Figure 3
From: Monatomic ions influence substrate permeation across bacterial microcompartment shells
Molecular occupancy and permeation through WT PduA in MD simulations. (A) Graphical depiction of the geometrical definitions used to estimate (blue cylinder) Nmol and dpore and (cyan cylinder) molecular permeation rates (see “Methods”). (B) Histograms of the average number of each molecular, Nmol, at various displacements along a 0.7 nm-radius cylinder aligned with the PduA pore axis, dpore, referenced such that the average position of PduA S40 Cα atoms are at dpore = 0 nm. Data shown separately for water and 1,2-propanediol (PD) in simulations with and without salt, and for Cl- and Na+ in simulations with and without PD. Vertical bars represent standard errors across three repeat simulations. (C) Spatial distribution functions of Cl- in the WT PduA pore. Residue S40 is shown for clarity. Yellow grid lines and solid surface enclose regions with time- and ensemble-average Cl- densities greater than 10- and 30-times bulk values, respectively. Data are from the three simulations lacking metabolites. (D) Representative conformation with two Cl- ions in the pore, coordinated by backbone amide groups of S40 residues. (E) Rates of bidirectional molecular permeation through the PduA pore. Permeants are labeled on the abscissa and simulation conditions are noted above each bar.
