Fig. 6: MD simulations of ion-binding to NHA2ΔN.
From: Structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2
a, Density of sodium ions over 716 ns of simulation f-01-0 during which one sodium ion spontaneously entered the binding site in protomer A. The [NaCl] bulk concentration was 150 mM and ions were free to diffuse. At the start of the simulation, both D277 and D278 were deprotonated in protomer A (right). Protomer B (left) had D277 protonated (neutral), while D278 remained in the carboxylate form (negatively charged). The arrow indicates the outward-facing entrance funnel through which ions diffuse to the binding site. The NHA2 dimer, shown in side view along the membrane, is presented in cartoon representation colored white; the membrane was omitted when preparing the figure for clarity. b, Sodium ion density, as in a, but when either Asp277 is deprotonated and Asp278 is protonated (protomer A, left) or both aspartates are protonated (protomer B, right) (based on simulation f-23-1). Ions do not enter the lysosolic funnel regions (highlighted with dashed circles). c, Side view from the dimerization domain (omitted) on the putative sodium-binding site, drawn from the last frame of the MD simulation. The sodium ion is shown as a yellow sphere, sodium-coordinating residues are indicated in bold, and other residues near the binding site are labeled for context. Water molecules within 3 Å of the sodium ion were included, with only one present in this snapshot at the end of the MD trajectory. d, Top view (from the lysosolic side), with elements as in c, with the addition of the dimer domain helices in light green. e, The shortest distance of any sodium ion to any carboxylate oxygen in either D277 or D278: time series (left) and histogram (right). f, Coordination of the bound sodium ion. The average contributions of oxygen atoms from different residues to the first hydration shell of the bound sodium ion, n1, identify the binding site residues. ‘OD*’ indicates the additive contributions from both the Oδ1 and Oδ2 carboxylate oxygen atoms; ‘water’ from any water molecules. n1 < 0.001 are not shown.
