Protein Modeling C

[TheGenius]

Yes the commands done in the console worked very nice thx! Unfortunately it looks like almost all the side chains are polar. And when you try to select the ones that are nonpolar you get 0, so I don't think it would be a very good creative addition. Any Thoughts?

What command are you using?
If you use "select sidechains and not polar" you should get more than zero.

[Mithrandir]

Yes the commands done in the console worked very nice thx! Unfortunately it looks like almost all the side chains are polar. And when you try to select the ones that are nonpolar you get 0, so I don't think it would be a very good creative addition. Any Thoughts?

What command are you using?
If you use "select sidechains and not polar" you should get more than zero.

Yeah your right. I was typing in "nonpolar" instead of "not polar". There are some sidechains that are polar and some that are not polar.

[gigaboo]

I know this is probably really simple and I'm just an idiot, but what is the command in Jmol to display things that I've hidden?

[TheGenius]

"undo" will usually work.
If you've used the "display" or "hide" comands, you can also use "display all".

[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?

[Phenylethylamine]

Yeah usually the floating balls represent certain molecules. In the 2wbu I think it represents water molecules. The red ones are red as Phenylethylamine said, but there are probably also two small hydrogen atoms.

In Jmol, hydrogen atoms are typically not displayed (there may be a way to make them show up, but I doubt it; it wouldn't be very useful), just implied. Water therefore shows up just as its central oxygen.

If you look at the scoring guide last year you get points for representing which parts are beta pleated sheets and alpha helixes. You get no additional points for color coding them if you already have them folded in the correct way. The only advantage is that if you color code them then you don't have to worry about you secondary structures being shaped correctly.

Even if you color code your secondary structures, the judges will still want to see that they are folded correctly. Color coding could be a backup in case some of your secondary structures get a little bent out of shape, but it cannot replace correct folding.

[starpug]

The gray spheres represent the Zinc Ion part of the Zinc Finger.

Zinc molecules perhaps?

No, zinc ions. Cys2/His2 zinc fingers have a Zn+2 ion coordinated by two cysteines and two histidines.

I realized they were ions 10 minutes later and changed my post. Sorry.

[mathemaniac]

I'm starting to learn a lot more about this protein, but I have 2 questions about the functions of some parts. First of all, what does the Zinc Ion DO? I'm aware that it is a ligand, but what is its function? 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?

In any case, I'm glad to have learned enough about Klf4 to be able to ask relevant questions this time around.

[gigaboo]

I'm confused. On the state protein site, it makes me think that the chain it shows is fragments 75-157, but when I try to select that it doesn't seem right. What am I missing? Also, could anyone tell me exactly where the zinc fingers attach?

[gigaboo]

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.