基于GROMACS软件的本科生酶工程创新实验项目设计——微生物谷氨酰胺转胺酶在水溶液中的分子动力学模拟

Innovative Experiment Project for Undergraduates Based on GROMACS Software:Molecular Dynamics Simulation of Microbial Transglutaminase in Water

基于分子动力学模拟软件GROMACS设计了微生物谷氨酰胺转胺酶在不同温度水环境下的分子动力学模拟实验,通过计算模拟过程中酶蛋白主链动力学,分子内氢键数目,回转半径以及溶剂可接触表面积的变化,分析温度对酶的结构与功能造成的影响。该模拟实验可帮助学生:(1)掌握蛋白质分子在水溶液中动力学模拟的方法;(2)理解温度对酶结构稳定性和活性造成的影响;(3)了解分子运动特性的生物学的意义;(4)学习酶工程研究的新手段。

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 Kand 500 Kby 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.