Using PyMOL to Explore the Effects of pH on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided-Inquiry Biochemistry Activity: Guided Inquiry Activity: PyMOL to Explore Protein Interactions
Using PyMOL to Explore the Effects of pH on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided-Inquiry Biochemistry Activity: Guided Inquiry Activity: PyMOL to Explore Protein Interactions
复制标题
使用 PyMOL 探索 pH 对免疫球蛋白 G 和蛋白 A 之间非共价相互作用的影响：引导探究生化活动：引导探究活动：PyMOL 探索蛋白质相互作用
DOI：
10.1002/bmb.21066
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发表时间：
2017
影响因子：
1.4
通讯作者：
Page, Richard C.
中科院分区：
文献类型：
--
作者：
Roche Allred, Zahilyn D.;Tai, Heeyoung;Bretz, Stacey Lowery;Page, Richard C.
学生对非共价相互作用、pH和pKa等基本概念的理解对于本科生生物化学课程的成功至关重要。我们开发了一个引导式探究活动，以帮助学生在非共价相互作用和pH/pKa之间建立联系。学生通过检查免疫球蛋白G（IgG）和蛋白A的一级和三级结构来探索这些概念。学生使用PyMOL，一个开源的分子可视化应用程序，以（1）确定氢键和盐桥之间和蛋白质内在生理pH值和（2）应用他们的pH/pKato的知识，这些蛋白质在pH值4和pH值11的缔合速率常数数据。实验室活动是在一个学期的生物化学实验室内进行的，该实验室为联合卫生学科、工程和生物科学专业的学生提供。几个扩展更先进的学生进行了讨论。学生的整体表现突出了他们成功完成标记和识别非共价相互作用等任务的能力，并揭示了在不同pH/pK条件下分析非共价相互作用的困难。学生完成活动后的评价表明，他们感到挑战，但也认识到活动的潜力，以帮助他们获得有意义的理解之间的非共价相互作用，pH值，pKa和蛋白质结构的连接。© 2017由国际生物化学和分子生物学联合会，45（6）：528-536，2017。
Students' understandings of foundational concepts such as noncovalent interactions, pH and pKaare crucial for success in undergraduate biochemistry courses. We developed a guided‐inquiry activity to aid students in making connections between noncovalent interactions and pH/pKa. Students explore these concepts by examining the primary and tertiary structures of immunoglobulin G (IgG) and Protein A. Students use PyMOL, an open source molecular visualization application, to (1) identify hydrogen bonds and salt bridges between and within the proteins at physiological pH and (2) apply their knowledge of pH/pKato association rate constant data for these proteins at pH 4 and pH 11. The laboratory activity was implemented within a one semester biochemistry laboratory for students majoring in allied health disciplines, engineering, and biological sciences. Several extensions for more advanced students are discussed. Students' overall performance highlighted their ability to successfully complete tasks such as labeling and identifying noncovalent interactions and revealed difficulties with analyzing noncovalent interactions under varying pH/pKaconditions. Students' evaluations after completing the activity indicated they felt challenged but also recognized the potential of the activity to help them gain meaningful understanding of the connections between noncovalent interactions, pH, pKa, and protein structure. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):528–536, 2017.