Protein Modeling C

pabalan
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Re: Protein Modeling C

Postby pabalan » February 20th, 2012, 3:15 pm

and another thing, is the part of the toober covered by the blue endcap regarded as the first amino acid? or is the first visible 2 cm of the toober the first amino acid of the chain?

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Re: Protein Modeling C

Postby theyankee » February 20th, 2012, 4:22 pm

Hey guys, sorry if this question is really noobish, but I was put in this event recently with no prior knowledge of proteins (or too much biology in general, it really isn't my thing).

In the model for caspase-3, would we have to show the helices in chain A for residues 224-226 and 271-273, and in chain B for 315-317? Or is that not needed? On the PDB sequence display it shows them as light pink helices that aren't labeled as alpha helices, but on JMOL they're colored pink like the rest of the helices.

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Re: Protein Modeling C

Postby Agggron » February 20th, 2012, 5:20 pm

@ palaban: The 2 cm that the endcap covers is counted as the first amino acid. So if you make a bend right after the endcap, that separates the first and second amino acids. I think this is significant since on chain B the beta sheet around residues 294-295 are very close to the red endcap, so just make sure that the judges can tell where the end is and where the beta sheet is.

@ theyankee: From what I can see on the Jmol environment on chain A there's one alpha helix from 207-225, but maybe it's two helices put together: one regular helix from 207 to 221, and a 3-10 helix from 221 to 225? Either way, I think you should show them as helices, just have them structured a little differently - earlier in this thread someone mentioned 3-10 helices as having less of a turn (sorry my description isn't really accurate). I think the other residues you mentioned are also helices (not sure if they are 3-10) that you should show. Good luck! :)

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Re: Protein Modeling C

Postby theyankee » February 20th, 2012, 5:23 pm

Thanks for your reply, but yes, all of the helices I specified were 3/10... so does that mean I should make them bigger/smaller?

EDIT: I'm taking the sequences based on DSSP, is that accurate? Because I don't know how to find the residue number of an amino acid on JMOL.

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Re: Protein Modeling C

Postby Agggron » February 20th, 2012, 5:39 pm

As far as I know 3/10 helices are "looser", so they have fewer amino acids per turn. Correct me if I'm wrong though. :x

Um...for Jmol most of the time I just hover over a particular amino acid to find its residue number. Usually it says something like [CYS]285{xxx...], so I would know it's cys-285.

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Re: Protein Modeling C

Postby theyankee » February 20th, 2012, 5:43 pm

Hmm... It doesn't seem to do that for me on any browser.

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Re: Protein Modeling C

Postby Agggron » February 20th, 2012, 5:46 pm

D: What browser are you using? I use Firefox on my laptop - and at the competition we had to use Safari on Macs - both of which worked. :3

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Re: Protein Modeling C

Postby TheWiseGirl » February 20th, 2012, 5:48 pm

Thanks for your reply, but yes, all of the helices I specified were 3/10... so does that mean I should make them bigger/smaller?

EDIT: I'm taking the sequences based on DSSP, is that accurate? Because I don't know how to find the residue number of an amino acid on JMOL.
From what I've heard you make the 3/10 helices have 3 amino acids per turn versus the usual 3.6.

So the 3/10 helices are from residues 224-226 and 271-273 in chain A, and 315-317 in chain B, correct? Should we label these different on the model, or simply mention it in our notecard?

And my second question is, Caspase-3 is shown to have a chain A,B,C,D,E,F. I realize we're only supposed to model A and B, and C/D is the second monomer. However, E and F are different. Which is XIAP? And what's the other chain then? Chain F has 2 parts to it as well. I'm getting extremely confused with those 2 (chains E and F).
I'm quirky like a quark.

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Re: Protein Modeling C

Postby Agggron » February 20th, 2012, 5:53 pm

I think both Chains E and F are supposed to be representations of XIAP - at least, that's what I showed on our prebuild. I know Chain E for sure is XIAP - since at regionals they specified so - and that chain interacts with A and B. I feel like C, D, and E comprise a separate identical portion?

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Re: Protein Modeling C

Postby theyankee » February 20th, 2012, 6:37 pm

I've encountered a problem... the 3/10 helices are 2 amino acids long, therefore when I twist them, they have to be really tight -_-


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