Protein Modeling C

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FullMetalMaple
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Re: Protein Modeling C

Postby FullMetalMaple » May 9th, 2011, 7:42 pm

What's the major groove?
My coach explained it to me like this: you know how in biology textbooks, DNA is drawn as a perfect helix, each strand precisely bonded to its complement? It's actually not quite like that - there are "gaps" and such in a DNA strand. The bigger gap is the major groove; the smaller, the minor. It's easier to understand if you find a picture of it.

Unfortunately, I'm not sure about your other question...

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Re: Protein Modeling C

Postby kwijiborjt » May 9th, 2011, 10:17 pm

What's the major groove?
My coach explained it to me like this: you know how in biology textbooks, DNA is drawn as a perfect helix, each strand precisely bonded to its complement? It's actually not quite like that - there are "gaps" and such in a DNA strand. The bigger gap is the major groove; the smaller, the minor. It's easier to understand if you find a picture of it.

Unfortunately, I'm not sure about your other question...
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.
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Re: Protein Modeling C

Postby TheWiseGirl » May 10th, 2011, 12:30 am

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?
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Re: Protein Modeling C

Postby Biology » May 10th, 2011, 7:57 am

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.

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Re: Protein Modeling C

Postby paradoxgirl » May 10th, 2011, 1:13 pm

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.
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Re: Protein Modeling C

Postby butter side up » May 10th, 2011, 3:25 pm

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.
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Re: Protein Modeling C

Postby The Eviscerator » May 10th, 2011, 4:18 pm

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?

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Re: Protein Modeling C

Postby Biology » May 10th, 2011, 4:23 pm

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.
Yes, It's just hydrogen bound to the DNA. I didn't know the specific binding amino acids though.

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Re: Protein Modeling C

Postby butter side up » May 10th, 2011, 4:35 pm

Yes, It's just hydrogen bound to the DNA. I didn't know the specific binding amino acids though.
I would assume that there may be other (especially positively charged) amino acids involved, but arginine is definitely the most influential one. It helps to know this when positioning amino acids- arginines almost all point toward the DNA.
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Re: Protein Modeling C

Postby TheWiseGirl » May 10th, 2011, 11:43 pm

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.
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