A Brownian dynamics model for the chromatin fiber.

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI:10.1093/bioinformatics/13.3.271

L Ehrlich, C Münkel, G Chirico, J Langowski

{"title":"A Brownian dynamics model for the chromatin fiber.","authors":"L Ehrlich, C Münkel, G Chirico, J Langowski","doi":"10.1093/bioinformatics/13.3.271","DOIUrl":null,"url":null,"abstract":"Motivation: 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.Results: 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.Availability: 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/.","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 3","pages":"271-9"},"PeriodicalIF":0.0000,"publicationDate":"1997-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.3.271","citationCount":"24","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computer applications in the biosciences : CABIOS","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioinformatics/13.3.271","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 24

Abstract

Motivation: 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.

Results: 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.

Availability: 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/.

查看原文本刊更多论文

染色质纤维的布朗动力学模型。

动机:我们在Woodcock等人的模型的基础上描述了染色质纤维折叠的布朗动力学模型(Proc Natl Acad Sci USA, 90, 9021-9025, 1993)。该模型考虑了DNA的弹性特性以及静电相互作用和核小体排斥-体积相互作用。溶剂被描述为一种粘性介质，静电相互作用通过屏蔽库仑势。结果:核小体二聚体和四聚体的流体动力学性质及其对溶剂离子强度的依赖关系可以用该模型精确地再现。离子强度依赖于迁移率的变化可归因于连接体DNA不同片段之间的静电排斥的部分筛选。对于25个核小体的线性结构，纤维状结构的形成发生在几百微秒的时间尺度上。该模型是通过创建用户定义的数据类型实现的。使用这种所谓的面向对象范例，可以在仿真、分析和可视化上下文中实现高度的组件重用。可用性:所描述的软件可以根据作者的要求获得。更多信息可以在WWW上找到:/(/)www.dkfz-heidelberg.de/Macromol/ehrlich / chrotin .htm/。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Computer applications in the biosciences : CABIOS

自引率

0.00%

发文量