Uncertainty Quantification of Bacterial Microcompartment Permeability

Andre Archer; Brett J. Palmero; Charlotte Abrahamson; Carolyn E. Mills; Nolan W. Kennedy; Danielle Tullman-Ercek; Niall M. Mangan

arXiv · 2509.23445

Uncertainty Quantification of Bacterial Microcompartment Permeability

Andre Archer·Brett J. Palmero·Charlotte Abrahamson·Carolyn E. Mills·Nolan W. Kennedy·Danielle Tullman-Ercek·Niall M. Mangan

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Abstract

Salmonella expresses bacterial microcompartments (MCPs) upon 1,2-propanediol exposure. MCPs are nanoscale protein-bound shells that encase enzymes for the cofactor-dependent 1,2-propanediol metabolism. They are hypothesized to limit exposure to the toxic intermediate, propionaldehyde, decrease cofactor involvement in competing reactions, and enhance flux. We construct a mass-action mathematical model of purified MCPs and calibrate parameters to measured metabolite concentrations. We constrain mass-action kinetic parameters to previously estimated Michaelis-Menten parameters. We identified two distinct fits with different dynamics in the pathway product, propionate, but similar goodness of fit. Across fits, we inferred that the MCP 1,2-propanediol and propionaldehyde permeability should be greater than 10^{-6} and 10^{-8} m/s, respectively. Our results identify parameter ranges consistent with prevailing theories that MCPs impose preferential diffusion to 1,2-propanediol over propionaldehyde, and sequester toxic propionaldehyde away from the cell cytosol. The bimodality of the posterior distribution arises from bimodality in the estimated coenzyme-A (CoA) permeability and inhibition rates. The MCP permeability to CoA was inferred to be either less than 10^{-8.8} m/s or greater than 10^{-7.3} m/s. In a high CoA permeability environment with low rates of CoA inhibition, enzymes produced metabolites by recycling (NAD+)/(NADH). In a low CoA permeability environment with high rates of CoA inhibition, enzymes required external NAD+/H to produce metabolites. Dynamics are consistent with prevailing hypotheses about MCP function to sequester toxic propionaldehyde, and additional collection of data points between 6 and 24 hours or characterization of enzyme inhibition rates could further reduce uncertainty and provide better permeability estimates.

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Andre Archer, Brett J. Palmero, Charlotte Abrahamson, Carolyn E. Mills, Nolan W. Kennedy, Danielle Tullman-Ercek, Niall M. Mangan. 2025-09-27. Uncertainty Quantification of Bacterial Microcompartment Permeability. https://arxiv.org/abs/2509.23445

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