脱氧核糖核酸柔性的分子动力学模拟:Amber bsc1和bsc0力场的对比研究

脱氧核糖核酸(DNA)的结构柔性对DNA生物功能的实现具有重要作用,全原子分子动力学模拟是一种研究DNA结构柔性的重要方法.DNA的分子动力学力场在Amber bsc0基础上有了进一步的发展,即Amber bsc1.本文采用基于最新bsc1力场和先前bsc0力场的分子动力学模拟对DNA的宏观柔性和微观柔性进行对比研究,发现力场的改进对DNA宏观柔性参量的预测有一定改善,即所预测的拉伸模量和扭转-伸缩耦合比与实验值更为接近,而弯曲持久长度和扭转持久长度两种力场结果皆与实验值一致.微观分析发现,除了滑移量稍变大,bsc1力场得到的微观结构参量如扭转角和倾斜角与实验值更为接近,且新力场下DNA宏观柔性的改善与DNA的微观结构参量及其涨落紧密相关.     

To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?

Nucleic acids are negatively charged biomolecules, and metal ions in solutions are important to their folding structures and thermodynamics, especially multivalent ions. However, it has been suggested that the binding of multivalent ions to nucleic acids cannot be quantitatively described by the well-established Poisson-Boltzmann(PB) theory. In this work, we made extensive calculations of ion distributions around various RNA-like macroions in divalent and trivalent salt solutions by PB theory and Monte Carlo(MC) simulations. Our calculations show that PB theory appears to underestimate multivalent ion distributions around RNA-like macroions while can reliably predict monovalent ion distributions. Our extensive comparisons between PB theory and MC simulations indicate that when an RNA-like macroion gets ion neutralization beyond a "critical" value, the multivalent ion distribution around that macroion can be approximately described by PB theory.Furthermore, an empirical formula was obtained to approximately quantify the critical ion neutralization for various RNAlike macroions in multivalent salt solutions, and this empirical formula was shown to work well for various real nucleic acids including RNAs and DNAs.