Abstract
The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic R free factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various possible states and see which fits the crystallographic raw data best. Applications to ferrochelatase, cytochrome c 553, alcohol dehydrogenase, myoglobin, and methylmalonyl coenzyme A mutase are described.
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