Discover and read the best of Twitter Threads about #pymol
Most recents (2)
Guess who’s back? 👀 That’s right, it’s Keith Robison (@OmicsOmicsBlog)! He’s taking the mic once again to share some lessons from SARS-CoV-2 #sequencing data.
@OmicsOmicsBlog 1/ Hi again! Keith here, with a few plots and visualizations based on @GISAID data. Here’s a 🧵 on an intriguing set of SARS-CoV-2 mutations that is catching some attention online: deletions within NSP1. Let’s dive in.
2/ Many have paid attention to viral mutations on the Spike protein, b/c it’s an important target for the immune response, the antigen used in many vaccines & the target of therapeutic monoclonal antibodies. Spike has been the most active protein in terms of mutations arising.
We drew a couple of figures to illustrate our thoughts about mutation Y453F. We used our models of the "canonical" SARS-CoV-2 RBD bound to human and ferret ACE2 as a base, and use ferret ACE2 because it is virtually identical to European mink in this region of the protein.
In all figures, we show only 3 amino acids important to understand this mutation: ACE2 position 34 (white) and RBD positions 453 (orange) and 455 (pink). Some special atoms of each amino acid are colored red (oxygen) or blue (nitrogen) when necessary.
Human ACE2 bound to SARS-CoV-2. Y453 makes a hydrogen bond with H34 (red/blue spheres) and hydrophobic contacts with L455. All three amino acids stabilize each other through these bonds/contacts and contribute to a stronger interaction between the two proteins. 
