Using PyMOL to Understand Why COVID-19 Vaccines Save Lives

Celia Maya

doi:10.1021/acs.jchemed.2c00779

Using PyMOL to Understand Why COVID-19 Vaccines Save Lives

J Chem Educ. 2023 Feb 28;100(3):1351-1356. doi: 10.1021/acs.jchemed.2c00779. eCollection 2023 Mar 14.

Author

Celia Maya^{1

2}

Affiliations

¹ Instituto de Investigaciones Químicas (IIQ), Departamento de Química Inorgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 49, 41092 Sevilla, Spain.
² Facultad de Química, Universidad de Sevilla, Aptdo 1203, 41071 Sevilla, Spain.

Abstract

Chemistry and biochemistry instructors must help students to develop the ability to visualize and manipulate 3D biomolecular structures and critically analyze them and their relationship to their functions. To do this, representative systems must be strategically selected to stimulate students' motivation. Since the World Health Organization declared a global pandemic caused by a new beta-coronavirus, called SARS-CoV-2 in early 2020, huge efforts are being taken by researchers to learn in depth how this virus works and a lot of scientific results are continuously reported. Many of them focus on the structural features of the viral spike glycoprotein and their relation with the vaccine development. This paper presents a series of workouts that deep into the structural characteristics of the spike protein S SARS-CoV-2 virus and the structural features involved in its infection process, using free online resources such as the PDB and the computer program PyMOL. This type of activity is intended to engage structural biology students in examining these macromolecules and others to help establish procedures for controlling COVID-19 and other future infectious diseases. PyMOL session files and student activities are provided.