Quantifying selective metabolite transport for the bacterial microcompartment from Haliangium ochraceum with molecular dynamics simulations

Abstract

Bacterial microcompartments (BMCs) are protein-based organelles found in diverse bacteria that encapsulate a sequence of enzymes to accelerate specific metabolic pathways and limit toxicity by confining intermediate products. To facilitate catalysis in BMCs, reactants and products must transit across the protein shells, which are made up of multimeric protein tiles. Quantifying the permeability for transport of small molecules across the shell is a key engineering consideration to design novel catalytic microcompartments. We examine the permeability of reactants and products for two reaction pathways, the degradation of 2-aminophenol by AmnAB and the reduction of nitrite to ammonium by NrfA, through a computational lens to quantify permeability for these metabolites at the nanoscale. From Hamiltonian replica exchange umbrella sampling simulations, we determine that the energetic barriers to permeation for the relevant metabolites along both pathways are small, with permeability coefficients in the range of 0.1–4 cm s⁻¹. The high permeabilities calculated for each metabolite through the inhomogeneous solubility diffusion model are corroborated by enzyme activity measurements in vitro that point to enzymatic activity within the shell system. We expand on these findings by quantifying the scale of transport and catalysis that can be supported by in vitro BMC systems. The results highlight the importance of substrate permeability across BMCs within a biological context, and represent steps toward generating synthetic shells or bioengineering novel nanoreactors.