Protein Modeling C

[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.

I can send you my state 3rd if you want. I don't think we could have gotten 3rd without your posts and contributions to the wiki. I can't wait to compete against you at nationals.

Thank you! Instead, you could post pictures of your state 3rd on the image gallery

[Mithrandir]

I am really sorry that you didn't win. There's just no way I would have gotten fourth if you hadn't answered all of my questions and explained what the pigeon was actually going on in this event. Considering that I got like 27th last year, I was really surprised that I placed. Your explanation clears stuff up though because I did all the obvious additions. Did anybody else use their regionals prebuild to make chains C and D?

[Phenylethylamine]

I am really sorry that you didn't win. There's just no way I would have gotten fourth if you hadn't answered all of my questions and explained what the pigeon was actually going on in this event. Considering that I got like 27th last year, I was really surprised that I placed. Your explanation clears stuff up though because I did all the obvious additions. Did anybody else use their regionals prebuild to make chains C and D?

Thank you!

My Regionals prebuild was the basis of my States prebuild, actually, but I asked one of my school's other teams for their Regionals prebuild and used that to make chains C and D.

[TheWiseGirl]

This is probably a dumb question, but I was googling PARP and there are a few different ones within the family; we are focusing on PARP1, correct? Thanks!

*Edit: Also, what's a conformational shift?

[Phenylethylamine]

This is probably a dumb question, but I was googling PARP and there are a few different ones within the family; we are focusing on PARP1, correct? Thanks!

*Edit: Also, what's a conformational shift?

Yes, the one we're looking at is PARP-1, formerly known just as PARP (before the other members of the family were discovered.

A conformational shift is a change in the shape of a protein. It can be induced by a change in pH, a change in temperature, the binding of a ligand, interactions with another protein, etc.

[TheWiseGirl]

This is probably a dumb question, but I was googling PARP and there are a few different ones within the family; we are focusing on PARP1, correct? Thanks!

*Edit: Also, what's a conformational shift?

Yes, the one we're looking at is PARP-1, formerly known just as PARP (before the other members of the family were discovered.

A conformational shift is a change in the shape of a protein. It can be induced by a change in pH, a change in temperature, the binding of a ligand, interactions with another protein, etc.

Thanks Phenyl! You know, if/when my team goes to nats I need to get your autograph...you're my protein modeling hero!

[FullMetalMaple]

Thanks Phenyl! You know, if/when my team goes to nats I need to get your autograph...you're my protein modeling hero!

Can I second that? (Okay, so maybe nats is a long shot for us, but you never know...)

[Phenylethylamine]

Thanks Phenyl! You know, if/when my team goes to nats I need to get your autograph...you're my protein modeling hero!

Can I second that? (Okay, so maybe nats is a long shot for us, but you never know...)

Aww, you're making me blush.

Seriously, though, it means a lot to me when people come up to me (or my Protein team) at competitions and ask, "Are you Phenylethylamine?" and thank me for my help. I like knowing that I'm actually helping people learn more about proteins and, secondarily, do well on the event (although given that the people who take my advice consistently do better in competition than I do, some people on my team keep telling me to stop helping everyone so much xD).

[TheWiseGirl]

Thanks Phenyl! You know, if/when my team goes to nats I need to get your autograph...you're my protein modeling hero!

Can I second that? (Okay, so maybe nats is a long shot for us, but you never know...)

Aww, you're making me blush.

Seriously, though, it means a lot to me when people come up to me (or my Protein team) at competitions and ask, "Are you Phenylethylamine?" and thank me for my help. I like knowing that I'm actually helping people learn more about proteins and, secondarily, do well on the event (although given that the people who take my advice consistently do better in competition than I do, some people on my team keep telling me to stop helping everyone so much xD).

Haha, if we do ever meet up I'll probably forget how to pronounce "Phenylethylamine" and ask "Are-you-the-gal-who's-really-good-at-proteins-and-has-a-purple-flower-avatar?" And FullMetalMaple, if one of us makes it to nats we'll mail each other copies of the autograph But back to fawning, Phenyl, you are seriously one of the best contributors on the site in general

On another note, I'm studying for State right now and I feel like I'm overdoing it; I mean, I've read 3 different sites about nucleophiles, 2 sites about specific protein domains, and probably have 50 pages of useless information in my study binder. I've done rather well on the Invitational tests, and was confident on the Regional test; I know I shouldn't worry about random stuff being on the State test because MSOE writes it. So am I just being paranoid here?

[flyingwatermelon]

So a few quick questions:

1) For the beta sheet are the "kinks" in the model that we place them exactly on the amino acid lines? |amino acid| 2cm

2) For the rest of the structure that isn't beta sheets/pi helices/alpha helices, do we attempt to model them in the way Jmol has it arranged in backbone format? Or is it up to our discretion...

3) How do you model pi helices? Same way as alpha?

Edit: Reading the forums, I'm not sure whether they're 3/10 helices or pi?