User:ScienceBubble/sandbox

Blue copper protein types structure

The chemical structure of Type 1- Blue Copper Protein

Blue Copper Proteins, a class of Type 1 copper proteins, are small proteins containing a cupredoxin fold and a single Type I copper ion coordinated by two histidine N-donors, a cysteine thiolate S-donor and a methionine thioether S-donor. In the oxidized state, the Cu⁺² ion will form either a trigonal bipyramidal or tetrahedral coordination. The Type 1 copper proteins are identified as blue copper proteins due to the ligand to metal charge transfer an intense band at 600 nm that gives the characteristic of a deep blue colour present in the electron absorption spectrum.

The protein structure of a Type 1 blue copper protein, amicyanin, is built off of polypeptide folds that are commonly found in blue copper proteins β sandwich structure. The structure is very similar to plastocyanin and azurin as they also identify as Type 1 copper proteins. They are also similar to one another due to the geometry of the copper site of each copper protein. The protein azurin has a trigonal bipyramidal geometry with elongated axial glycine and methoinione sulfur ligands. Plastocyanins have an additional methionine sulfur ligand on the axial position. The main difference of each copper protein is that each protein has different number and species of ligand coordinated to the copper center.

Electronic structure of the Blue Copper Protein type I Copper Complexes

The strong bond between the copper ion and the cysteine sulfur allows for the non-bonded electron on the cysteine sulfur to be present on both the low/high spin state copper ion, d_x²-d_y² orbital and the p-orbital of the cysteine sulfur. Most copper (II) complexes will exhibit the Jahn-Teller effect when the complex forms a tetragonal distortion of an octahedral complex geometry. With blue copper proteins, a distorted tetrahedral complex will be formed due to the strong equatorial cysteine ligand and the weak axial methionine ligand. The two neutral histidine ligands are positioned by the protein ligand so the geometry is distorted tetrahedral. This will cause them not to be able to coordinate perfectly as tetrahedral or a square planar.

Inner and Outer Sphere Metal Coordination

The cysteine sulfur copper (II) ion bonds range from 2.6 to 3.2 Å. With the reduced form, CuI, protein structures are still formed with elongated bonds by 0.1 Å or less. with the oxidized and reduced protein structures, they are superimposable. With amicyanin, there is an exception due to the histidine being ligated and it is not bound to copper iodide. In azurin, the Cysteine112 thiolate accepts the hydrogen bonds from the amide backbone of Asparagine47, and Phenylalanine114, and Histidine46 donates a hydrogen bond to the carbonyl backbone of Asparagine10. The Cysteine84 thiolate of plastocyanin accepts a hydrogen bond from a amide backbone, Asparagine38, and Histidine37 interacts strongly with the carbonyl backbone of Alanine33 and more weakly with the carbonyl backbone of Leucine5, Glycine34, and the amide backbone of Phenylalanine35.

Blue copper protein ligand field effect

Energy Diagram representing the blue copper protein ligand field effect (Solomon et al., 2004)

The orbital degeneracy is removed due to the asymmetric ligand field. The asymmetric ligand field is influenced by the strong equatorial cysteine ligand and the weak axial methionine ligand. The reorganization of the oxidized, Cu⁺², state, at the blue copper protein active site will be minimized due to the fact that at the oxidized, Cu⁺², state, the Jahn-Teller effect will be ineffective. In Figure 2, an energy level diagram is present to show the three different ideal geometries and its degenerate states. (i) represents the energy level diagram of a tetrahedral geometric structure with a T₂ degenerate ground state. This is due to the Jahn-Teller distortion from the oxidation. (ii) represents the energy level diagram of a C_3v symmetric structure with a ²E degenerate ground state. This resulted due to the thioether bond being elongated in the reduction site of the blue copper protein. The unpaired electrons leads to the Jahn-Teller effect. (iii) represents the energy level diagram of the ground states not being on an equal level. This shows that there is no presence of the Jahn-Teller effect. This is due to the strong equatorial donor and weak axial donor interactions. (iv) represents the difference in distance between the d_xy and d_x²_-y² .