Fig 1.
Proton pumping by rotary and alternating access mechanisms.
H+ transport, against a transmembrane pH and electric potential (Δψ) gradient, is driven by the hydrolysis of ATP to ADP. (a) In the rotary mechanism, hydrolysis of ATP causes the rotation of the transmembrane ring which leads to proton transport across the membrane. (b) In the alternating access mechanism, ATP hydrolysis produces allosteric conformational changes that transport protons across the membrane.
Fig 2.
Minimalistic kinetic models of possible ATP-driven H+ pump mechanisms.
Coupling ratio of 3:1 H+:ATP is shown here. See S1 File for 2:1 coupling ratio. Two possible proton transport mechanisms, (a) rotary and (b) alternating access, based on one of six possible sequences of reactions (event orders) for nucleotide and phosphate binding/unbinding in the ATP-driven proton pumping cycle. Results are qualitatively similar for other event orders. See S1 File and Fig 4(b).
Fig 3.
Kinetic models of all possible proton transport orders for ATP-driven H+ pump mechanisms based on one of six possible nucleotide and phosphate binding/unbinding sequences in the ATP-driven proton pumping cycle.
Coupling ratio of 3:1 H+:ATP is shown here. See S1 File for 2:1 coupling ratio. Results are qualitatively similar for other event orders. See S1 File and Fig 4(b).
Fig 4.
Rotary mechanism is faster than other possible mechanisms across a wide range of driving conditions.
(a) Average rates for the different mechanisms showing that the rates are quantitatively similar to experiment (∼60 H+/s [1]), and that the rotary mechanism is faster on average. (b) Average ratio of H+/s relative to the rotary mechanism showing that the rotary mechanism is also faster across a wide range of conditions. (c) Average ratio for extensive and systematic variations in model assumptions showing that results are qualitatively similar. Results shown here for 3:1 coupling ratio are qualitatively similar for 2:1 coupling ratio (see S1 File). Average ratio is the geometric average of individual ratios of pumping rates relative to the rotary mechanism for each set of condition, i.e. the ratio is calculated for each condition and then averaged across all conditions. Error bars show standard error of the mean when sampling over a range of conditions.
Fig 5.
Free energy landscape for rotary and alternating access mechanisms.
Free energy (FE) calculated using Eq (5) for a representative set of parameters from the optimization protocol, and typical physiological conditions. See S1 File. The steps in the proton pumping cycle correspond to those in Fig 2, with labels. “+ATP” is the ATP binding step, “->ADP” the ATP to ADP hydrolysis step, “-Pi” and “-ADP” the Pi and ADP unbinding steps, “+H+” the H+ binding step on the cytosol side, and “-H+” the H+ unbinding step on the “out” side of the membrane. For the example shown, the maximum FE climbs are 3.1 and 6.7 kcal/mol for the rotary and alternating access mechanisms, respectively, with corresponding rates of 42 and 10 H+/s, for the same driving potential ΔGdriv based on conditions described in S1 File.