The BASIL cure: Using structure to predict function in protein biochemistry.

Abstract

We have developed an undergraduate biochemistry lab curriculum based on authentic inquiry. This course-based undergraduate research experience (CURE) allows a large number of students to gain skills often learned only in the traditional one-on-one mentor-student research model by bringing a research project into the undergraduate teaching lab. The Biochemistry Authentic Scientific Inquiry Lab (BASIL) uses a combined computational and wet lab approach to study proteins of known structure but unknown function. Over 3800 structures in the Protein Data Bank (PDB) have unknown function. Students following the BASIL curriculum use a combination of sequence and structure alignment tools to study these structures with the goal of identifying possible enzymes. They then use molecular docking to predict what model substrates fit near a proposed active site. Students can produce the target enzymes in the lab using standard wet-lab biochemistry techniques for expression and purification, and they then perform kinetic assays with model substrates selected from their docking studies. We have successfully used this curriculum in biochemistry lab courses for majors and non-majors. The curriculum is modular and can be used as a whole or individual parts may be incorporated into an existing course - either lecture or lab. Curriculum materials are available free-of-charge at basilbiochem.org. We are currently investigating how this curriculum can be used in a variety of academic settings, and we welcome new collaborators. We can offer synchronous support via virtual meetings and asynchronous support via Slack. This project is supported in part by NSF IUSE 2141908.