Molecular dynamics of ALDH1/2

Members of the aldehyde dehydrogenase (ALDHs) superfamily have unique characteristics at their substrate binding site, where they catalyze the NAD+-dependent oxidation of aldehydes to their respective carboxylic acids. Molecular dynamics simulations, performed with the GROMACS 2022 package, have investigated the dynamics of the substrate binding site, using ALDH1 (PDB ID: 6B5G) and ALDH2 (PDB ID: 5L13) crystallographic structures. The tetrameric structures were simulated for 100 ns in: (1) APO (without any ligand bounded) state; (2) NAD-bounded state; (3) subtrate-bounded state; and (4) NAD- and substrate-bounded state. A total of 101 frames were extracted at regular intervals of 100 ps from the molecular dynamics trajectory. The ligands were removed from the substrate binding site after production to ease analysis.