Geometry optimisations in the protein

The best way to study the geometry of the blue copper proteins is to perform geometry optimisations in the protein using combined quantum chemical and molecular mechanical n thods. We have recently initiated a series of such calculations using the program COMQum [57], which uses the B3LYP method for the active site and the Amber force field [40] for the rest of the protein [26]. Some of the results of these calculations are shown in Table 4. 

For the Cu-Swet bond length, the results are less clear. In all cases, the bond is elongated, and for the oxidised structures, it is in excellent agreement with experimental structures. However, for reduced plastocyanin, the Cu-Smci bond becomes too long, 339 pm, compared to -290 pm. This is most likely due to the flexibility of the bond, combined with problems in the classical force field. Apparently, the molecular mechanics part of the calculations is not accurate enough to describe the fine-tuned interplay between methionine group, the copper ion, and the surrounding enzyme. 

At first, these improved structures could be taken as evidence for protein strain. However, the ComQum calculations involve effects that are normally not considered as strain, e.g. the change in the dielectric surrounding of the copper 

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