Ehrlich L, Münkel C, Chirico G, Langowski J
Division of Biophysics of Macromolecules, DKFZ, Heidelberg, Germany.
Comput Appl Biosci. 1997 Jun;13(3):271-9. doi: 10.1093/bioinformatics/13.3.271.
We describe a Brownian dynamics model for the folding of the chromatin fiber based on the model of Woodcock et al. (Proc Natl Acad Sci USA, 90, 9021-9025, 1993). The model takes into account the elastic properties of the DNA as well as the electrostatic interaction and nucleosomal excluded-volume interaction. The solvent is described as a viscous medium, the electrostatic interactions by a screened Coulomb potential.
The hydrodynamic properties and their dependence on the solvent's ionic strength are accurately reproduced by the model for nucleosome di- and tetramers. Ionic strength-dependent changes in mobility can be attributed to partial screening of the electrostatic repulsion between different segments of linker DNA. Formation of fiber-like structures occurs on time scales of several hundred microseconds for a linear configuration of 25 nucleosomes. The model was implemented by creating user-defined data types. Use of this so-called object-oriented paradigm allowed for a high degree of component reuse in simulation, analysis and visualization contexts.
The described software is available on request from the authors. Additional information can be found on the WWW at http:/(/)www.dkfz-heidelberg.de/Macromol/ehrlich /chromatin.htm/.
我们基于伍德科克等人（《美国国家科学院院刊》，90，9021 - 9025，1993年）的模型描述了一种用于染色质纤维折叠的布朗动力学模型。该模型考虑了DNA的弹性特性以及静电相互作用和核小体的排除体积相互作用。溶剂被描述为粘性介质，静电相互作用由屏蔽库仑势描述。
该模型准确再现了核小体二聚体和四聚体的流体动力学特性及其对溶剂离子强度的依赖性。迁移率随离子强度的变化可归因于连接DNA不同片段之间静电排斥的部分屏蔽。对于25个核小体的线性构型，纤维状结构在几百微秒的时间尺度上形成。该模型通过创建用户定义的数据类型来实现。使用这种所谓的面向对象范式允许在模拟、分析和可视化环境中高度重用组件。
所述软件可根据作者要求提供。更多信息可在万维网http:/(/)www.dkfz - heidelberg.de/Macromol/ehrlich /chromatin.htm/上找到。
