Examining COVID-19 Variants through PyMOL, a Research Tool Offered at the University
The B.1.1.7 variant, also known as the Alpha variant, of the SARS-CoV-2 virus has been a topic of interest due to its increased infectiousness. This variant primarily affects the spike (S) protein, with specific mutations in its receptor-binding domain (RBD) enhancing its binding affinity to the ACE2 receptor on human cells.
One such mutation is N501Y, which has been identified as a key factor in the variant's increased infectiousness. This mutation allows the spike protein to bind more tightly to ACE2, facilitating more efficient viral entry.
To better understand these structural and interaction changes at the atomic level, researchers often use PyMOL, a powerful molecular visualization software. PyMOL can be downloaded from the internet and accessed through the University Sonicwall VPN.
With PyMOL, users can load the 3D structures of the spike protein—both wild-type and variant forms—and the ACE2 receptor. They can then highlight mutations such as N501Y in the spike protein structure, visualise the spike-ACE2 binding interface, compare conformational differences between wild-type and variant spike proteins, illustrate electrostatic surface changes caused by mutations, and generate detailed images or animations for presentations or further structural analysis.
For instance, the command "color red, sele" colours the selected amino acid in red on the PyMOL structure, while "select resi 501" highlights the amino acid 501 on the spike protein structure.
PyMOL is a valuable resource for students, particularly those in the Molecular Biology department, and is heavily used in biology and chemistry. In fact, a recent article in The New York Times provides visualizations of mutations and different variants of SARS-CoV-2.
It's important to note that the spike protein mediates viral entry by its RBD interacting with the ACE2 receptor. The spike protein of SARS-CoV-2 is made of three identical subunits, which are collectively referred to as "the spike protein". COVID-19, a disease caused by the virus SARS-CoV-2, enters human cells using this spike protein.
Variants of SARS-CoV-2 have different mutations on the spike protein, and PyMOL can be used to visualize these differences in various coronavirus variants. The B.1.1.7 variant is thought to be 30-50 percent more infectious than other variants, largely due to the mutation N501Y in the RBD, which makes the binding between the spike protein and the ACE-2 receptor tighter.
In summary, PyMOL is a powerful tool for visualising the structural and interaction changes in the spike protein of the B.1.1.7 variant, helping us better understand the molecular basis of increased affinity due to these mutations and variant-specific behaviour.
(Nanako Shirai, Natural Sciences Correspondent)
- Junior students in the Molecular Biology department often use PyMOL, a software for molecular visualization, to better understand the structural differences between the spike protein of the SARS-CoV-2 virus and its variants.
- In contrast to the junior paper, a senior thesis might focus on the impact of specific mutations, such as N501Y, on the binding affinity of the spike protein to the ACE2 receptor, contributing to the increased infectiousness of the B.1.1.7 variant.
- Understanding the relationship between fitness-and-exercise regimens, health-and-wellness, and medical-conditions is essential. However, PyMOL, a tool for visualizing molecular structures, sheds light on the science behind the increased infectiousness of the B.1.1.7 variant by illustrating the changes in the spike protein's structure and interaction with the ACE2 receptor.
