Myoglobin structure

The protein that I've chosen to look at is myoglobin, which incidentally was the first protein structure to be found. Here is a picture of the structure:


Myoglobin binds carries oxygen in muscles, and binds oxygen at the heme group. The heme group is a porphyrin, which contains an iron atom at the centre. Porphyrins are aromatic molecules which are highly conjugated, usually deeply coloured and like to form complexes with other atoms. In this case, it is iron. The heme group is the red group of atoms at around the middle of the structure. Oxygen molecules bind directly to the iron atom.

The heme group is stabilised by hydrophobic interaction between the pyrrole rings in the porphyrin and hydrophobic amino acids in the interior of the protein. Additionally, a nitrogen atom from a histidine residue above the plane of the heme ring is coordinated with the iron atom, which also stabilises the interaction. I was able to find this particular histidine atom, and while it is still hard to see, it is one of the light green residues with the pentagon-like shape at the end of it in this picture, situated above the plane of the heme ring:

In order to better see the heme group and the binding site, I also made a ribbon structure. The iron atom in the centre of the heme group can easily be seen.

Proton Pump

To add to our discussion last week's chapter (Ch 2), I thought I'd put up something on proton pumps. Below is a video with voice-over giving a simple explanation, and p56-57;59 from Ch 2 has some generic information on ion pumps.


And here is the full 3D structure of 3B8C, a P-type proton pump, determined from X-ray crystallography experiments.


Right-click on the Jmol applet above to interact with the structure (highlight domains, calculate hydrogen bonds, show surface et cetera). If you want to visualise how this might fit into the cell membrane, try colouring residues by charge (e.g Select→Protein→Basic Residues (+), Color→Surfaces→Blue||Color→Structures→Cartoon→Blue ).

(Edit: If the above widget fails, or you want to look examine this in more detail, you can view the structure here.)