期刊检索

  • 2019年第17卷
  • 2018年第16卷
  • 2017年第15卷
  • 2016年第14卷
  • 2015年第13卷
  • 2014年第12卷
  • 2013年第11卷
  • 第1期
  • 第2期

主管单位 工业和信息化部 主办单位 哈尔滨工业大学 主编 任南琪 国际刊号ISSN 1672-5565 国内刊号CN 23-1513/Q

期刊网站二维码
微信公众号二维码
引用本文:吴超,陈竞哲.Bromodomains识别并结合配体的机理研究[J].生物信息学,2019,17(1):39-44.
WU Chao,CHEN Jingzhe.Study on the mechanism of Bromodomains identification and binding of ligands[J].Chinese Journal of Bioinformatics,2019,17(1):39-44.
【打印本页】   【HTML】   【下载PDF全文】   查看/发表评论  下载PDF阅读器  关闭
←前一篇|后一篇→ 过刊浏览    高级检索
本文已被:浏览 27次   下载 83 本文二维码信息
码上扫一扫!
分享到: 微信 更多
Bromodomains识别并结合配体的机理研究
吴超1,2,陈竞哲2
(1.上海大学 物理系 上海 200444;2.上海大学 量子与分子结构中心,上海 200444)
摘要:
关于酵母重组蛋白内的Bromodomain识别乙酰化赖氨酸的研究近年来受到广泛的关注,但是其识别配体并与之相紧密结合的机理有待进一步的研究。本文采用2015年开发的结合位点拓扑学方法(FCTM)和分子动力学模拟的方式对Bromodomains识别并结合配体的机理进行了充分研究,其中分子动力学模拟时间达24 ns。通过FCTM方法发现结合位点的几何结构具有高度的凹性,且其alphaspace达到了131。分子动力学模拟的结果显示:在模拟的过程中结合位点表面的脯氨酸(Pro66)始终对配体保持着强的分子间相互作用,同时pocket内的水分子分布对配体的氢键网络也一直存在影响。以上结果表明Bromodomains识别并结合配体有两个重要因素:蛋白结构域自身的几何结构和配体受到来自于结合位点表面的氨基酸分子相互作用和pocket内水分子的氢键网络作用。
关键词:  Bromodomains  结合位点分子拓扑学方法  分子动力学模拟
DOI:10.12113/j.issn.1672-5565.201807002
分类号:Q71
文献标识码:A
基金项目:国家自然科学基金(No.11674212).
Study on the mechanism of Bromodomains identification and binding of ligands
WU Chao1,2 ,CHEN Jingzhe2
(1. Department of Physics,Shanghai University, Shanghai 200444, China; 2. International Center for Quantum and Molecular Structure,Shanghai University, Shanghai 200444, China)
Abstract:
The research of the recognition of acetyl-lysine through Bromodomains in yeast remodeler has attracted wide attention in recent years. However, the mechanism of recognition and combination between Bromodomains and ligands needs further study. Fragment-centric topographical mapping (FCTM) and molecular dynamics simulation were used to study the mechanism in this paper, in which the simulation time was 24 ns. The geometric structure of the binding sites was highly concave and its alphaspace reached 131 by FCTM. The results of the molecular dynamics simulation show that the proline (Pro66) on the surface of combinational site always maintained a strong intermolecular interaction with the ligand during the simulation, and the distribution of water molecules within the pocket also existed on the hydrogen bond network of the ligand. The above results indicate that there are two important factors of Bromodomains to identify and bind ligands: The geometric structure of the protein domain itself and the continuous interaction of ligands with amino acid molecules on the surface of the binding site and pocket internal water molecules.
Key words:  Bromodomains  Fragment-centric topographical mapping (FCTM)  Molecule dynamics simulation

友情链接LINKS