Ray Gigi B, Cook J Whitney
Department of Chemistry, University of West Georgia, Carrollton, Georgia 30118.
Biochem Mol Biol Educ. 2005 May;33(3):194-201. doi: 10.1002/bmb.2005.494033032449.
A biochemical molecular modeling project on heme proteins suitable for an introductory Biochemistry I class has been designed with a 2-fold objective: i) to reinforce the correlation between protein three-dimensional structure and function through a discovery oriented project, and ii) to introduce students to the fields of bioinorganic and coordination chemistry. Students are asked to identify several unknown heme proteins based on a careful analysis of covalent and noncovalent interactions at the active site of each protein, focusing on amino acid reactivity and H-bonding networks. Starting with the three-dimensional crystal structures of four unknown proteins, students isolate and examine the coordination environment of the iron center in order to predict the relative reactivity toward dioxygen (O(2) ) or hydrogen peroxide (H(2) O(2) ). The central question of the project is to determine how the same iron protoporphyrin IX cofactor can be used by four different proteins to carry out diverse reactions, from electron transfer, to reversible oxygen binding to hydrogen peroxide activation. Pedagogical reasons for implementation of this biomolecular discovery-based activity and student evaluations are discussed. In addition to developing many of the three-dimensional visualization skills needed to successfully learn biochemistry, students also learn to use the versatile MOE molecular modeling program (Molecular Operating Environment), become familiar with metalloprotein reactivity, and are introduced to computational biochemistry research.
一个适合于生物化学入门课程的关于血红素蛋白的生物化学生物分子建模项目已被设计出来，其目标有两个：一是通过一个以探索为导向的项目加强蛋白质三维结构与功能之间的关联；二是向学生介绍生物无机化学和配位化学领域。要求学生基于对每种蛋白质活性位点处共价和非共价相互作用的仔细分析来鉴定几种未知的血红素蛋白，重点关注氨基酸反应性和氢键网络。从四种未知蛋白质的三维晶体结构开始，学生分离并检查铁中心的配位环境，以便预测对氧气（O₂）或过氧化氢（H₂O₂）的相对反应性。该项目的核心问题是确定相同的铁原卟啉IX辅因子如何被四种不同的蛋白质用于进行从电子转移到可逆氧结合再到过氧化氢活化的各种反应。讨论了实施这个基于生物分子探索的活动的教学原因以及学生评估情况。除了培养成功学习生物化学所需的许多三维可视化技能外，学生还学会使用多功能的MOE分子建模程序（分子操作环境），熟悉金属蛋白反应性，并被引入计算生物化学研究领域。
