Predicting the optimum temperature of <beta>-agarase based on the relative solvent accessibility of amino acids

Publication date: Available online 11 April 2016 Source:Journal of Molecular Catalysis B: Enzymatic Author(s): Yunmeng Chu, Zhiwei Yi, Runyin Zeng, Guangya Zhang It is of great significance to investigate the amino acids in different solvent accessibility parts of β-agarase responsible for its thermal stability, which may help for understanding the structural basis of thermophilic β-agarase and developing practical strategies for reengineering new one. We systematically analyzed the amino acids distributed in the internal, intermediate and external states of β-agarases and found 21 significant differences in the three states by t-test. Among them, Glu, His and charged residues in the internal part and Tyr in the external part are critical for the stability at high temperature. Based on it, we developed a support vector regression model to predict the optimal temperature of β-agarases with the 21 significant factors as input vector and the results are encouraging. The mean-absolute error (MAE) and root-mean-square error (RMSE) in the 10-fold cross-validation are 3.80°C and 5.46°C, respectively. In addition, we experimentally verified three β-agarases with the optimal temperature as 45°C, 50°C and 50°C, and the predicted temperatures were 47.2°C, 47.4°C, and 49.9°C, respectively. Graphical abstract

Source: Journal of Molecular Catalysis B: Enzymatic - April 19, 2016 Category: Biochemistry Source Type: research