A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms
Fig 5
Enhanced discrimination driven by an ion leak.
(A) For the model of Fig 4, the substrate, ion, and decoy flux are shown for a varying chemical potential difference of the driving ion. Note the negligible decoy flux relative to the substrate flux near −4kBT. Inset is the kinetic pathway diagram of the model at a specific chemical potential difference (−4kBT, vertical line) of the ion. (B) The same discriminative model as in (A), but with the energy barrier between the ion-only bound states in the inward and outward conformations raised by 100kBT, effectively shutting off the ion leak. Both the substrate and decoy fluxes increase. Inset is the kinetic pathway diagram of the model with the leak removed, resulting in two symmetrical pathways for substrate and decoy transport. (C) Comparing the ratio of substrate to decoy flux (selectivity) for the same model with and without an ion leak. With the ion leak, the selectivity approaches infinity due to the negligible decoy flux. In contrast, removing the ion limits the selectivity to the expected equilibrium-like value of eΔΔG=1. Note that the sign change of the selectivity is due to the change in substrate and decoy flux direction.