Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO₂ in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate ([Formula: see text]), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic [Formula: see text]-carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to [Formula: see text] relative to CO₂. To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO₂-concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO₂ assimilation in a crowded model carboxysome. Despite a relatively high CO₂ permeability of approximately 10^-2 cm/s across the carboxysome shell, the shell proteins reflect enough CO₂ back toward rubisco that 2,650 CO₂ molecules can be fixed by rubisco for every 1 CO₂ molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.