Hemocyanin structure

I was curious to see whether there were any obvious similarities in the subunit interactions of hemocyanin and hemoglobin. I downloaded 1NOL.pdb of Hazes et al. (1993). They reported it as a homohexamer and so I tried to dock the structure as a compact hexamer. In the crystal the hexamer has a large central cavity, which is unsatisfactory on physical grounds (see the first post of this Blog). Docking of a hexamer was unsatisfactory but a tetramer docked very well.
I have added the tetramer to the Gallery. The implication is that the tetramer has a physiological role.
Like hemoglobin, hemocyanin has an extensive aromatic network linked to the oxygen binding sites. Unlike hemoglobin the network does not appear to link oxygen binding sites on adjacent subunits. It is also unclear how the reported reverse Bohr effect could work.

Hemoglobin of the goose.

I have placed the R state and T state of hemoglobin from the Bar-Headed Goose, Anser indicus, in the Gallery. Inositol hexaphosphate is the polyanionic effector of avian hemoglobins and I have included a molecule of inositol hexaphosphate in the polyanion binding site of the T state. The positive charges of the polyanion binding site can be visualised by following the instructions in the Gallery. It can be seen that there are more positive charges than in human hemoglobin. The number of positive charges able to interact with the inositol hexaphosphate is more than appears at first sight, because allowance must be made for the flexibility of lysine side-chains. The larger number of positive charges accords with the fact that the avian effector has more negative charges than does diphosphoglycerate, the effector in human hemoglobin.

The Gallery can be accessed by clicking on the Title of this Post.

Quaternary Isomers of Hemoglobin

Perhaps a suitable term for the T state and R state conformations of hemoglobin would be "Quaternary Isomers". I have previously described them as interchangeable by subunit exchange. Subunit exchange is geometrically equivalent to concerted rotation of each subunit about its radial axis by 120º and perhaps this would be the preferred pathway of isomerisation in nature. For an α₂β₂ tetrahedron there are 3 different quaternary isomers. For vertebrate hemoglobins, a clockwise rotation of each subunit of the R state by 120º produces the T state with a polyanion binding site. An anticlockwise rotation of each R state subunit by 120º produces an alternate T state without an intact polyanion binding site. The alternate T state probably has a minor role physiologically. In the presence of the appropriate polyanion effector the isomerisation equilibrium would shift towards the main T state.
I have placed all 3 isomers in the Gallery.