Protein Modeling C

[Gemma W]

Does anyone know what the restriction numbers are for the onsite build for states, the TAL effectors? Thanks

For onsite builds at all levels, you do not find out the specific section until you arrive at the competition. You might be able to make an educated guess based on the location of important structural features, but I would be familiar with the whole thing.

[annaphase]

Does anyone know what the restriction numbers are for the onsite build for states, the TAL effectors? Thanks

The point is that we don't know, so we can't practice until we get there

[Gemma W]

So on the CBM website (as well as in other sources) it talks about the TALE proteins as having two alpha helices connected by a loop, and the two hypervariable residues that are contained in the loop and read DNA. However, in the picture and in the Jmol visualization of the protein, the residues in question seem to be at the end of one helix. What loop are they talking about?

[colorado mtn science]

hey guys just a quick question... what exactly is a beta bridge and how do you fold a beta bridge on the toober? i have looked this up for a while and can't seem to find anything.

Thanks,
Vane

A beta bridge is a beta sheet (made from two beta strands connected with H bonds) where each beta strand is one residue long.

[Celestite]

So on the CBM website (as well as in other sources) it talks about the TALE proteins as having two alpha helices connected by a loop, and the two hypervariable residues that are contained in the loop and read DNA. However, in the picture and in the Jmol visualization of the protein, the residues in question seem to be at the end of one helix. What loop are they talking about?

They're talking about the tip of the loop connecting the alpha helices.

You can see it more clearly in this picture.

[ellpida13]

Hey guys, I've noticed that there seems to be two sets of the FokI protein when I download the pdb file into Jmol (see the attached picture of 2fok A selected / restricted, with cartoon on and backbone at 1.5).
Can anyone explain to me why this occurs? If this is correct, do we need to reflect the second set in our pre-build model?

Thanks!

[fozendog]

Restrict it to chain A with the command:
restrict *A

That is all you need for the base pre-build model.

[bernard]

Restrict it to chain A with the command:
restrict *A

That is all you need for the base pre-build model.

If you want to do it all in one command, "restrict 421-560:A"

[ellpida13]

I see what I was doing wrong now. Thank you fozendog and bernard for the help!

[Gearbox]

I know this is a bit of a reach, but is anyone here from Huron High School in Ann Arbor, they were recently at the Mentor Invitational and their protein was freaking amazing, especially with the copper DNA model that they built. I was wondering if anyone from that team could give me some pointers on how they built the DNA. Thanks!