First, just a friendly reminder, since there seem to be a lot of new people posting in this thread:
Please read the entire thread before asking your questions. Many similar questions have already been addressed in detail.
And from what I've read on the forum it seems like a lot of people are confused about which ones the 3/10 helices are. But if you look at the protein on jmol on the PDB website and color by secondary structure the 3/10 helices show up as a purple color. Am I missing something? It just seems like a lot of people are super confused, which makes me wonder if I've got something wrong...
3/10 helices show up as a darker, more purple color in newer versions of Jmol, like what you'd find on the PDB website, or what you'd get if you downloaded standalone Jmol now.
However, in older versions of Jmol, like what they're using in the online prebuild competition environment
, 3/10 helices show up as the same color as alpha helices. This is presumably the source of the confusion.
If you are using the online prebuild environment and you are confused about where the 3/10 helices are, try looking at the protein on the PDB site instead.
As for what
3/10 helices are: they're just another kind of helix, which is vastly less common than the alpha-helix. They have three residues per turn instead of 3.6 residues per turn, which makes them tighter
than alpha-helices, not looser. All the 3/10 helices in this protein are exactly three residues in length, and therefore should be exactly one turn.
If you use colors to label your secondary structures, it might make sense to differentiate between alpha-helices and 3/10-helices; however, if you rely on the accuracy of your folding to identify your secondary structures, the tighter helix should make the difference clear.
1) What's a beta bridge? How is it different from a beta sheet?
A beta bridge is an isolated residue that forms hydrogen bonds with its neighbors in a way similar to how beta sheet residues bond to each other. We do not have to show beta bridges in our model
– their only function is to slightly increase the stability of the structure, and they don't look like much.
2) Why is chain C of Caspase (which is identical to chain A) apparently 144 amino acids versus 143? That's what the sequence map on PDB said at least.
The ends of chains can be hard to resolve via x-ray diffraction, because they're typically more mobile than the rest of the protein – so all that happened here is that they managed to resolve 144 residues of chain C, but only 143 of chain A. In reality, the two chains are identical.
3) On the sequence map for chain A (and others) there are some SNP's. Do they affect the structure/function of the protein in any way, or is it just there to show people that there have been mutations there before?
The particular single nucleotide polymorphisms (SNPs) that you see on the sequence map
don't really affect the structure or function of the protein; they just mean that some percentage of the population has a different residue at that position, which still maintains the functionality of the protein.
However, another SNP is pretty important to the event this year: Nic Volker's disease was caused by a very, very rare SNP in his XIAP gene, which rendered his XIAP proteins non-functional. Note that because this SNP is not common, it does not appear in the sequence summary for XIAP (chain E) at all; you can read about it on the CBM site