RNA碱基对的分子动力学模拟

Molecular Dynamics Simulation of RNA Base Pair

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.