Protein Modeling C

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Re: Protein Modeling C

Postby sci-man » February 25th, 2012, 6:00 pm

has anyone double checked whether XIAP is just chain e or both e and f?
never found out.

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Re: Protein Modeling C

Postby Agggron » February 25th, 2012, 6:56 pm

When you are looking at the prebuild environment you are looking at two dimers put together, and there is a XIAP for each dimer. Thus, there is one XIAP represented by Chain E, and another XIAP represented by Chain F.

Also, I'm sorry about the confusion with the tighter/looser 3-10 helices. I really don't know why I thought having less residues per turn meant a looser helix, so thanks for clearing that up. D:

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Re: Protein Modeling C

Postby Phenylethylamine » February 25th, 2012, 8:51 pm

On the regional test, one of the questions on the regional test had to do with Cys203 and Arg233.
It asked for the importance of these amino acids to XIAP.

How do you deal with these questions, what commands do you do?
I know they are bound to come up during states.
EASTstroudsburg gave a good explanation for how to see where each amino acid is (side note: if you like your Jmol visualization to be nice and neat, you can use "select [number] and sidechain" and then "wireframe 200" – or "spacefill 200", as EAST said – to just show the sidechain, without the amino and carboxyl groups sticking out from the backbone).

However, in order to find out the importance of the amino acids, you're probably going to have to do some research in advance. Knowing where they are is a big help, as it can give you general clues about function (e.g., located on the outside makes it more likely to be a residue that bonds to another molecule, located on the inside makes it more likely to be a stabilizing residue, located in a pocket makes it likely to be an active site residue), but just that isn't enough to give a detailed, full-points answer.

My advice is to treat the on-site like it's a pre-build. Read up on the on-site before competition, and try to come up with several residues that could possibly be asked and what you would write for each. For example, anyone who read the molecular story information on the CBM site should have been able to guess that CYS203 would be one of the residues highlighted on the Regional on-site.
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Re: Protein Modeling C

Postby pabalan » February 26th, 2012, 12:26 am

SILLY, BUT SOMEWHAT NECESSARY QUESTION ALERT: how long are your guys' endcaps?

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Re: Protein Modeling C

Postby Phenylethylamine » February 26th, 2012, 6:36 am

SILLY, BUT SOMEWHAT NECESSARY QUESTION ALERT: how long are your guys' endcaps?
This year, in my prebuild kit, I got endcaps that were more or less exactly 2 cm long, and are very cylindrical, made of thin, matte plastic. This was the first time I'd seen endcaps like that – in past years, the kit has included shorter (maybe 1-1.5 cm), more rounded endcaps made of a thicker, more rubbery material. The ones I got this year with the Regional on-site were also the short/rubbery kind.

If you're making them from scratch, I would say they can be anywhere up to 2 cm – it's not stated that they have to cover the entire first amino acid, and the short/rubbery kind that they give doesn't.
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Re: Protein Modeling C

Postby Allinea » February 26th, 2012, 8:35 am

My advice is to treat the on-site like it's a pre-build.
I can't believe I haven't realized that <facepalm>. Thank goodness I've been paying attention in Bio class lately, we're just getting to knockout mice and just went through protein synthesis. My research for state is now much more streamlined :)
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Re: Protein Modeling C

Postby EastStroudsburg13 » February 26th, 2012, 12:06 pm

For people who have used jewelry wire, what gauges have you used? I know it says 22 gauge, but to me that seemed kind of small and difficult to keep in shape. I'm using 12 gauge as a creative addition, which to me is a lot stronger and sturdier.
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Re: Protein Modeling C

Postby Phenylethylamine » February 26th, 2012, 2:03 pm

For people who have used jewelry wire, what gauges have you used? I know it says 22 gauge, but to me that seemed kind of small and difficult to keep in shape. I'm using 12 gauge as a creative addition, which to me is a lot stronger and sturdier.
If by "it" you mean the Protein Modeling Wiki or previous comments in this/past years' threads, the only reason it says 22 gauge is because that's what I personally like to use – it's actually quite sturdy, without being too hard to bend, and it's fairly unobtrusive (so it doesn't clutter up your model).

I typically only use wire for support, though – in place of cross-linkers (because I think it looks nicer, and because it allows me to attach parts that aren't exactly one cross-linker-length away from each other) – and to attach my protein to the base. I'm not using it for sidechains or anything like that (I usually use pipe cleaners). I prefer thinner wire in part because it fades into the background when it's just for structural integrity; it doesn't look like it's supposed to be representing anything (although I do always clarify on my card that no, those are not supposed to be bonds...). For anything load-bearing, I wind two strands of wire together, but none of the materials typically involved in this event are particularly heavy. I've never had any problems with my wire bending in ways I don't want it to.

If you're using 12-gauge, it sounds like you're using jewelry wire for a very different purpose than I am.
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Re: Protein Modeling C

Postby EastStroudsburg13 » February 26th, 2012, 2:38 pm

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.
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Re: Protein Modeling C

Postby TheWiseGirl » February 26th, 2012, 11:35 pm

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