Protein Modeling C

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TheWiseGirl
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Re: Protein Modeling C

Post by TheWiseGirl » May 11th, 2011, 8:27 pm

The Eviscerator wrote:On the 3 inch by 5 inch notecard, does the information have to be handwritten or can we type it up and then glue the printed words onto a notecard. Also, is only one side allowed to be used or both?

And how many hydrogen bonds between klf4 and DNA have you guys been finding? There are 7 that I've found that I'm pretty sure about right now, and another 9 that I'm not so sure about because the sidechain doesn't point directly at the DNA or the sidechain is a little bit far from the DNA.
At state I hand wrote it and made the notecard one sided because my teammates and I weren't sure about the whole "judges cannot touch model" thing. But I was planning on typing and printing it out, maybe making it stand up to utilize both sides so that way judges can see both sides without having to move the card. But that is a really good question. I am wondering about that too...

As for hydrogen bonds our modeler found 5.
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Re: Protein Modeling C

Post by kwijiborjt » May 11th, 2011, 8:37 pm

Both sides are fine. I'm not sure how you could possibly judge this event without touching the models. And i think that the hydrogen bonds are more than five and less than sixteen.
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Re: Protein Modeling C

Post by The Eviscerator » May 11th, 2011, 8:53 pm

kwijiborjt wrote:Both sides are fine. I'm not sure how you could possibly judge this event without touching the models. And i think that the hydrogen bonds are more than five and less than sixteen.
So can we type it up?

I found some residue sidechains that I think hydrogen bonded to the DNA sugar-phosphate backbone instead of to the nucleotides. Did you find any of these and does this actually even happen?

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Re: Protein Modeling C

Post by kwijiborjt » May 12th, 2011, 12:33 am

Typing should be fine. I didn't find multiple residues, but it's possible. if you measure bond lengths the distance between hydrogen bond donors and acceptors are usually about 3-4 angstromsish. Direction should also be a clue (you can figure this out for yourself... it's nontrivial).
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Re: Protein Modeling C

Post by butter side up » May 12th, 2011, 12:16 pm

My coach has proctered several protein modeling competitions and says that as a rule, judges actually prefer the notecard to be typed whenever possible. Our notecard has explinations about the function of the protein and the important structures (hydrophobic cores, zincs, alpha helices and beta sheets, etc.) typed on the back and small samples of all our materials with handwritten labels. We also usually tape two notecards together so we don't have to redo the sample part every time we redo the explanation part (which is often.)

EDIT: From my coach: As far as the info goes, putting the important portions, like the intro to each section, in a different color font is also helpful to the judges and allows them to find things faster and easier.
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Re: Protein Modeling C

Post by The Eviscerator » May 13th, 2011, 8:26 pm

Just to clarify: other residue sidechains (say for example tyrosine, a non-charged hydrophillic amino acid) besides arginine interact with dna, right?

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Re: Protein Modeling C

Post by kwijiborjt » May 14th, 2011, 8:56 am

The Eviscerator wrote:Just to clarify: other residue sidechains (say for example tyrosine, a non-charged hydrophillic amino acid) besides arginine interact with dna, right?
Yes side chains other than arginine interact with DNA. I'm not sure that tyrosine is one of them in this case.
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Re: Protein Modeling C

Post by The Eviscerator » May 14th, 2011, 9:09 am

I looked at 1nkp (c-myc the nationals on-site build) and the rcsb site says there are 8 chains, but in the jmol on the rcsb site, there were only 4. Can someone explain?

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Re: Protein Modeling C

Post by Phenylethylamine » May 14th, 2011, 9:32 am

The Eviscerator wrote:Just to clarify: other residue sidechains (say for example tyrosine, a non-charged hydrophillic amino acid) besides arginine interact with dna, right?
I see one tyrosine that could be interacting with the DNA backbone based on its position, and possibly a couple serines (one by the backbone, another by one of the bases), but apart from those, I'm only seeing positively charged sidechains (i.e., arginine, lysine, and histidine*) involved with the DNA.

*Histidine is not always positively charged, and most charts show it as uncharged polar. However, there are a few cases when it becomes positively charged, and when it's involved in hydrogen bonds is one of them.
The Eviscerator wrote:I looked at 1nkp (c-myc the nationals on-site build) and the rcsb site says there are 8 chains, but in the jmol on the rcsb site, there were only 4. Can someone explain?
I can see two different ways you could have counted only four chains in that file: either you're not counting the DNA (which makes up four of the eight named chains in 1NKP), or you're not counting the duplicates (there's two copies of each chain in 1NKP). If you use the command "color chain", you should see eight different colors indicating the eight different chains.
butter side up wrote:My coach has proctered several protein modeling competitions and says that as a rule, judges actually prefer the notecard to be typed whenever possible. Our notecard has explinations about the function of the protein and the important structures (hydrophobic cores, zincs, alpha helices and beta sheets, etc.) typed on the back and small samples of all our materials with handwritten labels. We also usually tape two notecards together so we don't have to redo the sample part every time we redo the explanation part (which is often.)
I also typically type my notecards, including the key (for which I also use small samples of my materials, partly because it's the easiest way to identify what's what and partly because it just looks cool), and leave spaces to glue the bits of materials afterward.

I usually do my notecard at the last minute before competition, and not just because of procrastination: I don't want to redo it multiple times, because it's a fairly effort-intensive process (especially gluing all those little pieces of pipe cleaner onto the card >.<), so I want to make sure the model is finished and contains everything it's going to contain before I try to make the card.

Edited for errors.
Last edited by Phenylethylamine on May 15th, 2011, 3:06 pm, edited 1 time in total.
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Re: Protein Modeling C

Post by proton28 » May 15th, 2011, 10:32 am

Does anyone have the link for the PDB c-myc jmol? i was looking for it to practice with but i cant find it... thanks!

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