Protein Modeling C

[Phenylethylamine]

Ah, never mind, I'm looking at the rules and it lists 12-gauge wire as a potential replacement for the Toober for the backbone. I guess I saw 22 so much that I thought that it was what was mentioned in the rules. I agree, they're very different purposes, and 22 gauge is good for connecting, since they're not a fixed distance.

Yeah, one of our B teams actually used 12-gauge wire for their backbone last year at Regionals; the entire protein ended up being noticeably smaller, even with the same 2 cm per residue scale, and they had a lot of difficulty attaching things to it. However, it did hold its shape pretty well, without requiring anywhere near as much support as Toobers do. On the whole, though, I'd say Toobers are vastly easier to use (I mean, it's just foam with a wire core, which is probably in the vicinity of 14-gauge – at least, it looks a bit smaller than 12-gauge).

@Phenylethylamine: THANK YOU THANK YOU THANK YOU THANK YOU for answering all of my questions!!!!

You're very welcome

[EastStroudsburg13]

I'd also say that the Toober is better, but as an addition, I prefer the wire rather than getting another Toober, partially because it's a whole lot cheaper.

[pabalan]

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!

[jmb04]

Okay so I have now read this entire thread as well as many other sources on the internet and I still haven't made myself positive about the active site of chains A and B of caspase-3... I realize XIAP is a zinc finger, and it is an allosteric inhibitor but all the confusion about ALA285 is really bothering me. Could anyone help me with the active site because I am completely lost on the matter. Also if CYS285 is the cleaving site of the protease, would it be a good idea to show a small portion of another protein that contains an ASP that is being cleaved or not?

[EastStroudsburg13]

@pabalan: I've usually put in information about the pre-build, the on-site builds, and the main topic in sections on my reference sheet, since that usually encompasses almost everything in the event. I'll usually put some jmol images and the PDB sequences in this section. This year, you should probably put information about Nic Volker's story, since that'll almost certainly appear on tests. Lastly, some general information about proteins, like each of the sidechains, which ones are hydrophobic, any charges, etc.

@jmb04: The active site is CYS285. ALA285 was a mistake in the jmol. I'd think that it would be a good idea to show a substrate being cleaved as a creative addition.

[Bluerang1]

With Caspase-3 or proteins as a whole, how do we know where to put the crosslinks?

[jmb04]

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?

[Phenylethylamine]

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).

[jmb04]

If XIAP is a competitve inhibitor then what residues are important to the active site it blocks? and what are the other residues other than cys 285 that are involved in the series of active sites?

[paradoxgirl]

If XIAP is a competitve inhibitor then what residues are important to the active site it blocks? and what are the other residues other than cys 285 that are involved in the series of active sites?

That's your job to find out! If you have a specific question (such as the cys 285/ ala 285 confusion) then this is the place to ask for help, but researching your creative additions is a huge part of this event. Its what sets you apart from other teams (who may not have researched as much as you). Its your chance to show how much you know about your protein.

My advice is to do a PubMed search for your prebuild protein, or perhaps the prebuild along with one of its substrates. You may find articles that mention the two of them working together (and amino acid residues involved in that process). An easier way: google it.