Fig. 6: The F–F′ loop moves downward during DHB’s conformational transition.
From: Molecular dynamics simulations elucidate the role of the F–F′ loop in substrate entry into CYP3A4
a Top: Schematic diagram illustrating the conformational changes of DHB and the F–F′ loop. Bottom: Two distinct pathways leading to stable DHB conformations with the psoralen head oriented toward the heme group, captured by independent, unbiased MD simulations. Time evolution of RMSD values for DHB and the F–F′ loop during MD simulations 3-5 (b) and 3-6 (c). All trajectory frames were aligned to the crystal structure prior to RMSD calculation. d, e Conformational transitions of the F–F′ loop during the simulations. The loops colored red, pink, light blue, and dark blue correspond to states I, II, III, and IV in b (d) or c (e), respectively. The overall enzyme structure is taken from the crystal structure, with the F–F′ loop shown in green. Final DHB structures (cyan) from trajectories 3-5 (f) and 3-6 (g), each aligned to the crystal structure (green)35.
