Sodium is an allosteric modulator of odorant receptors

Initial topology, parameter, and coordinate files of the Molecular Dynamics (MD) simulations of seven odorant receptors (ORs). Seven receptors were simulated: Class I: OR51E1, OR51E2 Class II: OR1A1, OR2W1, OR5K1, OR8D1, OR11A1 Each receptor was simulated in four protonation state and in two conformational state (active and inactive-like): deprotonated (-/-act): D2.50 and D/E3.39 deprotonated monoprotonated (H/-act): D2.50 protonated only protonated (H/Hact): D2.50 and D/E3.39 protonated inactive (-/-inact): D2.50 and D/E3.39 deprotonated bound to Na+ We used OpenMM (v8.0) as the molecular engine and CHARMM36 as the force field. Three independent replicas of 1 µs each were run per system (XTC format), stored with the following naming scheme: dry_aligned_rep_<replica_num>.xtc. Water molecules, ions, and membrane atoms (POPC: phosphatidylcholine) were removed from the original trajectories and topology before upload. The dry protein topology is provided as dry_prot.pdb. The initial topology and coordinate files (structure.psf, structure.pdb) are stored in the input_structure/ subfolder of each system. MD protocol and additional material related to this work are available at: https://github.com/anicoli/OR_sodium