Protein Modeling C

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garrett247
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Help With Protein Modeilng "Creative Addons"

Postby garrett247 » February 14th, 2011, 9:49 pm

Hello:
We've ordered the mini-toobers and used the JMol program to modeling the pre-build protein (Klf4). What I'm having trouble with is the "creative add-ons". According to the Science Olympiad Wiki:
...the model must also include "creative additions" that showcase the function of the selected protein. Students must decide for themselves which sidechains and/or ligands are important to the protein's function and should be displayed. These additions must be explained on a two-sided, 3x5 index card, along with a paragraph explanation of how they are relevant to the protein's function, and submitted with the model, typically at impound.
Does anyone have any idea what this means? What sorts of "add-ons" are they talking about? Most importantly, which parts the protein do we need to add add-ons for?

It also says:
Klf4 is a DNA transcriptional factor characterized by its three Cys2 His2 zinc fingers. It can promote or repress the expression of other protein-coding genes, notably that of Nanog, another factor involved in pluripotency. It can also up-regulate its own expression, forming a positive feedback loop. It binds to the gene sequence CACCC.
Does any of that need to be modeled?

Thank you in advance for your help!
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Re: Protein Modeling C

Postby Gillen » February 14th, 2011, 9:57 pm

I modeled the zinc fingers, the DNA, and plan on modeling the sidechains on the helices that interact with the DNA. I just made little sidechains and wired them to the mini-toober. For the notecard, you just explain what creative additions you modeled and why they matter to the protein's function.

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Re: Protein Modeling C

Postby garrett247 » February 15th, 2011, 12:32 am

I modeled the zinc fingers, the DNA, and plan on modeling the sidechains on the helices that interact with the DNA. I just made little sidechains and wired them to the mini-toober. For the notecard, you just explain what creative additions you modeled and why they matter to the protein's function.
Thanks for your quick reply! How would you find which sidechains/helices interact with the DNA? Also, are there any materials that you recommend making the sidechains/DNA/zinc fingers/etc. out of?
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Re: Protein Modeling C

Postby Phenylethylamine » February 15th, 2011, 12:19 pm

2 Questions:
1 - What is the exact section of the 2GT0.pdb protein to be made on-site
2 - How do you open the 2GT0.pdb file on jmol
Replies are appreciated.
1. That information isn't public- you'll find out when you get to competition. The rules specifically say that you're modeling Oct4, though, and there's a bunch of other non-Oct4 stuff in the PDB file as well, so you know that you'll be modeling one of the Oct4 pieces (actually, the PDB file says Oct1. I'm not sure who's right, although I'd put my money behind the PDB. But that's what they're referring to).
2. Have you read the Protein Modeling Wiki? If you read that and are still confused, what have you tried so far?
I modeled the zinc fingers, the DNA, and plan on modeling the sidechains on the helices that interact with the DNA. I just made little sidechains and wired them to the mini-toober. For the notecard, you just explain what creative additions you modeled and why they matter to the protein's function.
Thanks for your quick reply! How would you find which sidechains/helices interact with the DNA? Also, are there any materials that you recommend making the sidechains/DNA/zinc fingers/etc. out of?
I'd try researching the properties of specific sidechains (there might be a useful link on the wiki, I don't remember exactly), then showing in Jmol the ones that sound like they might interact with DNA well. If they are known to interact with other molecules and are in the right spot (i.e., in contact with the DNA), they probably are the ones that interact with the DNA.

I've had good results using pipe cleaners for sidechains; other useful materials (for sidechains, ligands, etc) include jewelry wire, Model Magic, cardboard, paper, and really just about any craft supply. My model is all supported by 22-gauge jewelry wire, because I make jewelry (or at least I did, before my protein model took over my beading table) and therefore have a lot of experience with what it can do; I typically use Model Magic for ligands, and my model is on a foamcore base. At the end of the competition season, I'll post pictures in the Image Gallery (I meant to do this with my hemagglutinin model from last year, but sadly it was damaged before I got a chance).

Also, the notecard needs to do two things: show what each addition is, and explain what each addition means. In other words, it needs to have a legend, just stating things like "purple pipe cleaners = histidine" or however you want to show it, and it also needs to have a paragraph that explains why you chose to show those histidines, or whatever it is that you focused on for your creative additions.
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Re: Protein Modeling C

Postby garrett247 » February 15th, 2011, 4:49 pm

I'd try researching the properties of specific sidechains (there might be a useful link on the wiki, I don't remember exactly), then showing in Jmol the ones that sound like they might interact with DNA well. If they are known to interact with other molecules and are in the right spot (i.e., in contact with the DNA), they probably are the ones that interact with the DNA.

I've had good results using pipe cleaners for sidechains; other useful materials (for sidechains, ligands, etc) include jewelry wire, Model Magic, cardboard, paper, and really just about any craft supply. My model is all supported by 22-gauge jewelry wire, because I make jewelry (or at least I did, before my protein model took over my beading table) and therefore have a lot of experience with what it can do; I typically use Model Magic for ligands, and my model is on a foamcore base. At the end of the competition season, I'll post pictures in the Image Gallery (I meant to do this with my hemagglutinin model from last year, but sadly it was damaged before I got a chance).

Also, the notecard needs to do two things: show what each addition is, and explain what each addition means. In other words, it needs to have a legend, just stating things like "purple pipe cleaners = histidine" or however you want to show it, and it also needs to have a paragraph that explains why you chose to show those histidines, or whatever it is that you focused on for your creative additions.
Thank you so much! I was very confused and now I understand what to do.
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Re: Protein Modeling C

Postby Phenylethylamine » February 16th, 2011, 2:43 pm

Thank you so much! I was very confused and now I understand what to do.
No problem. That's what the boards are for. Feel free to ask any further questions you have.
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Re: Protein Modeling C

Postby Mithrandir » February 16th, 2011, 5:26 pm

Does anybody know if we should include the side chains that they included in their example of a Zinc finger? They gave an example of a Znf in their video on how to construct a protein. Also I was reading about how there are primarily four different kinds of Znf, does anybody know which one we have to model? Did anybody show some of the side chains of DNA?
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Re: Protein Modeling C

Postby French_Toast » February 16th, 2011, 5:42 pm

A question regarding the onsite build, here. It may be stupidly obvious and I just can't figure it out, but it can't hurt to ask.

In the jmol program, how do you view where the add-ons are located? Is there a way of knowing by looking at the basic structure(which I ended up building fine), or is there something in the program that will show them?

Like I said, probably a stupid question, but one that would be really useful to know, so I don't have to lose out on half of the points of that section again. Thanks in advance, though.
2011 Events: Anatomy & Physiology, Disease Detectives, Ecology, Microbe Mission, Mission Possible, Optics, Birds, Protein Modeling, Technical Problem Solving
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Re: Protein Modeling C

Postby Gillen » February 16th, 2011, 5:53 pm

I believe if you go to the menu in the lower right corner, under style there is bonds. That shows the entire molecular structure. Its easiest to make sense of if you use the trace scheme for the backbone (under style and then scheme).

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Re: Protein Modeling C

Postby paradoxgirl » February 17th, 2011, 9:04 am

My model is all supported by 22-gauge jewelry wire
At an invitational my school went to, one of our teams was docked points because our protein was held up by wood stakes (attached to the Styrofoam base) and the judges told us that they must be able to pick up the protein and move it around. Is suspending it from a "ceiling" with wire legal? I do not think there is anything in the rules about this (and it was only an invitational, so the judges may have been in the wrong).
Our DNA part of the model will probably be supported from underneath by wooden stakes (or suspended) because that has not been a problem, I think the issue was that the protein could not be separated from the rest of the display.
What are your thoughts on this? I'm concerned this will be sprung on all of us at competition, and anyone supporting their model with attachments will be second-tiered.
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