Protons in small spaces: Discrete simulations of vesicle acidification
Fig 5
Effects of vesicle radius and steady state pH on H+ and pH fluctuations as predicted from our DS model.
(A&B) The standard deviation in the free proton count of DS model simulations (σ(NH)) as a function of vesicle radius with the lumenal/bath pH set to 5.5 (panel A) or as as a function of lumenal/bath pH with the radius fixed at 150 nm (panel B). (C) The instantaneous free proton count over time and corresponding count histogram for the common DS model simulation to panels A-D (diamonds) with r = 150 nm and pH = 5.5. (D&E) The standard deviation in pH of DS model simulations (σ(pH)) as a function of vesicle radius with the lumenal/bath pH set to 5.5 (panel D) or as as a function of lumenal/bath pH with the radius fixed at 150 nm (panel E). Dashed lines in A, B, D, and E scale as expected based on free proton count and pH scaling with volume and pH as described in the main text. (F) Standard deviation in steady state pH as a function of lumenal pH for vesicles undergoing active proton pumping. The proton pump rate was adjusted to achieve different internal pH values, each curve corresponds to a different size vesicle (r = 100, 150, 200, and 250 nm). The inset is a histogram of free proton counts for the r = 150 nm, pH = 5.45 data point (diamond). For all panels, the simulations of the DS model were run for 750 s at equilibrium with the bath pH, with no active pumping (except panel F), and PH = 4.6 × 10−5 cm/s. All other parameters can be found in Table 1.