Protein Modeling C

[FullMetalMaple]

Hey, my partner and I are doing this event for the first time; what are the red and blue end caps for? ^^;;

The blue cap is the amino terminus (N-terminus) of the protein. It represents the first amino acid in your model. The red cap is the carboxylic acid terminus (C-terminus), which represents the final amino acid.

[Phenylethylamine]

Again, a reminder: Please read the entire thread before posting, so you do not duplicate a question that was already asked.

Hey, my partner and I are doing this event for the first time; what are the red and blue end caps for? ^^;;

I refer you to this post:

I am confused about how you determine which ends the blue cap and red cap go on. Can somebody explain this to me?

The blue cap goes on the amino terminus: the low-numbered end. The red cap goes on the carboxy terminus: the high-numbered end.

Here's an easy mnemonic to remember this: In alphabetical order, you go from blue to red, so the blue one goes at the beginning (low number), and the red one goes at the end (high number). This also works for remembering which end is amino and which is carboxy; amino comes before carboxy alphabetically, so the amino terminus is the end with the lower number and the carboxy terminus is the end with the higher number.

To find them in Jmol, you can just look at the little info box on the side of the online competition environment (or the sheet that came with the Toobers, or the CBM site, or any of the various other places that mention this) and use the numbers it says (e.g., this year's prebuild says 148-296 for chain A, and 310-401 for chain B, so you'd use 148 and 296 as the ends for A and 310 and 401 as the ends for B).

Then use the commands:
select *a and 148
color blue
select *a and 296
color red
select *b and 310
color blue
select *b and 401
color red

That will show you where the ends are in the 3D structure, and will also make them the right colors.

The way I figure it in Jmol:
color group

After that, hover over one end to figure out the amino acid number and the cap of the same color on that end, other cap on the other end. Sometimes the chain ends before both red and blue are present, and you just have to go on whatever color is there (red or blue)... unless I've been doing it wrong all season.

That's a perfectly fine way of doing it, too, but this way doesn't involve the guesswork of making sure you've found the end and that you're interpreting the colors correctly (especially since sometimes neither red nor blue is present, particularly when you're looking at a fragment of a protein rather than a whole one). "color group" could still be the easiest way if you didn't know what the numbers of the ends of the chains were.

[BoldlyGoingNowhere]

I was just placed in this event two weeks before state. I am with two people who (fortunately) know pretty much what they're doing, but I have no idea what's going on... Can anyone just give me a basic idea of the MOST IMPORTANT things to study so I can help them as much as I can?

[Phenylethylamine]

I was just placed in this event two weeks before state. I am with two people who (fortunately) know pretty much what they're doing, but I have no idea what's going on... Can anyone just give me a basic idea of the MOST IMPORTANT things to study so I can help them as much as I can?

Make sure you know your basic protein and general chemistry facts (structure of an amino acid, relative strength of different types of bonds, protein primary/secondary/tertiary/quaternary structure, etc), so you can do the easy questions, leaving your partners more time to work on the hard ones and the on-site.

It could also be good to familiarize yourself with this year's prebuild protein (caspase-3) and the states onsite (PARP), for which I recommend reading this thread and the [wiki]Protein Modeling/Apoptosis[/wiki].

Actually, in general, reading this thread and the Protein Modeling Wiki as a whole is a great place to start.

[gsheni]

Based on the thread suggestions, I modeled Chain C,D. Now I want to show these as creative additions.
How would I show that?
I can show Chain E inhibiting Chain A,B. But what about Chain C,D?
Or
Should I leave out the chain C,D?

[FullMetalMaple]

Based on the thread suggestions, I modeled Chain C,D. Now I want to show these as creative additions.
How would I show that?
I can show Chain E inhibiting Chain A,B. But what about Chain C,D?
Or
Should I leave out the chain C,D?

What you want to do is really up to you - they're creative additions for a reason. Looking at the national rubric from 2010 should help you because that year, another part of the Jmol file could be modeled as a creative addition.

Also, there's a chain of XIAP for each unit of caspase-3.

Sorry if I don't seem too helpful: I don't want to give away everything to others because your model is your own. It's not mine. (Also, I seem to mess up a lot with the advice I give people here. XD)

EDIT: Also, for those who wanted to read this article on PARP, it's now viewable.

[Phenylethylamine]

Based on the thread suggestions, I modeled Chain C,D. Now I want to show these as creative additions.
How would I show that?
I can show Chain E inhibiting Chain A,B. But what about Chain C,D?
Or
Should I leave out the chain C,D?

What you want to do is really up to you - they're creative additions for a reason. Looking at the national rubric from 2010 should help you because that year, another part of the Jmol file could be modeled as a creative addition.

As a general rule, anything else in the Jmol file is a good place to start looking for potential creative additions. As for how to show chains C and D, the best place to start would be by simply placing them correctly relative to your model of chains A and B. Remember, chains C and D are identical to chains A and B – all their interactions (with each other, and with things around them) are the same, too. I don't recommend showing the exact same things on both copies, though, as that's pretty much redundant and doesn't add anything new to your model. You could just let your chains C and D be a creative addition on their own without any additional adornment.

Also, there's a chain of XIAP for each unit of caspase-3.

Yes, as I think was mentioned earlier in this thread, chain E is the XIAP molecule inhibiting the caspase-3 unit made up by chains A and B; chain F is the XIAP molecule inhibiting the caspase-3 unit made up by chains C and D. Although note that this doesn't mean you have to show both, even if you are showing both units of caspase-3.

Sorry if I don't seem too helpful: I don't want to give away everything to others because your model is your own. It's not mine. (Also, I seem to mess up a lot with the advice I give people here. XD)

Hey, I don't want to give you the impression that the advice you're giving is wrong – it's usually right! But sometimes I think of something related that you just didn't mention, and I feel like I can add to your answer. Doesn't mean what you said was wrong

[FullMetalMaple]

Sorry if I don't seem too helpful: I don't want to give away everything to others because your model is your own. It's not mine. (Also, I seem to mess up a lot with the advice I give people here. XD)

Hey, I don't want to give you the impression that the advice you're giving is wrong – it's usually right! But sometimes I think of something related that you just didn't mention, and I feel like I can add to your answer. Doesn't mean what you said was wrong

No problem! I wasn't getting that impression - I appreciate that you add to what I say. It's helpful for everyone.

[Dragonshark]

We got second in this event at States, only losing by three-fourths of a point...

[Phenylethylamine]

I spent between twenty and forty hours on my prebuild between Regionals and States, adding multiple creative additions and a huge amount of detail; I read all about PARP, and we came out of the test/onsite feeling that we completely nailed both. We were certain we'd medaled, and thought we had a significant chance of the elusive first place.

So we were rather surprised when we didn't medal, and turned out to have gotten ninth.

In retrospect, I'm guessing this was my fatal mistake: I didn't realize that it wasn't going to be the same event supervisor as last year. Last year's supervisor (who some of you may remember as kwijiborjt) wanted detail, detail, detail – chemically accurate, high-level creative additions. So that's how I built my model, with heteroatoms of relevant residues shown in CPK colors, and different colored thread corresponding to different types of bonds between residues, and so on. I tried to make my creative additions creative, with some more complex stuff in addition to the obvious additions, trying to show a deeper understanding of the protein's function. And I think some of it may have gone over the heads of the judges, who were probably judging the event for the first time and adhering exactly to the grading guidelines issued by MSOE. My more advanced creative additions wouldn't have been on the list of likely/suggested creative additions (which event supervisors are encouraged to look beyond at their own discretion), and may not have received any points. Similarly, my explanations for why the highlighted residues in the onsite were important (which came straight from the primary citation for 3OD8.pdb) may have been too technical and might not have gotten as many points as a more general explanation.

It's a shame – I think this is a better event when there's room to push your understanding farther – but at the same time, it's a good reminder that you should never rely too heavily on a particular supervisor's grading/writing style for your strategy in any event.