Protein Modeling C

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Phenylethylamine
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Re: Protein Modeling C

Postby Phenylethylamine » December 13th, 2010, 2:47 pm

Okay I don't know if anyone else has been to a competition yet but when we went we never got a score for our prebuild or on site. They were graded and were counted towards our scores but the judge/proctor never gave us the results for anything except the onsite exam... has this happened to anyone else? Is this the norm? I was just bummed cause I worked really hard on the prebuild and I wanted to see how it did... Overall though I felt the competition was a really good one, the test was espicially awesome!
Typically, the only competition at which you will ever receive any scores for any event is an Invitational. Depending on where you live (and how well your coach knows the event supervisors), it might be possible to find out more specifically how you did at Regionals, and possibly a few events at States (although that's much less likely). But the usual method is that teams only know their rank, and nothing about their raw score. It's unlikely that you will have more information than that, for this event or any other. It can be annoying, but returning specific score sheets to all the teams would probably be a logistical nightmare.
We have read and read and read but we are clueless as to how to make the computer model into a 3-D, physical model. Maybe it's really simply and we are just missing something small...but we really need some guidance!!
The computer model is essentially a guide to help you figure out how to twist your Mini-Toober into the shape of the protein; there's no way to directly convert it to a physical model. I recommend highlighting your alpha helices and beta sheets in Jmol ("select helix", "color [colorname (red is usual for helices)]"; "select sheet", "color [colorname (yellow is standard for beta sheets)]"). This combined with the Structure Summary page from the PDB (which shows the complete sequence of the protein and its secondary structures by residue) will allow you to figure out what residues are part of a helix or beta sheet, and therefore correctly fold the secondary structures. In order to fold the tertiary structure, you basically have to just examine the Jmol image and try to replicate it as best you can.
I just need one clarification. The DNA present in the computer model: that counts as a extra thing for the model, right? And would we have it separate from the protein or intertwine it in some way?
Based on the kinds of additions mentioned in last year's prebuild rubric, which is now available online, it seems like the DNA would certainly count as an addition. Given how vital it is to the protein's function, I would certainly include it.

I keep meaning to put a lot of this information on the wiki, but I haven't gotten around to it yet...
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Re: Protein Modeling C

Postby aubrey048 » December 13th, 2010, 3:28 pm

I have a couple questions in regards to the Protein Modeling event . . .

1. Is there any simple guide to using Jmol anywhere? I have tried typing in color-related commands and such in the program and nothing works!

2. Is there anywhere where I can buy CHEAP Mini-Toobers?? (Not 50 dollars please!!)

Thanks!
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Projected 2011-2012 Events: Anatomy, Microbe Mission, Disease Detectives, Tower, Optics, Helicopter.
Past Events: Anatomy (7th), Helicopter (6th), Mission Possible (1st), Write It Do It (4th, 8th), Ornithology (5th).

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Re: Protein Modeling C

Postby aubrey048 » December 13th, 2010, 5:50 pm

Another question . . .

What exactly do you DO to model the proteins??? Do you stick tacks in the toobers for molecules? Are we representing the molecular structure? And how exactly can you build such a complex Klf4 protein from the image on the computer? Any tips??? (Sorry, I'm new to this event.)
Plotting the function of the universe for efficiency without your permission.

Projected 2011-2012 Events: Anatomy, Microbe Mission, Disease Detectives, Tower, Optics, Helicopter.
Past Events: Anatomy (7th), Helicopter (6th), Mission Possible (1st), Write It Do It (4th, 8th), Ornithology (5th).

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Re: Protein Modeling C

Postby Vizard007 » December 13th, 2010, 6:01 pm

Another question . . .

What exactly do you DO to model the proteins??? Do you stick tacks in the toobers for molecules? Are we representing the molecular structure? And how exactly can you build such a complex Klf4 protein from the image on the computer? Any tips??? (Sorry, I'm new to this event.)
Well, there are kits out there, so with the supplies they give you, you should be able to make the part of the protein that you are required to make. I dont' think you would need anything extra.
It's so easy, even a Badger could do it.

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Re: Protein Modeling C

Postby quizbowl » December 13th, 2010, 6:53 pm

Another question . . .

What exactly do you DO to model the proteins??? Do you stick tacks in the toobers for molecules? Are we representing the molecular structure? And how exactly can you build such a complex Klf4 protein from the image on the computer? Any tips??? (Sorry, I'm new to this event.)
Well, there are kits out there, so with the supplies they give you, you should be able to make the part of the protein that you are required to make. I dont' think you would need anything extra.
While yes that is true, just by making a bit more can really push one over the top. Dont overkill though - last year a nice display was a wood frame to suspend it in midair.
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Re: Protein Modeling C

Postby ajwilliams2011 » December 15th, 2010, 1:38 pm

Okay...so if you look at the JMOL of the protein structure on PDB they show the alpha particle as those curly pink parts. Does that mean we curl our mini toobers to resemble those curly parts?
2010-2011 Events: Protein Modeling, Disease Detectives, Ornithology, Ecology, and Experimental Design.

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Re: Protein Modeling C

Postby Phenylethylamine » December 17th, 2010, 3:39 pm

Okay...so if you look at the JMOL of the protein structure on PDB they show the alpha particle as those curly pink parts. Does that mean we curl our mini toobers to resemble those curly parts?
Yes, those "curls" are the alpha helices, and yes, you curl your Mini-Toober into that shape.

For anyone who's having difficulty figuring out how to fold the model, this is a great resource.
I have a couple questions in regards to the Protein Modeling event . . .

1. Is there any simple guide to using Jmol anywhere? I have tried typing in color-related commands and such in the program and nothing works!

2. Is there anywhere where I can buy CHEAP Mini-Toobers?? (Not 50 dollars please!!)

Thanks!
1. Unfortunately, there aren't many good Jmol tutorials out there for people who have never used the program before; I've been meaning to create something of the sort and put it on the Protein Modeling Wiki, but haven't gotten around to it (junior year is busy >.<). Hopefully I'll have time to do that soon.
In the meantime, if you have any specific questions, don't hesitate to ask.

2. Here. They have affordable kits specifically for the event.
Another question . . .

What exactly do you DO to model the proteins??? Do you stick tacks in the toobers for molecules? Are we representing the molecular structure? And how exactly can you build such a complex Klf4 protein from the image on the computer? Any tips??? (Sorry, I'm new to this event.)
You do not have to represent the complete molecular structure of the protein; you just have to show a) the alpha-carbon backbone of the protein and b) "creative additions"- i.e., other parts of the protein or things it interacts with that are important to what it does. The whole point of the model is to showcase the protein's function.

That being said, you can use tacks, pipe cleaners, pom-poms, beads, wire, dowels... any craft materials, really, to represent the things you choose to show.
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Re: Protein Modeling C

Postby ajwilliams2011 » December 20th, 2010, 8:06 am

Let me start out by saying that anyone from another state (not IN) does not have to worry about sharing some hints with my because my team will not make it past states, if it even makes it past regionals (we are having some major dedication problems this year). So please, don't be scared to help me because you think we might beat you somewhere along the line...trust me, we won't.

That being said...HELP!

I have the basic structure made but I am unsure what kind of extras I need to include and how I am supposed to find information about them. I know I should probably include the DNA, but what other things should be included? Sidechains? How do I know which ones to include?

Feel free to reply back on the board or PM me.

Please keep in mind-- I am not a complete idiot, but I was totally thrown into this event and it is not my specialty field at all.
2010-2011 Events: Protein Modeling, Disease Detectives, Ornithology, Ecology, and Experimental Design.

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Re: Protein Modeling C

Postby Phenylethylamine » December 20th, 2010, 12:49 pm

I have the basic structure made but I am unsure what kind of extras I need to include and how I am supposed to find information about them. I know I should probably include the DNA, but what other things should be included? Sidechains? How do I know which ones to include?
This is always a difficult question. There's no one answer– there could be multiple ways of showcasing the protein's function. Try your standard resources: Wikipedia, Google, PDB Molecule of the Month... Just from a cursory search of "KLF4", I found:
All KLF family members are characterised by their three Cys2 His2 zinc fingers located at the C-terminus [...] separated by a highly conserved H/C link.
You might want to show the sidechains of those Cys2 His2 zinc fingers, for example.

Google search results are a little harder to navigate, but with some effort, you should be able to find more useful information about KLF4. It doesn't look like Molecule of the Month has ever featured KLF4 (although it has featured the Oct and Sox transcription factors that we have as the on-site at one of the competitions, don't remember which), but there's an article on zinc fingers that could be helpful. Keep searching; there should be some information out there that can help you.

Generally speaking, it's probably a good idea show disulfide bonds if there are any; other sidechains should be shown, again, only if they're relevant to the protein's function. Anything the protein acts upon can be shown (in this case, the DNA), and if there's a clear way of showing the interaction itself (e.g., bonds, attractions, or repulsions between the protein and its substrate/target), that could also be a good thing to show.

Feel free to reply back on the board or PM me.
Just a note for future reference (that applies to all events, not just this one): if you are asking for/giving relatively general advice on the event, stuff that could be useful to everyone, please keep it on the board so everyone can benefit from it.
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MA State Science Olympiad Tournament
MIT Invitational Tournament
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Re: Protein Modeling C

Postby aubrey048 » December 22nd, 2010, 6:52 am

Thanks for answering my questions, Phenylethylamine! I'm sure I will have more soon!

(Also, you can give me any hints you'd like; I'm from a TINY homeschooling team in north Alabama that will not make it past the first level of competition!)
Plotting the function of the universe for efficiency without your permission.

Projected 2011-2012 Events: Anatomy, Microbe Mission, Disease Detectives, Tower, Optics, Helicopter.
Past Events: Anatomy (7th), Helicopter (6th), Mission Possible (1st), Write It Do It (4th, 8th), Ornithology (5th).


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