大学化学 >> 2019, Vol. 34 >> Issue (2): 81-89.doi: 10.3866/PKU.DXHX201805027

国外化学教育 上一篇    下一篇

将生物信息学与有机化学结合初探酶促反应原理与实践——介绍一个国外本科生实验并讨论其相关问题

田杰1,王志鹏1,2,*(),马新雨2,蒋振雄1,许兵3   

  1. 1 Department of Biology, Texas A & M University, College Station, TX 77840, United States
    2 Department of Chemistry, Texas A & M University, College Station, TX 77840, United States
    3 Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX 77840, United States
  • 收稿日期:2018-05-16 发布日期:2019-02-26
  • 通讯作者: 王志鹏 E-mail:zwang44@bwh.harvard.edu

Study of Enzymatic Reaction with the Combination of Bioinformatics and Organic Chemistry: An Introduction and Discussion of an Undergraduate Experiment Abroad

Jie TIAN1,Zhipeng A. WANG1,2,*(),Xinyu MA2,Zhenxiong JIANG1,Bing XU3   

  1. 1 Department of Biology, Texas A & M University, College Station, TX 77840, United States
    2 Department of Chemistry, Texas A & M University, College Station, TX 77840, United States
    3 Department of Plant Pathology and Microbiology, Texas A & M University, College Station, TX 77840, United States
  • Received:2018-05-16 Published:2019-02-26
  • Contact: Zhipeng A. WANG E-mail:zwang44@bwh.harvard.edu

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摘要：

21世纪是生命科学与信息科学高速发展的时代，化学作为理科的中心学科与此二者均有紧密的联系。伴随着各种交叉学科的诞生与发展，将信息科学技术整合有机化学方法并用于认知生物大分子进而解决生命科学问题也是大势所趋，而在生物化学与化学生物学基础教学中引入相关内容也具有前瞻性与必要性。国外化学本科的基础教育也切合时宜地以一个生物信息学的最常用软件PyMOL为例设计相关实验，让学生在了解反应中的有机化学机理的基础上，学习酶的三维结构，并探究酶催化该反应的原因。此设计结合了有机化学、生物化学、生物信息学、蛋白质结构生物学等多学科，可以加深学生对多肽与蛋白质的高级结构的认识，并为今后的生物化学学习与研究打下基础，同时有利于培养学生对于化学的兴趣，可谓一举多得。这对于培养交叉学科人才，做出开创性研究极为重要。对国内生物有机化学实验的设计有借鉴作用。

关键词: PyMOL, 生物信息学, 脱羧酶, 二磷酸甲瓦龙酸, 本科生实验

Abstract:

The 21st century witnesses the most rapid development of life science and computer science. As the core of current scientific research, chemistry forms an integration in close combination with other subjects including biology and information science. With the appearance and development of various interdisciplinary subjects, integrating the methodology of computer science and organic chemistry is becoming one of the main trends to understand biomacromolecules and then to solve problems in life science. Therefore, it is also enterprising and necessary to introduce relative contents to fundamental biochemistry and chemical biology education. An organic experiment has been designed and carried out, right at the time point, for the undergraduate education with chemistry related majors based on a commonly used software named as "PyMOL". The experiment allows students to study the three-dimensional structure of a typical enzyme and with their solid understanding of organic chemistry mechanisms to investigate how the enzyme can catalyze a specific reaction. As a combination of multiple fields as organic chemistry, biochemistry, bioinformatics, protein structural biology, etc., this experimental design can largely enhance the students' understanding of higher-order protein structures, which lays the foundation of the biochemistry education and research. This experiment kills two birds with one stone, since it can also greatly intrigue students in chemistry learning. This is important to train all the promising students of interdisciplinary majors to initiate their innovative study. It's worthy to be introduced to bioorganic experimental design in China.

Key words: PyMOL, Bioinformatics, Decarboxylase, Diphosphomevalonate, Undergraduate experiment