黑曲霉α-L-鼠李糖苷酶Rha1的二级结构预测及三级结构模拟

Secondary Structure Prediction and Three-dimensional Structure Simulation of the Recombinant α-L-Rhamnosidase Rha1

摘要:

本文研究了酶的结构，有利于进一步了解酶的功能，通过对α-L-鼠李糖苷酶Rha1二级结构分析及三级结构模拟，为该酶进行理性设计提供基础。采用GORⅢ、PHD等九个二级结构预测方法对Rha1的二级结构进行分析和预测。结果显示，Rha1二级结构为 23.51% α-螺旋，29.77% β-折叠，46.71%无规则卷曲，具有一个与GH78家族相似的(α/α)6桶状结构域及两个β三明治折叠片结构域。利用Swiss-Model以单模板建模的方法构建了Rha1的三维结构模型。根据二级结构的结果，将Rha1分为三个结构域，利用Modeller 9.15以多模板分段建模、结构域拼接的方法构建了该酶的三维结构模型，并对其进行能量最小化优化。利用Ramachandran图以及Verify_3D评估对两种方法构建得到的Rha1的三维结构模型进行评价，其中Swiss-Model构建得到的模型未通过评价，Modeller 9.15构建得到的Rha1的三维模型结构合理，通过评价。α-L-鼠李糖苷酶Rha1模型的构建为今后深入研究该酶的结构与功能奠定了基础。

Abstract:

Exploration of enzyme structure can provide a better understanding of enzyme functions. This study aimed to analyze the secondary and tertiary structures of the α-L-rhamnosidase Rha1 and provide a basis for the rational design of this enzyme. Nine secondary structure prediction methods, including GORⅢ and PHD, were used to analyze and predict the secondary structure of Rha1. The results showed that Rha1 was composed of 23.51% α-helix, 29.77% β-sheet, and 46.71% random coil. Rha1 included three domains: a (α/α)6 barrel structure, similar to that of the GH78 family, and two β-sandwich domains. The Swiss-Model was used to simulate the three-dimensional structure of Rha1 with a single template. The results showed that Rha1 was divided into three domains. Modeller 9.15 was used to construct the three-dimensional structure of r-Rha1 with multi-template segment modeling and domain splicing. The new simulated r-Rha1 three-dimensional structure was optimized by energy minimization. The two models simulated using Swiss-Model and Modeller 9.15 were evaluated by Ramachandran plot and verify-3D, respectively. The results showed that the model simulated by Swiss-Model was not qualified, whereas the model simulated by Modeller 9.15 had a reasonable structure and passed the assessment. The construction of an α-L-rhamnosidase Rha1 model establishes a foundation for the further study of the structure and biological function of α-L-rhamnosidase Rha1.