Molecular dynamics simulations and thermodynamic studies of hemoproteins and their model compounds

Elucidation of the structures of molecular systems including biological systems such as peptides and proteins is crucial for investigating relations between structure, stability, function, thermodynamics, kinetics and mechanism. These relationships for biological molecules have been studied in a variety of areas. Two commonly used approaches in investigations of these complex biological molecules are molecular dynamics (MD) simulations and synthesizing model compounds.; In this dissertation, the MD simulations of three synthetic peptides, twelve model hemoprotein compounds and the rat outer mitochondrial (OM) and microsomal (Mc) cytochrome b₅ have been carried out to study dynamical behavior of structures and stabilities of the model compounds and two hemoproteins. The studied peptides have been designed to form α-helices when incorporated in novel hemoprotein model compounds, Peptide-Sandwiched Mesohemes (PSMs), which consist of two identical peptides [AcNH-A-A-E-X-A-E-A-H-A-A-E-X ′-A-CONH₂, with X = A, F or W, and X′ = K] covalently attached to a Fe(III) mesoporphyrin. The α to π helical transformation was observed in MD simulations of these synthetic peptides. The possibilities of transforming from α to π helical structures by the constituent peptides may influence the properties of the hemoprotein models. The results of MD simulations of PSMs, constructed from mesoporphyrin II or IX, and with (X′ = K) or without Lys-propionate linkages (X′ = A) allow us to assign structural roles to the two types of peptide-porphyrin covalent bonds. The presence of His-iron bonds is sufficient to maintain the proximity of the peptides to the porphyrin. The additional Lys-propionate bonds are needed for preventing the rotation of the peptides around the porphyrin to maintain the α-helical structure. Thermodynamic studies of carbon monoxide binding to the hemoprotein models indicate that the higher helix content of PSM (X = W, X′ = K) relative to PSM (X = A, X′ = K) results from hydrophobic effects. From the MD simulation of rat outer mitochondria) (OM) and microsomal (Mc) cytochrome b₅ (cyt b₅), both proteins exhibit limited mobility, while remaining close to their experimental initial structures. The investigation of the flexibility of both OM and Mc cyt b₅ demonstrate that the PSMs are well designed hemoprotein models and eventually may provide us with a way of designing hemoprotein model compounds and an insight of structural relations to biological function.