Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory for Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA.
Phys Chem Chem Phys. 2009 Dec 7;11(45):10619-32. doi: 10.1039/b910794k. Epub 2009 Sep 15.
Of special interest in molecular biology is the study of structural and conformational changes which are free of the additional effects of the environment. In the present contribution, we report on the ultrafast unfolding dynamics of a large DNA macromolecular ensemble in vacuo for a number of temperature jumps, and make a comparison with the unfolding dynamics of the DNA in aqueous solution. A number of coarse-graining approaches, such as kinetic intermediate structure (KIS) model and ensemble-averaged radial distribution functions, are used to account for the transitional dynamics of the DNA without sacrificing the structural resolution. The studied ensembles of DNA macromolecules were generated using distributed molecular dynamics (MD) simulations, and the ensemble convergence was ensured by monitoring the ensemble-averaged radial distribution functions and KIS unfolding trajectories. Because the order-disorder transition in free DNA implies unzipping, coiling, and strand-separation processes which occur consecutively or competitively depending on the initial and final temperature of the ensemble, DNA order-disorder transition in vacuo cannot be described as a two-state (un)folding process.
在分子生物学中，特别感兴趣的是研究不受环境额外影响的结构和构象变化。在本研究中，我们报告了在真空中对大量 DNA 大分子聚集体进行多次温度跳跃的超快展开动力学，并与 DNA 在水溶液中的展开动力学进行了比较。使用了一些粗粒化方法，如动力学中间结构（KIS）模型和均方位移径向分布函数，在不牺牲结构分辨率的情况下，对 DNA 的过渡动力学进行了描述。使用分布式分子动力学（MD）模拟生成了所研究的 DNA 大分子聚集体，通过监测均方位移径向分布函数和 KIS 展开轨迹，确保了聚集体的收敛性。由于自由 DNA 中的有序-无序转变意味着拉链、缠绕和链分离过程，这些过程根据聚集体的初始和最终温度连续或竞争地发生，因此真空状态下的 DNA 有序-无序转变不能描述为一个二态（展开或折叠）过程。
