Course-based Undergraduate Research Module for Enzyme Discovery Using Protein Structure Prediction

Kelz, Jessica I.; Takahashi, Gemma R.; Safizadeh, Fatemeh; Farahmand, Vesta; Crosby, Marquise G.; Uribe, Jose Luis; Kim, Suhn H.; Sprague-Piercy, Marc A.; Diessner, Elizabeth M.; Norton-Baker, Brenna; Damo, Steven M.; Martin, Rachel W.; Kadandale, Pavan

A major challenge for science educators is teaching foundational concepts while introducing their students to current research. Here we describe an active learning module developed to teach protein structure fundamentals while supporting ongoing research in enzyme discovery. It can be readily implemented in both entry-level and upper-division college biochemistry or biophysics courses. Pre-activity lectures introduced fundamentals of protein secondary structure and provided context for the research projects, while a homework assignment familiarized students with 3D visualization of biomolecules using UCSF Chimera, a free protein structure viewer. The activity is an online survey in which students compare structure elements in papain, a well-characterized cysteine protease from Carica papaya, to novel homologous proteases identified from the genomes of an extremophilic microbe (Halanaerobium praevalens) and two carnivorous plants (Drosera capensis and Cephalotus follicularis). Students were then able to identify, with varying levels of accuracy, a number of structural features in cysteine proteases that could expedite the identification of novel or biochemically interesting cysteine proteases for experimental validation in a university laboratory. Student responses to a post-activity survey were largely positive and constructive, describing points in the activity that could be improved and indicating that the activity helped them learn about protein structure.