Protein Modeling C

[gsheni]

I see on the rules that it says one 3”x5” note card.
What if you have more information that can fit on the notecard?

[FullMetalMaple]

Use the back and write or type small. I had a lot to explain on my notecard at my regional and just wrote small on the back (okay, so you probably shouldn't have that much information, but...).

[Phenylethylamine]

Thanks for the help so far everyone
I was wondering,
http://www.pdb.org/pdb/explore/biologyA ... ureId=1I3O
In the Protein Details section, it shows a list of GO IDs for Chains A and C.
Are those ID corresponding to amino acids, which then is corresponding to a definition?

Not quite. Those IDs correspond to entries in the Gene Ontology database, which is basically a glossary of gene/protein terms; they're each a term that is relevant to this protein structure.

So they don specifically tell the function of each amino acid, they just tell functions of the whole chain A and C.
I was wondering where nucleophile came on the regional test and it seems that it came from that page.
You think its worth memorizing those things or having on the note sheet?

They don't refer to any particular amino acid, correct; they are various terms that are related to this entire protein complex (caspase-3 in complex with XIAP) in one way or another.

That is one place that the term "nucleophile" is mentioned, true, but you could also have found it various other places (notably, the Wikipedia article on cysteine proteases has an excellent description of how they work, which explains how the nucleophile concept fits in there).

It could be good to be familiar with the concepts listed there, since a lot of them are things about apoptosis or cysteine proteases that could show up on an event, but it's a pretty general list. It could be a good place to start if you're looking for topics, though.

Is the Wikipedia article accurate for the active site? Because on the PDB it says that the residue at 185 is Ala. I've also seen other sources that say the active site Cysteine is Cys163 and the PDB says there's a Gly at 163. Is anyone able to shine some light on this?

The active site residue is Cys285. The alanine is there for crystallization purposes for research; it's really a cysteine. The reason it's numbered 285 instead of 163 is because 285 comes from caspase-1 numbering, I believe. It's the same residue, though.

Yes, CYS163 and CYS285 are the same thing, just under different numbering systems. For the purposes of this event, we are using 1I3O.pdb, which is numbered in the latter way (i.e., it's CYS285). This numbering system is, as FullMetalMaple mentioned, based on caspase-1: all caspases can be numbered this way, in order to look at the similarities between them (this is why we have residues 381A through 381H in there – there's an entire loop of residues in caspase-3 where there's only one residue in caspase-1).

If you go back and read through this thread, you'll see extensive discussion of why there's an alanine there in the file, and why it actually should be a cysteine.

I see on the rules that it says one 3”x5” note card.
What if you have more information that can fit on the notecard?

You have to fit all your information on the notecard somehow. You can definitely use both sides. You can also make your text smaller, but remember that it still has to be readable. You may just have to make your explanations more concise.

While you can try putting text on the model itself, remember that the judges are looking at a whole lot of models and may not be inclined to read a bunch of details written on your model after having already looked at your card.

[Dragonshark]

This is just a quick question that probably isn't very important, but does anyone know the name of Nic Volker's disease? Or was it too rare/novel to have been even assigned a name?

[FullMetalMaple]

He has XLP (X-linked lymphoproliferative disorder). I think about one in a million males (females can't get it, because they have two X chromosomes) have it, so it's rare, but not so rare it doesn't have a name.

[Phenylethylamine]

He has XLP (X-linked lymphoproliferative disorder). I think about one in a million males (females can't get it, because they have two X chromosomes) have it, so it's rare, but not so rare it doesn't have a name.

Note that not all cases of XLP are caused by XIAP deficiency. More than half (~60%) are caused by a mutation in a completely different protein. While roughly one in a million males are predicted to have the disease, there have only been about 400 cases reported (ever). The "chronic hemorrhagic colitis" (the bowel problems that Nic had) seems to be unique to the XIAP type of XLP (XLP-2), though.

[gsheni]

What about finding specific residues for PARP1, the on site model for states?
I have looked in google scholar and have come up empty.

[Phenylethylamine]

What about finding specific residues for PARP1, the on site model for states?
I have looked in google scholar and have come up empty.

Try downloading 3OD8.pdb and looking at it in Jmol, with sidechains on ("select protein and sidechain"; "wireframe 200"). If you know the function of PARP (and there's some information about it in the [wiki]Protein Modeling/Apoptosis[/wiki]), you may be able to come up with a few residues that appear to be important, based on the position of their sidechains.

[Helicase]

I want to do some creative additions to the Pre-build besides XIAP (chain c), but I can't really think of any. Would the connection (wherever that is) between chain a and b be a creative addition? Or what about the numbers on the number map http://cbm.msoe.edu/includes/jmol/SOJmo ... berMap.pdf
here? The numbers on the chart are different than the numbers on http://www.pdb.org/pdb/explore/remediat ... sPerPage=3
so would they be creative additions?
Also- where can i find reliable information on caspase-3 besides wiki? Sorry for all of the questions, help would be appreciated!

[Helicase]

I want to do some creative additions to the Pre-build besides XIAP (chain c), but I can't really think of any. Would the connection (wherever that is) between chain a and b be a creative addition? Or what about the numbers on the number map http://cbm.msoe.edu/includes/jmol/SOJmo ... berMap.pdf
here? The numbers on the chart are different than the numbers on http://www.pdb.org/pdb/explore/remediat ... sPerPage=3
so would they be creative additions?
Also- where can i find reliable information on caspase-3 besides wiki? Sorry for all of the questions, help would be appreciated!

sorry i just realized that the numbers are indeed the same- but would including them on the build and included on the card be an addition?