RNA碱基对的分子动力学模拟

RNA碱基对的分子动力学模拟 Molecular Dynamics Simulation of RNA Base Pair 张勇 ZHANG Yong 1 first-author 王宇杰 WANG Yujie 1 张文炳 ZHANG Wenbing 1 武汉大学物理科学与技术学院 武汉大学物理科学与技术学院 School of Physics and Technology,Wuhan University School of Physics and Technology,Wuhan University RNA作为一种重要的生物大分子,其很多生物功能都与其结构有关.RNA碱基对的热力学性质和动力学性质是预测RNA结构的基础.本文采用全原子分子动力学方法模拟了RNA碱基对G—C在3种不同温度下的打开及闭合情况,统计分析了其打开和闭合几率.研究结果表明,随着温度的升高,碱基对G—C处于闭合状态的几率逐渐降低,处于打开状态的几率逐渐增加,而碱基对打开闭合状态的转换频率随着温度的升高而逐渐增加,并且形成碱基配对的3组原子间的氢键距离分布变宽. Ribonucleic acids is a kind of very important biological molecule,many biological functions of which are related to their structures.The thermodynamic and dynamic properties of the base pairs provide a foundation to predict the secondary structure of RNA.With the molecular dynamics simulation software GROMACS,we studied the probability of G—C base pair in the closed state or open state at three different temperature.The results showed that with temperature increasing the probability of G—C base pair in the closed state will decrease while that in the open state will increase;the conversion frequency between the open and closed state of the G—C base pair will increase and the distribution of the distance between the atoms that can form the hydrogen bond will become wide. RNA碱基对 分子动力学模拟 自由能 热力学 RNA base pair molecular dynamics simulation free energy thermodynamics 10.14188/j.1671-8836.2014.03.004 Q522 国家自然科学基金资助项目（31270761） 2014-03-01 2021-04-01 3 60