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