The alternating-access mechanism of transport of the Na+/Ca2+ exchanger

Conformational free-energy landscapes of a Na + /Ca 2+ exchanger explain its alternating-access mechanism and functional specificity

“…Conventional and enhanced-sampling MD simulations were carried out using GROMACS2018 or GROMACS 4.5.5 with PLUMED ( 48 – 51 ), at constant temperature (298 K), pressure (1 bar) and periodic-boundary conditions. The simulation systems ( 52 ) comprise the protein (with or without ions bound) embedded in a POPC lipid bilayer (of 208 molecules), ~15,000 water molecules and Cl − counterions, for ~80,000 atoms in total ( SI Appendix , Fig. S4 A ).…”

“…A methodology was developed to contrast the conformational ensembles obtained with our MD simulations with experimental measurements of hydrogen–deuterium exchange (HDX) carried out for WT NCX_Mj as well as the loop-elongation mutant 5L6-8 ( 52 ). This methodology builds upon a theoretical framework reported in a previous study ( 24 ) and is generally applicable to cases where multiple constructs and conformational states are evaluated; it explicitly accounts for the unknown degree of deuterium loss after quenching of the HDX reaction.…”

“…A comprehensive package of input and output files is available at https://github.com/Faraldo-Gomez-Lab-at-NIH/Download ( 52 ). Some study data available (Simulation data amounts to tens of terabytes; this data will be shared with researchers upon request).…”