Binding Interaction Activities Powered by Desmos

Abstract

Three computer-based activities focusing on fundamentals of binding interactions are described that are powered by Desmos, freely available web-based software. The software allows the instructor to monitor the progress of each student completing the activity by privately viewing their answers in real time, to enforce class pacing by modulating which parts of the activity are available at certain times, to acquire the full attention of the class for vital teaching moments by pausing the activity at will, and to promote learning by seamlessly graphing and fitting nonlinear data. Students learn that binding interactions are governed by kinetics and energetics which dictate affinities and binding curves. A generic binding interaction is used to derive an equation describing a hyperbolic-binding curve, and given binding curves are used to identify Kd values and relate them to relative affinities. This leads into a case study using myoglobin and oxygen where given binding curves are used to identify P50 values and relative values are justified via the energetics of the particular binding site. Last, students use nonlinear regression to fit imported binding data to the derived equation to construct a binding curve and determine the P50 affinity value. Students report acclimating to the Desmos environment quickly and an increased understanding of the relationship between Kd and binding affinity. After the activities, students are prepared for a lab analyzing hyperbolic binding and discussions on allosteric binding and sigmoidal curves. Ultimately, steps are laid out for instructors to try using Desmos, and thoroughly developed and assessed activities involving graphical biochemistry content are provided for use.