okay, so at this point, I am ready for this event in all respects but one: the notes! I have a basic idea as to what to include in them, but I was just wondering what participants on here have found particularly helpful to include, or what you guys felt were absolute necessities and/or found yourselves revisiting time and time again on there. I'd be ever so grateful for any and all feedback!
In my notes, I have the structure summary page of both the pre-build and the on-site, some random protein background knowledge that I probably don't need but haven't bothered to take out, essentially the entire contents of the CBM site, and (probably most importantly) detailed background information about the on-site and pre-build.
With Caspase-3 or proteins as a whole, how do we know where to put the crosslinks?
This has come up on the thread a bunch of times, and I think I should probably put something about it on the Protein Modeling Wiki
, but here's the answer again:
The cross-linkers are for structural stability only, and do not have to represent anything in particular.
You can put them wherever two pieces of the protein come sufficiently close and need stabilizing.
That said, you could
use them to represent actual bonds if you chose; you would just have to specify that on your card.
Personally, I use them to hold together the protein when I'm first folding it, but replace them with wire stabilizers before competition (looks nicer, allows me to stabilize places where the gap isn't exactly one crosslinker-length). I also cut them in half and use them (attached to the end of double-twisted wire supports) to attach my protein to its base, so it will be removable for examination by the judges.
Thanks alot! so is that the only active site involved in the prebuild. Also, are both chains e and f allosteric inhibitors of chains a and b or is one the inhibitor of chains a and b and one the inhibitor of chains c and d?
Caspase-3 actually has a series of "active sites", in that it has a preference for a sequence of something like four consecutive residues in its substrate that bond loosely to four consecutive spots on its surface. However, you're correct in that peptide cleavage occurs only at that particular point, CYS285.
Chain E and F are identical; each is one copy of the XIAP BIR2 domain. Chain E is bound to (and therefore inhibits) the caspase-3 asymmetrical unit of chains A and B, while chain F is bound to chains C and D (this should be apparent if you look at the Jmol visualization – use the commands "select all", "backbone 200", "color chain" and then mouse over each chain to see its letter).
An "allosteric inhibitor", for those who are not familiar with the term, is a molecule that prevents the function of a protein by binding somewhere other
than its active site (usually by changing the overall shape of the protein, rather than by simply blocking its active site). XIAP can act as an allosteric inhibitor for some proteins, but it is actually a competitive inhibitor
for caspase-3, meaning that it binds in the active site (thus competing with the normal substrate of caspase-3).