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3D structures of biomolecules are critical to understanding molecular mechanisms in core biological processes. Visualization of these dynamic processes can be challenging for students. However, this skill is critical for advancing their knowledge and reinforcing core concepts beyond the textbook. Thus, protein structure–function relationships serve as a learning outcome in many undergraduate biochemistry and molecular biology courses. The RCSB PDB database entries has grown to over 200K entries in past decade with an average increase of about 12K each year. This database will continue to grow as the methods of structural biology improve along with technological advances. It implies that a structural understanding of biomolecules is no longer a specialized theme, but an integral part of the curriculum. Furthermore, the ability to effectively evaluate and navigate structural data are skills needed in the modern academic and industrial workforce. During COVID-19, we expanded the protein-structure-function exploration (PSFE) initiatives at our primarily undergraduate HBCU. We focused on implementing PyMOL to advance interactive learning in virtual setting during pandemic hardship coupled with interactive engagement during extended lab and lecture sessions. PyMOL provided a way to dive into protein structures via the graphical user interface using basic functions as well as advanced functions that required text commands that could be combined into elaborate analysis scripts using procedural programming. The use molecular graphics software has been instrumental to infusing structural interpretation of molecular mechanisms that can lead to the formulation of new hypotheses. During the pilot phase of our PSFE initiative, we developed a plan to infuse our research involving modeling a helical sensory receptor, an oligomeric beta sheet transducer, and DNA-protein interaction as an introduction to PyMOL using a guided tutorial. The initial assessment was focused using semiquantitative queries that probed a student's understanding and appreciation of visualization and analysis of 3D structures. A subsequent approach focused on expansion of the preliminary activity towards similar structures in RCSB PDB database and utilizing a tutorial in addition to the use structural bioinformatics. Students then prepared a detailed structural analysis in form of a written report. The outcomes of the pilot PSFE were reported at the 2021 ASBMB "Teaching with Big Data" conference and ultimately published 1. Our PSFE initiatives have enhanced the rigor in our independent research, biochemistry, and molecular biology courses and labs. We have used crucial biomolecules in the central dogma to stimulate effective and inclusive engagement via visualization and structural approaches using PyMOL and the RCSB PDB database. Our initial results have shown increased not only increased performance in class, but also deeper and more meaningful discourse in their products. As we continue to improve our tutorials and methods, our future aims will include the use of more advanced features in PyMOL and develop modules that will reinforce these skills as well as implementation of the basic modules in earlier courses. 1 Trivedi,V.D.(2022) "PSFEProteinStructure-FunctionExplorationInitiativein Undergraduate Biochemistry and Independent Research Courses" Biochem. & Mol. Biol. Edu., 50 5, 473-475. Supported by BCU STEM Excellence scholarship program and previous support of NIH-NIGMS SCORE SC3GM113803 ended in 2020.
Trivedi et al. (Fri,) studied this question.