Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite Glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to modeling an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large datasets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately three orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least ten-fold higher than it would be in neat solution, and is the real driver for varying permeability estimates we obtain through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs.