Thursday, 21 June 2007


I stumbled across hemoglobin while I was studying for toxicology. The body's oxygen carrier is a pretty cool molecule. Here are some pictures that I drew in PyMOL during little "studying breaks". They are made from the XRD structure from Protein Data Bank. Thinking about it, it seems pretty cool that we can actually visualise molecular structures and that we get the same results when we model them in a computer.

On this one you can see the whole tetramer. The four heme groups are shown in yellow.

Heme is the center-piece of the molecule (or as they say prosthetic group). The O2 is right in the middle. Underneath is the Fe2+. It's bonded to the oxygen, the 4 nitrogens of the porphyrin ring, and the nitrogen of His87 which is the covalent connection to the protein (hence prosthetic group).

A hydrogen of His58 is very close to the O2. Good for it that it is bent away. You could imagine that linear CO wouldn't be quite as comfortable in there. This is probably one of the reasons why the affinity of hemoglobin for CO is much lower than that of isolated heme.

This is heme with its whole subunit. You can see how the two histidines (the covalently bonded one and the steric hindrance) come from different helices.

Doing all this makes me wonder which I like better quantum chemistry or theoretical biochemistry. I'll get to take a glance into both of them this summer hopefully. Maybe I'll know more then.


Anonymous said...

Thanks for the visuals. I am taking a sculpture welding class as a hobby. I am going to create a sculpture of the heme subunit for a project using metal rods and steal bearings. Your drawings help me visualize the final project.

Felix said...

oh, that sounds very interesting. if you put up a photo of that somewhere, let me know