...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Iterative approach to computational enzyme design
【24h】

Iterative approach to computational enzyme design

机译：计算酶设计的迭代方法

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

A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants'. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner,but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MO and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes.
机译：酶催化催化任意反应的计算设计的一般方法是蛋白质设计领域的首要目标。最近，通过合成和筛选大量变体，已经为三种化学反应生产了经过计算设计的酶。在这里，我们提出了一种迭代方法，该方法导致了迄今为止消除Kemp的最高效催化计算设计酶的开发。先前建立的计算技术被用于生成初始设计HG-1，该催化剂没有催化活性。用分子动力学模拟（MD）和X射线晶体学分析对HG-1进行分析，结果表明，这种不活泼可能是由于结合水和活性位点内残基的高度柔性所致。该分析指导了我们设计流程的改变，使设计更深入了蛋白质的内部，并产生了一种活性的Kemp消除酶HG-2。该酶与过渡态类似物（TSA）的共晶结构表明，TSA结合在活性位点上，以催化相关的方式与预期的催化碱基相互作用，但相对于设计模型而言是翻转的。 MD对HG-2的分析导致了另外的点突变HG-3，使活性进一步提高了三倍。这种计算酶设计的迭代方法，包括对有活性和无活性设计进行详细的MO和结构分析，有望对酶催化的基本原理有更全面的了解，并进一步促进了可靠生产活性酶的发展。

著录项

  • 来源
  • 作者

    Heidi K. Privet; Gert Kiss; Toni M. Lee; Rebecca Blomberg; Roberto A. Chica; Leonard M. Thomas; Donald Hilvert; Kendall N. Houk; Stephen L. Mayo;

  • 作者单位

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125;

    Department of Chemistry and Biochemistry,University of California, Los Angeles, CA 90095;

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125;

    Laboratory of Organic Chemistry, Eidgenossische Technische Hochschule Zurich, CH-8093 Zurich,Switzerland;

    Division of Biology, California Institute of Technology, Pasadena, CA 91125;

    Howard Hughes Medical Institute, California Institute of Technotogy, Pasadena, CA 91125;

    Laboratory of Organic Chemistry, Eidgenossische Technische Hochschule Zurich, CH-8093 Zurich,Switzerland;

    Department of Chemistry and Biochemistry,University of California, Los Angeles, CA 90095;

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125,Division of Biology, California Institute of Technology, Pasadena, CA 91125;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    computational protein design; de novo enzyme design; proton transfer;

    机译：计算蛋白设计;从头酶设计;质子转移;

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