Investigation by MD simulation of the key residues related to substrate-binding and heme-release in human ferrochelatase

Molecular dynamics (MD) simulations of three models based on the crystal structure of the E343K variant of human ferrochelatase were performed in this study. The “open” and “closed” conformations of the enzyme obtained by simulations are in agreement with the corresponding crystal structures. The snapshots and the structure analysis indicate that alterations of the hydrogen bonds and the positions of E347 and E351 lead to a conformational change in the π-helix. The hydrogen bonded form of residue R164 could be regarded as a signal indicating alteration of the active site conformation. When R164 forms a hydrogen bond with D95, the active site is closed, and when a hydrogen bond is formed with E171, the active site is open. Interestingly, the protoporphyrin with Fe²⁺ is observed to move noticeably out of the enzyme while the protoporphyrin lacking Fe²⁺ remains almost fixed. Alterations of the hydrogen bonds between the propionate of the heme and R115, K118 and S303 trigger movement of the heme out of the active site. Residues E347 and E351, which are located on the π-helix and form an acidic path leading to a salt bridge interaction with the propionate of the heme, accelerate the release process.