Maciejczyk Maciej, Spasic Aleksandar, Liwo Adam, Scheraga Harold A
Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Physics and Biophysics, Faculty of Food Sciences, University of Warmia and Mazury , 11-041 Olsztyn, Poland.
Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States ; Department of Biochemistry and Biophysics, University of Rochester Medical Center , Rochester, New York 14642, United States.
J Chem Theory Comput. 2014 Nov 11;10(11):5020-5035. doi: 10.1021/ct4006689. Epub 2014 Sep 22.
A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. , , 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole-multipole Debye-Hückel model. A very efficient -RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures.
提出了一种中等分辨率的DNA粗粒度模型。DNA链由通过弹性虚拟键连接的球形和平板刚体构成。势能函数的键合部分拟合到模型系统的平均力势。刚体是中性、带电和偶极珠子的集合。静电和范德华相互作用由我们最近开发的程序[Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A.,,, 1644]进行参数化。与溶剂和离子云的相互作用通过多极-多极德拜-休克尔模型进行近似。实现了一种非常高效的用于积分刚体运动的-RATTLE算法。这是第一个粗粒度模型，其中键合和非键合相互作用均从头进行参数化，并且能从分开的互补链折叠出稳定的双螺旋，最终构象接近实验确定结构的几何形状。
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