Heme enzymes energy surfaces

Some of the above mentioned studies also use two-layer ONIOM QM MM approaches to include the full protein in an MM description. Other examples of QM MM calculations of metal enzymes include heme oxygenase [89], nitrate reductase [90] and peptide deformylase [91]. Finally, we note that the ONIOM (I IF Amber) potential energy surface has been directly used in a molecular dynamics study (ONIOM/MD) of cytidine deaminase [92],... 

Many enzymes use redox centers to store and transfer electrons during catalysis. These redox centers can be composed of metals such as iron or cobalt, or organic cofactors such as quinones, amino acid radicals, or flavins. In order to fully appreciate the catalytic mechanisms of these enzymes, it is often necessary to determine the free energy required to reduce or oxidize their protein redox centers. This is called the redox potential. The measurement of enzyme redox potentials can be performed by either direct or indirect electrochemical methods. The type of electrochemistry suitable for a particular protein system is simply dictated by the accessibility of its redox center to the electrode surface. Because most reactions catalyzed by enzymes occur within hydrophobic pockets of the protein, the redox sites are often far from the surface of the protein. Unless an electron transfer path exists from the protein surface to the redox center, it is not feasible to use direct electrochemistry to measure the redox potential. Since only a few enzymes (most notably certain heme-containing enzymes) have such electron transferring paths and... 

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