核小体在张力诱导状态之间的动力学。
Nucleosome dynamics between tension-induced states.
机构信息
Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences, Zanjan, Iran.
出版信息
Biophys J. 2012 May 16;102(10):2235-40. doi: 10.1016/j.bpj.2012.04.012. Epub 2012 May 15.
Abstract
We studied the dynamical behavior of a mononucleosome under tension using a theoretical model that takes into account the nucleosomal geometry, DNA elasticity, nonspecific DNA-protein binding, and effective repulsion between the two DNA turns. Using a dynamical Monte-Carlo simulation algorithm, we demonstrate that this model shows a behavior that for an appropriate set of parameters is in quantitative agreement with data from micromanipulation experiments on individual nucleosomes. All of the parameters of the model follow from the data obtained from two types of pulling experiments, namely, constant force and constant loading rate ensembles.
摘要
我们使用一种理论模型研究了拉伸下单核小体的动力学行为，该模型考虑了核小体的几何形状、DNA 的弹性、非特异性 DNA-蛋白质结合以及两个 DNA 转角之间的有效排斥。使用动态蒙特卡罗模拟算法，我们证明该模型对于一组适当的参数，其行为与单个体细胞核小体的微操作实验数据具有定量一致性。该模型的所有参数都来自两种类型的拉伸实验，即恒力和恒加载速率系综，从这些实验中获得。
相似文献
1
Nucleosome dynamics between tension-induced states.核小体在张力诱导状态之间的动力学。
Biophys J. 2012 May 16;102(10):2235-40. doi: 10.1016/j.bpj.2012.04.012. Epub 2012 May 15.
2
Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability.DNA内在曲率和柔韧性在决定核小体稳定性中的双重作用。
J Mol Biol. 1999 Mar 12;286(5):1293-301. doi: 10.1006/jmbi.1998.2575.
3
Nucleosome interactions in chromatin: fiber stiffening and hairpin formation.染色质中的核小体相互作用：纤维硬化和发夹形成。
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Jul;70(1 Pt 1):011915. doi: 10.1103/PhysRevE.70.011915. Epub 2004 Jul 29.
4
Designing nucleosomal force sensors.设计核小体力传感器。
Phys Rev E. 2017 May;95(5-1):052402. doi: 10.1103/PhysRevE.95.052402. Epub 2017 May 8.
5
A lattice model for transcription factor access to nucleosomal DNA.转录因子与核小体 DNA 相互作用的点阵模型。
Biophys J. 2010 Oct 20;99(8):2597-607. doi: 10.1016/j.bpj.2010.08.019.
6
Structural mechanics of DNA wrapping in the nucleosome.核小体中 DNA 缠绕的结构力学。
J Mol Biol. 2010 Feb 19;396(2):264-79. doi: 10.1016/j.jmb.2009.11.040. Epub 2009 Nov 27.
7
Two DNA-binding sites on the globular domain of histone H5 are required for binding to both bulk and 5 S reconstituted nucleosomes.组蛋白H5球状结构域上的两个DNA结合位点对于与整体及5S重构核小体的结合均是必需的。
J Mol Biol. 2000 Nov 17;304(1):21-33. doi: 10.1006/jmbi.2000.4205.
8
Multiscale modeling of nucleosome dynamics.核小体动力学的多尺度建模。
Biophys J. 2007 Mar 1;92(5):1457-70. doi: 10.1529/biophysj.106.094805. Epub 2006 Dec 1.
9
A deformation energy-based model for predicting nucleosome dyads and occupancy.一种基于变形能量的预测核小体二分体和占有率的模型。
Sci Rep. 2016 Apr 7;6:24133. doi: 10.1038/srep24133.
10
Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.弯曲诱导的扭波与核小体 DNA 的结构。
Phys Rev Lett. 2018 Aug 24;121(8):088101. doi: 10.1103/PhysRevLett.121.088101.
引用本文的文献
1
Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome.组蛋白在核小体中强制解缠绕和力猝灭重缠绕过程中的旋转不对称性。
Nucleic Acids Res. 2021 May 21;49(9):4907-4918. doi: 10.1093/nar/gkab263.
2
Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks.在核小体阻碍存在的情况下，特定于位点的 DNA-蛋白质相互作用的理论。
Biophys J. 2018 Jun 5;114(11):2516-2529. doi: 10.1016/j.bpj.2018.04.039.
3
On the role of inter-nucleosomal interactions and intrinsic nucleosome dynamics in chromatin function.论核小体间相互作用及内在核小体动力学在染色质功能中的作用
Biochem Biophys Rep. 2016 Feb 16;5:492-501. doi: 10.1016/j.bbrep.2016.02.009. eCollection 2016 Mar.
4
Tension-Dependent Free Energies of Nucleosome Unwrapping.核小体解旋的张力依赖性自由能
ACS Cent Sci. 2016 Sep 28;2(9):660-666. doi: 10.1021/acscentsci.6b00201. Epub 2016 Aug 23.
5
Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility.在由DNA局部柔韧性引导的张力下核小体的不对称解旋
Cell. 2015 Mar 12;160(6):1135-44. doi: 10.1016/j.cell.2015.02.001.
6
Unwinding and rewinding the nucleosome inner turn: force dependence of the kinetic rate constants.解开与重新缠绕核小体内侧转弯：动力学速率常数的力依赖性
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jan;87(1):012710. doi: 10.1103/PhysRevE.87.012710. Epub 2013 Jan 17.
本文引用的文献
1
The physics of chromatin.染色质物理学
J Phys Condens Matter. 2015 Feb 18;27(6):060301. doi: 10.1088/0953-8984/27/6/060301. Epub 2015 Jan 7.
2
Tension-dependent structural deformation alters single-molecule transition kinetics.张力依赖的结构变形改变了单分子的转变动力学。
Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1885-90. doi: 10.1073/pnas.1010047108. Epub 2011 Jan 18.
3
Nucleosome stability and accessibility of its DNA to proteins.核小体的稳定性及其 DNA 对蛋白质的可及性。
Biochimie. 2010 Dec;92(12):1722-8. doi: 10.1016/j.biochi.2010.08.008. Epub 2010 Aug 13.
4
Brownian dynamics simulation of DNA unrolling from the nucleosome.从核小体展开的DNA的布朗动力学模拟。
J Phys Chem B. 2009 Mar 5;113(9):2639-46. doi: 10.1021/jp806137e.
5
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.核小体波动调控RNA聚合酶II的转录动力学。
Science. 2009 Jul 31;325(5940):626-8. doi: 10.1126/science.1172926.
6
Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence.RSC和Mi-2介导的依赖ATP的核小体易位的多个方面受潜在DNA序列的指导。
PLoS One. 2009 Jul 23;4(7):e6345. doi: 10.1371/journal.pone.0006345.
7
Hidden Markov analysis of nucleosome unwrapping under force.力作用下核小体解旋的隐马尔可夫分析
Biophys J. 2009 May 6;96(9):3708-15. doi: 10.1016/j.bpj.2009.01.048.
8
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome.核小体中组蛋白与DNA相互作用的高分辨率动态图谱。
Nat Struct Mol Biol. 2009 Feb;16(2):124-9. doi: 10.1038/nsmb.1526. Epub 2009 Jan 11.
9
Effect of force on mononucleosomal dynamics.力对单核小体动力学的影响。
Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15871-6. doi: 10.1073/pnas.0607526103. Epub 2006 Oct 16.
10
Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF.使用核心组蛋白、核仁素结合蛋白1（NAP-1）和染色质组装因子（ACF）对组装在异源DNA上的核小体进行强制解聚。
J Mol Biol. 2005 Aug 5;351(1):89-99. doi: 10.1016/j.jmb.2005.05.058.
Zotero 插件