Protein Modeling C

[JonB]

I understand that endonuclease binds to DNA for transcription and genome editing purposes, but would a DNA molecule be reasonable to include in the pre-build? Also, besides the active sites, what other creative add-ons are available can we add to the model?

That's a tough call because the confirmation of endonuclease is different when DNA is bound to it. It seems like a logical add-on, but proves difficult when faced with the fact that the protein will be a different shape.

[ppran]

For building the nuclease domain I put the file in jmol. I restricted it to chain a and the proper residues, but when I got to show alpha helix and beta sheets it says 0. I am kind of stuck on what to do in order to go from this jmol to the mini toober. Also for the on site model of zinc finger when I say select zinc finger it says 0 atoms. Can someone please shed some light? Thanks

[Gemma W]

For building the nuclease domain I put the file in jmol. I restricted it to chain a and the proper residues, but when I got to show alpha helix and beta sheets it says 0. I am kind of stuck on what to do in order to go from this jmol to the mini toober. Also for the on site model of zinc finger when I say select zinc finger it says 0 atoms. Can someone please shed some light? Thanks

If you look at the bottom of the wiki, it has a link to a CBM video about modeling your toober from the jmol molecule. This link was broken in the past but has now been fixed.

[balsa]

has anyone used materials besides toobers / kwiktwist for this event? I want to use wire, but I'm not sure how one would add sidechains to a wire model. any suggestions?

[orchid]

So where can we find the information about the important sidechains for 2fok?

[teaforterry]

When the fokI endonuclease protein is loaded on jmol, first we use the console to eliminate all amino acids besides 421-560. Then, we are left with two biomolecules. At first they appeared to be the same, however, when selecting one of them to view, jmol displays biomolecule 2 as have 53 more atoms than biomolecule 1. Does anyone know which biomolecule we are supposed to be modeling our protein after? Thank you!

You need to specify that you want chain A,
Restrict *A
Don't forget to capitalize the "A"

This may seem like a silly question, but how do we know we only need to model biomolecule A? Thank you!

EDIT: Just kidding! I found it.

[heidi456]

Does anyone know where i could buy bulk mini-tuber? I'd like some extra on hand, and i don't want to buy the pre build kit again. But the only other non kit option is only 122 cm, which is too short.

[Gemma W]

I think the only retailer is the 3dmoleculardesigns site, and they only come in predetermined kits, but they have many other kit options if you think that would be helpful. I doubt any of them are less expensive, though.

[_vanemchir_]

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

[bernard]

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

According to Wikipedia, a β-bridge is a "single pair β-sheet hydrogen bond formation." Since it describes interactions between two β-pleated sheets, it would be tertiary structure. This site has a diagram that I think shows a β-bridge, though I'm not very sure since I couldn't find much about it on the internet.