Protein Modeling C

[AlphaTauri]

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.

[GCXC]

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?

[kwijiborjt]

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.

[GCXC]

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.

[The Eviscerator]

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.

[TheWiseGirl]

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.

[kwijiborjt]

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.

[The Eviscerator]

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?

[kwijiborjt]

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).

[butter side up]

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.