Journal:BAMBEd:A practical guide to teaching with Proteopedia:Supplementary 2
From Proteopedia
A practical guide to teaching with Proteopedia - Supplementary 2
Proteopedia contains comprehensive content that can be used as a 3D supplement throughout the first semester in a biochemistry course.
The page Proteopedia:Biochemistry in 3D gives suggestions of which pages might match a first semester biochemistry course particularly well. For example, during the section on protein structure, Proteopedia can be used to introduce the ‘levels’ of structure (i.e., primary, secondary, etc.) in both 2D and 3D (Introduction to protein structure). This page, developed by Ann Taylor, includes a number of leading questions and is leveraged to ‘flip’ the classroom and provide motivation to the student for learning structure. The questions embedded in the page serve to spark a conversation about protein structure. Two tutorials on the Ramachandran plot illustrate constraints on the protein main chain geometry that are difficult to teach without 3D visualization and difficult to learn without being able to manipulate a protein backbone to experience the clashes for certain phi/psi angle combinations Tutorial:Ramachandran principle and phi psi angles Tutorial:Ramachandran Plot Inspection. Hemoglobin illustrates protein function, ligand binding, and allostery (Hemoglobin, Ann Taylor/Hemoglobin). Glucokinase is another example (The Structure and Mechanism of Hexokinase).
These models and their Proteopedia pages visually illustrate the conformational changes that occur upon ligand binding and on regulator binding. A page on citrate synthase (Citrate Synthase, started as student-authored page) can be used during the citric acid cycle; it features an instructive morph of open to closed conformation to teach the concept of protein dynamics. This is a difficult concept to convey with static images, but on Proteopedia, Jmol can visualize the motion, making it easier to grasp.
