCHECK and Qmean.The structure of adenine and adenosine was optimized by Chem3D, and the amino acid composition of Curcin and Curcin C active site was predicted by UCSF Chimera.Finally, AutoDock was used for molecular docking to predict the interaction of two protein model with adenine and adenosine. The docking results showed that the interaction modes between the two proteins and adenine were similar, but the key amino acid Arg of Curcin did not participate in the interaction with the ligand. In addition, the binding energy of Curcin C to adenine and adenosine is lower than that of Curcin, and the difference between the binding energy of Curcin C to adenosine and adenine is also higher than that of Curcin.This result implies that the difference in activity between Curcin and Curcin C is related to the structural features at the active site, and the key amino acid Arg in Curcin C is closer to the binding sites of adenine and adenosine.This will lead to lower binding energy between Curcin C and the substrate, which is more conducive to the catalytic reaction.