Secondary Structure Prediction and Three-dimensional Structure Simulation of the Recombinant α-L-Rhamnosidase Rha1
WU Zhe-yu
YU Yue
GONG Jian-ye
LI Li-jun
NI Hui
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 Rhal 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 Rha 1 was composed of 23.51％ α-helix,29.77％ β-sheet,and 46.71％ random coil.Rha 1 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-Rhal 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 Rla1.
Keywords：α-L-rhamnosidasebioinformaticssecondary structurehomology modeling
Publication Date：2017-01-01
Online Publishing Date：2025-08-15(First online date of this platform, not the publication date of the document)
Pages：13( 62-73,227 )