Protein Modeling C

[starpug]

It might help if you go through the thread. It basically tells you what you need to represent.

There are three Amino Acids that you definitely want to represent and then you probably want to show the XIAP blocking the active site of Caspase 3 and maybe site that is cleaved by Caspase 3.

[Phenylethylamine]

My partner and I were just put on this event Tues., and looked at all the websites and are extremely confused, Our competition is Sat. Help!!

It's much easier to help when you have specific questions. What do you want to know?

WE would like to know how to do the prebuild mostly how to figure out what it supose to look like with additions from the stupid Jmol junk that only show s gray lines and where each amino acid and chain is and how to stand it up and such stuff like that

If you're wondering how to make the "stupid Jmol junk" show more than just "gray lines", check out the Jmol section of the Protein Modeling Wiki. Also, at the top of the online prebuild environment, there should be a link to a Jmol quick reference sheet if you want specific commands.

[Mithrandir]

So we were given a really nice magnet cysteine side chain from our regional on site. Are we allowed to use that for our state prebuild?

[Dragonshark]

So we were given a really nice magnet cysteine side chain from our regional on site. Are we allowed to use that for our state prebuild?

Yes, you're allowed to use the CBM-provided magnet sidechains on your prebuild, as long as you explain the significance of the residues you decide to include, on your notecard. However, they have a tendency to be shifted around, so be sure to double-check the positions of each sidechain before impounding.

[Phenylethylamine]

So we were given a really nice magnet cysteine side chain from our regional on site. Are we allowed to use that for our state prebuild?

Yes, you're allowed to use the CBM-provided magnet sidechains on your prebuild, as long as you explain the significance of the residues you decide to include, on your notecard. However, they have a tendency to be shifted around, so be sure to double-check the positions of each sidechain before impounding.

If I were you, I'd glue the magnet sidechain to the metal bracket attaching it to the Toober. Your model might be moved and jostled in the judging process, and not only can those magnet sidechains get shifted, they can also fall right off. Find a glue that can do metal-on-metal, and just put a drop of it between the magnet and the bracket – the magnet should hold it in place long enough for the glue to dry.

[bloopy]

Hi guys, does anyone know between which two cysteines the disulfide bond on the prebuild are? I tried to first look for it on the Internet and then just tried to eyeball it on the protein but I didn't see anything obvious, so I was just wondering if anyone was able to find it (if there even is one)? Thanks.

[EastStroudsburg13]

I don't think there are any disulfide bonds in the pre-build. If there were, it would be a very important addition, though.

[Phenylethylamine]

I don't think there are any disulfide bonds in the pre-build. If there were, it would be a very important addition, though.

No, there are no disulfide bonds in the pre-build. Here's a good way to check, in general:

restrict *a or *b // Only look at the relevant chains
color white
select cys and sidechain // Select all the cysteine sidechains
wireframe 200 // Make them visible
color red // Make them really visible

Now look for any two cysteines where the ends are nearly touching, with nothing else in between them (the main thing likely to be between two close cysteines is a zinc ion; you can use "select zn" and then "spacefill 400" to check if there's a zinc in there). That is most likely a disulfide bond.
The PDB used to show disulfide bonds with green dotted lines on its sequence summary pages, but it doesn't seem to anymore, for whatever reason. Maybe they decided it looked too cluttered. It was useful, but I haven't found any way of turning that back on.

As for using disulfide bonds as creative additions, in general (not that it's really relevant this year): yes, it's good to show disulfide bonds, because they're important to maintaining the protein's structure. But unless you know how each disulfide bond's contribution to the protein's structure is important to its function, simply showing the disulfide bonds does not demonstrate "the relationship between structure and function" in the protein, which is the point of the creative additions.

[Mithrandir]

I am confused about how you determine which ends the blue cap and red cap go on. Can somebody explain this to me?

[gsheni]

I have done some heavy research and it says that there should be two zinc ions on Chain E and F?
But Phenylethylamine said there should be one?