• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文学位 >The crystallization expert system Xtaldb, and its application to the structure of the 5'-nucleotidase YfbR and other proteins.
【24h】

The crystallization expert system Xtaldb, and its application to the structure of the 5'-nucleotidase YfbR and other proteins.

机译：结晶专家系统Xtaldb，及其在5'-核苷酸酶YfbR和其他蛋白质的结构中的应用。

获取原文
获取原文并翻译 | 示例
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Growing crystals is a critical step in the process of determining the 3-D structure of macromolecules by X-ray crystallography. While significant progress has been made in analyzing quantitatively crystallization experiments, in general, crystallization of biological macromolecules remains more of an art than a science. This work presents Xtaldb, an expert system for the quantitative analysis of crystallization experiments. Xtaldb provides tools for efficiently designing crystallization screens, tracks in a semiautomatic manner most of the parameters of the experiments, and provides sophisticated search, analysis, and data graphing tools. The algorithm used to produce balanced random screens is the fastest and most robust available. Xtaldb was tested on a set of six novel proteins that had failed to produce diffraction-quality crystals in a high-throughput structure determination pipeline. Of them, five yielded crystals diffracting to 3.5 A or better and three 3-D structures were elucidated. One of the three proteins was YfbR, a member of the HD-domain phosphohydrolase superfamily. Structural analysis of the 3-D structure and biochemical work confirmed phosphohydrolase activity. Further studies by a collaborator demonstrated that YfbR is a 5'-deoxynucleotidase. Xtaldb was used to produce two crystals of catalytically inactive YfbR mutants in the presence of metal cofactor and the substrates TMP or dAMP. The structures of the complexes explained the mechanism of the unique pattern of substrate selectivity, further supported by computational docking studies. The complex structures suggested a plausible atomic mechanism of catalysis for the enzyme, the first proposed mechanism for an HD-domain phosphohydrolase based directly from enzyme-substrate complex structures.
机译：晶体生长是通过X射线晶体学确定大分子3-D结构过程中的关键步骤。尽管在定量结晶实验分析方面已取得重大进展，但总体而言，生物大分子的结晶仍然是一门艺术，而不是一门科学。这项工作介绍了Xtaldb，这是一种用于结晶实验定量分析的专家系统。 Xtaldb提供了用于有效设计结晶屏幕的工具，以半自动方式跟踪了大多数实验参数，并提供了复杂的搜索，分析和数据绘图工具。用于产生平衡随机屏幕的算法是最快，最可靠的算法。 Xtaldb在一组六种新型蛋白质上进行了测试，这些蛋白质在高通量结构测定管线中未能产生衍射级品质的晶体。其中，五个产生的晶体衍射到3.5 A或更高，并阐明了三个3-D结构。三种蛋白质之一是YfbR，它是HD结构域磷酸水解酶超家族的成员。 3-D结构的结构分析和生化研究证实了磷酸水解酶的活性。合作者的进一步研究表明，YfbR是5'-脱氧核苷酸酶。 Xtaldb用于在金属辅因子和底物TMP或dAMP的存在下产生催化失活的YfbR突变体的两个晶体。配合物的结构解释了底物选择性的独特模式的机制，进一步由计算对接研究支持。复杂的结构表明了一种可能的酶催化原子机制，这是直接基于酶-底物复杂结构的HD域磷酸水解酶的首次提出的机制。

著录项

  • 作者

    Zimmerman, Matthew David.;

  • 作者单位

    University of Virginia.;

  • 授予单位 University of Virginia.;
  • 学科 Biophysics General.
  • 学位 Ph.D.
  • 年度 2008
  • 页码 149 p.
  • 总页数 149
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 生物物理学;
  • 关键词

  • 入库时间 2022-08-17 11:39:02

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号