Teaching enzymology with the Protein Data Bank: From pandemic to Paxlovid
RCSB Protein Data Bank is a rich open-access resource for introducing many aspects of protein structure and function into biochemistry courses. In addition to containing more than 200,000 biomacromolecule 3D structures, it also hosts PDB-101 training materials, the Molecule of the Month series and additional resources for exploring enzyme structure–function relationships.
Starting with an example of the SARS-CoV-2 main protease, we demonstrate how to use new PDB tools, notably interactive sequence and structure (1D-3D) views, ligand interactions and exploration of groups of protein to identify trends and understand structure–function relationships more deeply.
The introduction of each tool is followed by hands-on learning exercises and ideas for preparing a lesson plan using another enzyme. Viewers will learn to use PDB resources to create graphically rich, deeply annotated and engaging lessons about enzyme function for their upper-division undergraduate and graduate students and even administrators or funding agencies.
Speakers
![Stephen K. Burley](/getmedia/99949dd7-a5e2-4927-a9b6-454eeb496556/300x300-Stephen-Burley.jpg)
Stephen K. Burley
Director, RCSB Protein Data Bank; University Professor and Henry Rutgers Chair, Rutgers University
![Paul A. Craig](/getmedia/87d3fa64-eb3c-45a7-b8f3-77f02a919e19/300x300-Paul-Craig.jpg)
Paul A. Craig
Professor of chemistry and materials science, Rochester Institute of Technology
![Shuchismita Dutta](/getmedia/61b4cc93-764f-428c-9d48-63d65582d5a4/300x300-shuchismita-dutta.jpg)
Shuchismita Dutta
Scientific training, education and documentation lead, RCSB Protein Data Bank
Who should watch
- Faculty members who teach biochemistry courses that involve structure-function relationships at all levels.
- Graduate students and post-doctoral fellows who are interested in teaching and science communication.
Key takeaways
- Navigate the RCSB PDB website to visualize each 3D structure and explore various annotations mapped to it.
- Compare the shapes, interactions and functions of groups of PDB structure with similar sequences and/or similar structures.
- Use RCSB PDB data, tools and resources to enhance classroom instructions and build lessons for teaching about enzymes.