Protein Visualisation Practical Exercises Using Pymol in Multiple Year Levels of an Undergraduate Biochemistry Program

 

Shane Austin

Tested Studies in Laboratory Teaching, 2019, Volume 40

Abstract

Using Pymol to aid student visualization of proteins and protein stabilization features is a powerful tool in teaching protein biochemistry. Pymol often helps students move from abstract concepts such as hydrogen bonds and salt bridges, to visualizing how these bonds and other non-covalent features contribute to protein 3D structure and function. The practical exercises presented in this poster focus on building student’s competence using Pymol. In a second-year exercise, students are shown basic secondary features such as loops, sheets and helices. They explore how hydrogen bonds and other interactions contribute to these features and start to visualize unique features such as pi helices. While in a final year course exercise, students use Pymol as a tool to visualize the complex interactions between the various subunits of the oxidative phosphorylation machinery. Responses from students in the second-year course have been favorable over 2 years of running the practical. Most students are pleased with the exercises and find they reinforce the lecture content. While the advanced course practical has been run for one semester and has been received very favorably by biochemistry major students.

Keywords:  Pymol, protein visualization

The Ohio State University (2018)