Dynamic Simulations of the Hydrogen-bondings on the Proximal Side of the Heme in Terms of the ABEEM/MM Method

The structures of sperm whale myoglobin (Mb) and mutants were investigated in terms of the ABEEM/MM method. The molecular dynamic simulations showed that the bifurcated hydrogen-bondings in the proximal side of the heme in Mb were not stable. These simulations indicated that hydrogen-bondings could not determine the overall orientation of imidazole, which could be related to the histidine residue. The amide acids and the bulk of the imidazole can have effects on the flexibility of proximal ligands.