Clustering of SARS-CoV-2 membrane proteins in lipid bilayer membranes

We characterized M protein assembly within membranes using atomic force microscopy (AFM) of M proteins embedded in 2.25 μm × 2.25 μm suspended lipid bilayers that mimic the physiological composition of the ERGIC membrane. Data from these images and corresponding analyses are included in AFM_Data.zip. Additionally, an all-atom molecular dynamics (MD) simulation of the short form embedded in a lipid bilayer was performed using the CHARMM36m force field with the MD package GROMACS, version 2022. The full trajectory (excluding solvent molecules) is included as 7vgs_preproc_2_micros.xtc, with setup files in MD_Simulation_Files.tar.gz, and analyses scripts in MD_Simulation_Analysis.zip. To numerically solve the protein evolution equation, we create a finite difference script. All analyses were performed with python, where every script and all finite difference simulation data can be found in continuum_analysis.zip (variance_data.tar.gz is a subset of this simulation data separated due to size).