Molecular dynamics of microperoxidases in aqueous and nonaqueous solutions

We report an extended molecular dynamics study of the heme-containing peptide ''microperoxidase'' (MP), a model system of several heme-proteins. The most commonly studied forms of MP, the octa- and the undecapeptide, are studied both in pure water conditions and in mixed solvent (80% methanol and 20% water) conditions that stabilize the monomeric form. The equilibrium structures and their stability are visualized by graphical tools and analyzed in terms of the molecular shape, the vibrational amplitudes, and torsional angles along the backbone. The obtained structures are used to confirm the experimental data on aggregation of Urry and Pettegrew(7.8) by using simple geometric arguments based on the possible assemblies of several monomeric units in space. We have investigated in detail the H-bond network and the influence on the heme conformational properties. We have found that heme interacts with the peptide through H-bonds formed by the propionates, the axial histidine, and different partners of the peptidic chain. These interactions are regulated by the degree of exposure of HIS to the solvent. These results permit us to predict that the undecapeptide and the octapeptide can be good model systems for horseradish peroxidase and cytochrome c', respectively.