ABSTRACT

This report describes the implementation of a laboratory exercise for an advanced biochemistry or enzyme kinetics class at the undergraduate or graduate level, designed to improve understanding of protein conformational changes associated with the binding of a ligand. Students measure the fluorescence changes induced by the conformational transition of a glycoprotein (the Na,K-ATPase) upon addition of different ligands (Pi and BeF₃⁻) and analyse the results in order to determine the mechanism of the process. The results show that Pi and BeF₃⁻ present opposite effects on the observed rate constants (k_obs) with ligand concentration: k_obs decreases with [Pi] and increases with [BeF₃⁻]. This observation, together with the frequently used assumption that binding occurs under rapid equilibrium, led to propose different models for ligand-induced conformational transitions: a conformational selection for Pi and an induced fit for BeF₃⁻. In this paper, we show that if the rapid-equilibrium approximation for ligand binding is not assumed, a conformational selection mechanism can account for the effects of both ligands. This active-learning exercise serves as the basis for discussing the consequences of not being extremely cautious when invoking approximations about not-very-well-known systems and the importance of a correct understanding of models assigned to chemical processes.

摘要

本报告描述了本科或研究生水平的高级生物化学或酶动力学课程的实验室练习的实施，旨在提高对与配体结合相关的蛋白质构象变化的理解。学生测量添加不同配体（Pi 和 BeF ₃ ^-）后糖蛋白（Na,K-ATPase）的构象转变引起的荧光变化，并分析结果以确定该过程的机制。结果表明，Pi 和 BeF ₃ ^-对观察到的速率常数 ( k _obs ) 与配体浓度呈现相反的影响：k _obs随 [Pi] 减少而随 [BeF] 增加₃ ^- ]。这一观察结果，连同经常使用的结合发生在快速平衡下的假设，导致提出了不同的配体诱导构象转变模型：Pi的构象选择和BeF ₃ ^-的诱导拟合。在本文中，我们表明，如果不假设配体结合的快速平衡近似，则构象选择机制可以解释两种配体的影响。这种主动学习练习可作为讨论在调用关于不太知名的系统的近似值时过于谨慎的后果以及正确理解分配给化学过程的模型的重要性的基础。