Abstract
Na+/H+ antiporters exchange sodium ions and protons on opposite sides of lipid membranes. The electroneutral Na+/H+ antiporter NhaP from archaea Pyrococcus abyssi (PaNhaP) is a functional homolog of the human Na+/H+ exchanger NHE1, which is an important drug target. Here we resolve the Na+ and H+ transport cycle of PaNhaP by transition-path sampling. The resulting molecular dynamics trajectories of repeated ion transport events proceed without bias force, and overcome the enormous time-scale gap between seconds-scale ion exchange and microseconds simulations. The simulations reveal a hydrophobic gate to the extracellular side that opens and closes in response to the transporter domain motion. Weakening the gate by mutagenesis makes the transporter faster, suggesting that the gate balances competing demands of fidelity and efficiency. Transition-path sampling and a committor-based reaction coordinate optimization identify the essential motions and interactions that realize conformational alternation between the two access states in transporter function.
Highlights
Na+/H+ antiporters exchange sodium ions and protons on opposite sides of lipid membranes
Using this structure (PDB ID: 4D0A) as reference for targeted molecular dynamics (MD) (TMD) simulations to create an outward-open PaNhaP led to an incomplete conformational change
We used the refitted outwardopen MjNhaP1 model as a reference to construct the outwardopen conformation of PaNhaP by TMD simulations[16]
Summary
Na+/H+ antiporters exchange sodium ions and protons on opposite sides of lipid membranes. The archaeal PaNhaP and MjNhaP1 as well as human NHE1, which is linked to a wide spectrum of diseases from heart failure to autism[5] and has no structure solved yet, are electroneutral antiporters of the CPA1 family, exchanging one proton against one sodium ion. By adapting the transition-path sampling algorithm[11] to shooting trajectories from pre-defined transition regions[12], we determined continuous and unbiased transition trajectories between access states. These transition paths are the exceptional segments of equilibrium trajectories when rare events—here the exchange of ions— occur, and contain the mechanistic information about complex molecular processes[11,12,13,14]. Path sampling allows us to “watch” the transport cycle unfold, with H+ and Na+ as substrates, both at near-ambient temperature (37 °C) and at 100 ° C, the physiological temperature for P. abyssi
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