Protein of the Day #11: cystathionine gamma-lyase (CTH)

In a recent article in Science, Yang et al found that cystathionine gamma-lyase can produce hydrogen sulfide gas in mice, and that this seems to help control blood pressure. Since I'm interested in mammalian hibernation, this made me wonder about connections with another Science article from 2005 which showed that a torpor-like state of lowered body temperature can be induced in mice by a particular level of H2S exposure. This protein is very well conserved; below is an alignment with the mouse version with some mammals and the chicken. Normally it is involved in cysteine metabolism and presumably does not create H2S; there are some splice variants and perhaps the variants are important in this respect.

Protein of the Day #10: TRPV1

Mmmmm...spicy food. Wouldn't be as nice if we didn't have TRPV1, which responds to the capsaicin from hot peppers. Here is the predicted domain structure from the SMART database, with the transmembrane domains picked out (along with some ankyrin repeats):

Wordle Malaria

Wordle is a fun little site; I fed the OMIM entry for malaria susceptibility into it and got:

Protein of the Day #9: Retrocyclin

The defensins are an interesting protein family that is important in mammalian immune systems. It now seems that most mammals have some versions of the alpha- and beta-defensins, but only some primates have theta-defensins. In the human, there is a pseudo-gene for a theta-defensin that is post-translationally processed into a cyclic peptide called retrocyclin. It is possible that our loss of a functional retrocyclin contributes to our susceptibility to HIV and AIDS; its an interesting avenue for future gene therapy.

I can't find out too much about retrocyclin; since you pretty much have to use rhesus monkeys to study it, there isn't a lot out there yet. A good place to start is the OMIM entry for the alpha-defensins, and the paper by Cole et al.

Schlegel and the 600 cell

I just wrote a patch to do Schlegel diagrams (a sort of projection) of 4D polytopes in Sage. The 4D regular polytopes are an awful lot of fun to think about; below is a picture of the 600 cell as rendered by my new code. Its much more fun to play with it interactively - check it out.

Protein of the Day #8: Hemoglobin

So I should have called it "Protein of the Week". Ah well. Its the protein of the day, just not every day...

Hemoglobin: its a classic! Don't think that makes it boring. On the contrary, I think it remains a fascinating protein.

Its possible that it deserves the title of most-studied protein. Right now there are 4820 hemoglobin sequences at NCBI. It was discovered in 1851, and the structure solved in 1959 - I think that was the first protein structure found by x-ray crystallography. I could go on and on...

One of my interests in it at the moment is that hemoglobin is the food for the Plasmodium species that cause malaria. Amazingly, they synthesize their own heme groups. Hemoglobin is a funny food though, because of dealing with all those heme units, and Plasmodium has to accumulate hemozoin garbage.