Innovative Experiment Project for Undergraduates Based on GROMACS Software: Molecular Dynamics Simulation of Microbial Transglutaminase in Water
WU Nan1,2,3**, CUI Dan-Dan4, JI Bao-Cheng1,2,3, BAI Yan-Hong1,2,3
1. College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China;
2. Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou 450001, China;
3. Henan Collaborative Innovation Center for Food Production and Safety, Zhengzhou 450001, China;
4. Zhengzhou Yinglun Foreign Language School, Zhengzhou 450000, China
Abstract GROMACS software was used for designing a molecular dynamics simulation experiment for undergraduate student teaching. Microbial transglutaminase was selected as a target protein, which was solubilized and incubated in temperatures of 300 K, 400 K and 500 K by using computer simulation, respectively. The backbone dynamics, hydrogen bond, radius of gyration and solvent accessible surface area of the protein during simulation were calculated in order to analyze structural changes of microbial transglutaminase resulted from high temperature. This experiment helps students: (1) know how to simulate a protein in water; (2) understand the importance of the temperature affection to enzyme structure and function; (3) understand the biological significance of molecular dynamics; (4) learn a novel method for enzyme engineering.
WU Nan, CUI Dan-Dan, JI Bao-Cheng, BAI Yan-Hong. Innovative Experiment Project for Undergraduates Based on GROMACS Software: Molecular Dynamics Simulation of Microbial Transglutaminase in Water[J]. Chinese Journal of Chemical Education, 2021, 42(20): 102-107.
