Protein Modeling C

[mathemaniac]

I think the 2wbu file rounds it to the nearest 10, because I literally counted every amino acid on the protein (no life, only SciOly ) and it came out to perfectly 85.

[Flavorflav]

One more question. Has everyone else realized what 5 amino acids don't matter, because the 2wbu.pdb file has a 90-long strand. I think.

Phenyl answered this question back in October. Go to page 2.

[Frogger4907]

Why is there only one invitation protein test that the company made? We've had that same test like 3 times...

[barker9]

In the picture of the klf4 protein there are 10 DNA base pairs - are we supposed to include this DNA in our pre-build model?

[Gillen]

In the picture of the klf4 protein there are 10 DNA base pairs - are we supposed to include this DNA in our pre-build model?

You don't have to, but it would definitely be a good thing to include.

[Phenylethylamine]

I found the sidechains that interact with the Zinc molecules easy enough. But how are you guys finding the sidechains that interact with the DNA molecule? Are you just playing with the protein in jmol to find those side chains?

Try looking (in a biology textbook, or online) for detailed descriptions of the different amino acids. Certain sidechains are more likely than others to be involved in interactions with other molecules, including DNA. Then try looking in Jmol at where those sidechains appear in Klf4, and you'll probably find that they're in the right place to contact the DNA.

[I think there's a good detailed description of all the different amino acids in one of the links at the bottom of the Protein Modeling Wiki.]

First of all, what does the Zinc Ion DO? I'm aware that it is a ligand, but what is its function?

Basically, the zinc ion allows the protein to fold much more tightly than it otherwise could. The two histidines and two cysteines all bond to the zinc ion, drawing them far closer together than they could get without a ligand there. This compact structure allows the transcription factor to get close in the DNA's major groove in order to bind to the base pairs that it regulates.

For more information about zinc fingers, try reading this.

Simalarly, I know that the non-polar portions of the protein are hydrophobic and the polar portions are hydrophilic, but is the final purpose of those portions of the proteins just to repel and attract water?

If you look at the polar and nonpolar portions of a protein, especially a large protein with few ligands, in Jmol, you'll probably see that the hydrophilic/polar sidechains are mainly on the outside of the protein's tertiary structure, while the hydrophobic/nonpolar ones are mainly sheltered inside. Because most proteins fold in a watery environment, the hydrophobicity or hydrophilicity of the different sidechains helps determine the tertiary structure by causing the polar ones to end up outside, where they contact the external water (and in some cases allow the protein to be water-soluble), and the nonpolar ones aggregate inside, where they do not come into contact with the water.

Beyond that, polar vs. nonpolar sections of the protein could theoretically have some purpose in a protein's interactions with other molecules; you'd have to do more specific research to find out if this is the case in Klf4, but I haven't found anything about that in my research.

Why is there only one invitation protein test that the company made? We've had that same test like 3 times...

Because, like you said, the one company- the Center for Biomolecular Modeling at MSOE- makes all the tests. Most teams don't go to more than one invitational tournament, so it's not an issue most of the time. The regional tests are presumably the same in all the regions, too, and the state ones are the same in all the states.

I find it very refreshing to have the tests all made by a single group that knows the material well and can ask good questions on it; it takes the "bad/unfair event" possibility out of the equation. It also means there's a nice progression in terms of difficulty from regional to state to national level.

[gigaboo]

Whoa, I realized my stupidity. Thank you. For the test, will we need to know about the proteins for the flu, like it says, or will be tested more on the proteins we are doing this year?

[starpug]

I found the sidechains that interact with the Zinc molecules easy enough. But how are you guys finding the sidechains that interact with the DNA molecule? Are you just playing with the protein in jmol to find those side chains?

Try looking (in a biology textbook, or online) for detailed descriptions of the different amino acids. Certain sidechains are more likely than others to be involved in interactions with other molecules, including DNA. Then try looking in Jmol at where those sidechains appear in Klf4, and you'll probably find that they're in the right place to contact the DNA.

[I think there's a good detailed description of all the different amino acids in one of the links at the bottom of the Protein Modeling Wiki.]

I will be sure to check the macromolecule chapter of my Campbell's book.

[Phenylethylamine]

For the test, will we need to know about the proteins for the flu, like it says, or will be tested more on the proteins we are doing this year?

This year's test will only be on this year's proteins (as well as general protein information, but nothing about the flu). When you say "like it says", where are you looking?

[gigaboo]

The page http://cbm.msoe.edu/includes/pdf/SO/201 ... iption.pdf which is the on-site description this year says so. So either I found something you didn't know, or I'm dumb. I'm guessing the latter as you seem to be an expert in this event.