Atomistic MD simulation. The synthetic T=4 carboxysome cryo-EM structure was solvated in a water cube with side length 29 nm and prepared for simulation (SI Animation 1) with the CHARMM36m force field for proteins (70) using VMD .To track metabolite permeation, we add 500 mM concentrations of CO2, O2, HCO3 -, 3-PGA, and RuBP to independent simulation systems (SI Fig. ). After a brief equilibration period utilizing NAMD 2.14 , each simulation was converted using TopoGromacs to GROMACS for production simulations, which were 3 replicates for 500 ns each. Particle tracking and analysis was performed with pythonenabled VMD (71), extensively using numpy , scipy (