Protein Modeling C

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Re: Protein Modeling C

Post by butter side up » May 11th, 2011, 5:49 am

TheWiseGirl wrote:Trying to anticipate what type of questions they might ask at Nationals. For our regional and state test there were questions on the importance of the sidechains you were adding to the protein you were modeling. On last year's national test* there wasn't a question like that, but do you think they'll have something like that on this year's test?

*I know last year Protein Modeling was a trial event.
I think that there probably is a very good chance of something similar to that on the nats test. I have seen "what is the importance of [whatever amino acids you added to the on-site build] to the function or structure of the protein?" quite often. Also, as the level goes up, there seems to be many more genetics questions, and questions on the actual mechanisms of how Klf4 functions with the DNA, transcription factors, and the other proteins (Oct4, Sox2, Nanog, c-myc, etc.) That would probably be something else to study.
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Re: Protein Modeling C

Post by kwijiborjt » May 11th, 2011, 10:30 am

butter side up wrote:
Biology wrote:I didn't make it to nationals, but I still need to know something. How do you find which specific amino acids bind the DNA?
I've looked all over, but haven't been able to find them.
I am not sure about this, but my coach said that the DNA is not actually bound to the protein.
The arginine in Klf4 attracts the DNA because DNA has a slightly negative charge (being acidic) and arginine is positively charged.
We put something along those lines as the answer to a regionals test, and got full credit for it, so I would assume it is pretty close.
Your coach's description as you've relayed it is not correct and I would not give it full points on an exam.

The protein isn't covalently bonded to the DNA. It is hydrogen bonded. Several amino acids interact with the nitrogenous bases of the DNA via hydrogen bonds. This is bonding, so to say that DNA is not actually bound to the protein is incorrect. Also, hydrogen bonding is in some ways similar to charged interactions, but they are not the same. I would suggest researching how hydrogen bonding works, because your explanation makes it sound as if you think the binding of Klf4 to DNA is a charged interaction. Charge may play some role, but if this were enough for specific binding then any positively charged protein could bind to this region. Hydrogen bonding is key for selectivity.
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Re: Protein Modeling C

Post by kwijiborjt » May 11th, 2011, 10:36 am

The Eviscerator wrote:
paradoxgirl wrote:I know of 5 residues that bind to DNA, but I'm having trouble understanding a previous comment, that amino acids only interact with the sugar-phosphate backbone. If this were the case, how would transcription factors recognize DNA correctly?
It appears, in jmol, that the residues bind to the base pairs.
I didn't say that residues only interact with the sugar-phosphate backbone. I was asking if they did because I already knew that residues bind to the nitrogenous bases.
Also, I've only found 5 residues that bind to DNA too. Does anyone know if there are more than 5?

kwijiborjt, Would you recommend modeling the DNA sequence CACCC, or the one that shows up in jmol?
The identification of the CACCC region as a transcription factor binding site does not mean that these are the only bases that are involved in hydrogen bonding. I would say that modeling five hydrogen bonds should be sufficient to make the point, but it's not going to hurt you to model all of them (i don't think there are more than ten anyway...). You can figure out which residues hydrogen bond to the DNA using jmol and some background knowledge about hydrogen bonding.

There are some modeling problems with just doing one strand. This would make it more difficult to model the interaction of the protein and the DNA accurately. But it's up to your judgment and creativity. There are certainly lots of ways to make good models, and this is a lot of the fun of the event imo.

My poking around led me to think there might be one h-bond with the phosphate backbone. But I wasn't positive about it.
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Re: Protein Modeling C

Post by kwijiborjt » May 11th, 2011, 10:40 am

paradoxgirl wrote:I know of 5 residues that bind to DNA, but I'm having trouble understanding a previous comment, that amino acids only interact with the sugar-phosphate backbone. If this were the case, how would transcription factors recognize DNA correctly?
It appears, in jmol, that the residues bind to the base pairs.
I suspect we're probably thinking about the same residue.

Your question about specificity is logical, but there are more dynamics than just specificity going on in DNA-protein interactions. Some hydrogen bonding may enable specific binding, and other bonding may just lower the energy of the complex and stabilize the interaction. Not all hydrogen bonding exists for the purpose of specificity (e.g. internal hydrogen bonds in elements of secondary structure).
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Re: Protein Modeling C

Post by kwijiborjt » May 11th, 2011, 10:42 am

TheWiseGirl wrote:
kwijiborjt wrote: I would suggest getting a better definition of the major and minor grooves. Poke around on google and wikipedia for a bit, it should be readily available. Also *hint hint* you may want to think about this for your models. Only one team from NY did.
Sorry, just clarifying, you mean labeling the major and minor groove? Or the earlier mentioned Hydrogen bonds? Or both?
I was talking about your description of the major and minor grooves. But in my experience most people could probably use some extra background on hydrogen bonding too (and more specifically, exactly how it works and why it's not the same thing as ionic bonding).
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Re: Protein Modeling C

Post by AlphaTauri » May 11th, 2011, 12:49 pm

The Eviscerator wrote:kwijiborjt, Would you recommend modeling the DNA sequence CACCC, or the one that shows up in jmol?
Going to intrude for a second here: Use the sequence in Jmol, which I believe is CACCG. I believe (don't quote me on this) that by "CACCC sequence", they mean C/G or A/T pairs, not necessarily a specific nucleotide.
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Re: Protein Modeling C

Post by GCXC » May 11th, 2011, 2:39 pm

Hey everyone, I just had state and came in 3rd in Protein Modeling and 3rd overall so one spot out of Nationals, but the only real comments that the proctor gave me besides good things about my placement of zinc fingers, they said that the only thing that i had a mishap on was the placement of my DNA in the proper position compared to the protein itself. Oh and they liked the Hydrogen bonds that i showed in the beta pleated sheets and the alpha helices too.

Good luck to everyone at Nationals!

And any ideas on what next year's protein will be?
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Re: Protein Modeling C

Post by kwijiborjt » May 11th, 2011, 4:14 pm

GCXC wrote:Hey everyone, I just had state and came in 3rd in Protein Modeling and 3rd overall so one spot out of Nationals, but the only real comments that the proctor gave me besides good things about my placement of zinc fingers, they said that the only thing that i had a mishap on was the placement of my DNA in the proper position compared to the protein itself. Oh and they liked the Hydrogen bonds that i showed in the beta pleated sheets and the alpha helices too.

Good luck to everyone at Nationals!

And any ideas on what next year's protein will be?
As a general rule showing hydrogen bonds on alpha helices and beta sheets is probably not a good idea. The judging criteria say that you should not look favorably on superfluous additions. That kind of an addition isn't specific enough to the function of the protein to get creative addition points. However, if you do model every hydrogen bond it would suggest that you didn't understand the importance of certain ones that are relevant to function.
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Re: Protein Modeling C

Post by GCXC » May 11th, 2011, 5:53 pm

kwijiborjt wrote:
GCXC wrote:Hey everyone, I just had state and came in 3rd in Protein Modeling and 3rd overall so one spot out of Nationals, but the only real comments that the proctor gave me besides good things about my placement of zinc fingers, they said that the only thing that i had a mishap on was the placement of my DNA in the proper position compared to the protein itself. Oh and they liked the Hydrogen bonds that i showed in the beta pleated sheets and the alpha helices too.

Good luck to everyone at Nationals!

And any ideas on what next year's protein will be?
As a general rule showing hydrogen bonds on alpha helices and beta sheets is probably not a good idea. The judging criteria say that you should not look favorably on superfluous additions. That kind of an addition isn't specific enough to the function of the protein to get creative addition points. However, if you do model every hydrogen bond it would suggest that you didn't understand the importance of certain ones that are relevant to function.

I'm sorry I didn't specify, but yes I did only show a few hydrogen bonds not all because like you said that would be superfluous.
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Re: Protein Modeling C

Post by The Eviscerator » May 11th, 2011, 7:40 pm

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.

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