Ponomarev Sergei Y, Thayer Kelly M, Beveridge David L
Department of Physics, Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA.
Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14771-5. doi: 10.1073/pnas.0406435101. Epub 2004 Oct 1.
Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for convergence of each of the properties of interest. To address this issue, MD on a d(CGCGAATTCGCG) duplex in a dilute aqueous solution of water and 22 Na+ counterions was performed until convergence was achieved. The calculated first shell ion occupancies and DNA-Na+ radial distribution functions were computed as a function of time to assess convergence, and compared with relaxation times of the DNA internal parameters shift, slide, rise, tilt, roll, and twist. The sequence dependence of fractional occupancies of ions in the major and minor grooves of the DNA is examined, and the possibility of correlation between ion proximity and DNA minor groove widths is investigated.
抗衡离子在DNA的结构和功能中起着重要作用，分子动力学（MD）模拟为在分子水平上详细描述离子的动态结构提供了前景。然而，在DNA上进行MD模拟时，可移动抗衡离子的运动收敛得非常缓慢。要获得准确可靠的MD模拟，需要知道对于每个感兴趣的属性，收敛需要多少采样。为了解决这个问题，在含有水和22个Na+抗衡离子的稀水溶液中对d(CGCGAATTCGCG)双链体进行MD模拟，直到达到收敛。计算第一壳层离子占有率和DNA-Na+径向分布函数作为时间的函数来评估收敛情况，并与DNA内部参数位移、滑动、上升、倾斜、滚动和扭转的弛豫时间进行比较。研究了DNA大沟和小沟中离子占有率的序列依赖性，并探讨了离子接近度与DNA小沟宽度之间相关性的可能性。
