flyingwatermelon wrote:1) For the beta sheet are the "kinks" in the model that we place them exactly on the amino acid lines? |amino acid| 2cm
It doesn't matter exactly where in the amino acid you kink the Toober, but you should be consistent: adjacent kinks should be at the same point in the amino acids, so they fall 2cm apart.
Most "correctly", the kink should occur at the point where the sidechain extends outward (which could be good to know if they give you a sidechain to show that falls somewhere in a beta strand), but I do not believe that this is part of the grading criteria. Could be good to keep in mind anyway, though.
flyingwatermelon wrote:2) For the rest of the structure that isn't beta sheets/pi helices/alpha helices, do we attempt to model them in the way Jmol has it arranged in backbone format? Or is it up to our discretion...
You should try to follow what you see in Jmol as closely as possible. I recommend watching the video about folding 3D structure on the CBM site
for more detail.
TheGenius wrote:I am curious: Why do they make us use the applet version of Jmol instead of regular Jmol? Standalone Jmol is much better and more tolerable than the web version.
Note that the applet has improved considerably from last year: it used to be necessary to click "Execute" and then manually empty the field after each command.
chalker wrote:Probably because in many school computer labs it's hard to get administrator access in order to install new software. With the web version you can run it from virtually anywhere.
It doesn't need to be installed, though. The file will run on any computer with Java installed, like the web version, even on differing operating systems.
Some school computer labs make it very hard even to save files locally (e.g., they require all users to save everything to flash drives), or do not allow files that could potentially contain applications to be saved.
Probably more importantly, though, standalone Jmol is not totally straightforward to download, and many event supervisors may not be inclined to go to the (relatively small, I admit) extra effort to put it on twenty or thirty computers when they're being provided with a webpage that they just have to open. Some may not even be aware that standalone Jmol is a thing that exists (which sounds scary, but it was actually primarily developed to be used as a web applet, so you could be completely aware of how it works and still not fully cognizant of the fact that there's a standalone version).
At NY States, they gave us the choice of using standalone or the webapp, which was a pleasant surprise. I used standalone, but it was nice to have both options, because when something weird and anomalous showed up in the structure (no spoilers), I could check that it was, in fact, part of the structure and not some artifact of the platform.
Dragonshark wrote:Also, a piece of advice for the onsite in general: Do a 'practice fold' of the onsite before competition, and include some reference photos of the practice model in your notes. This allows you to familiarize yourself with the general structure of the protein and will allow you to fold it much quicker and more accurately. Also, including the photos will give you another thing to reference during the competition, especially if you find the onsite jmol version clumsy to work with (like it did at States).
Excellent advice. If you don't have another Toober, you can do a "mental" practice fold: 'Here's a helix, and then there's a beta strand that comes around next to this other beta strand over here, and then they're parallel to the helix, and then this other helix is over here at this angle, about this far away...' Do that a few times, and the onsite will go much more quickly in competition (although this year's States onsite is tiny and pretty easy; it took me literally fifteen minutes to fold, although I then took another five or so to check my work really carefully. I assume this is why the NY State Protein supervisor limited it to two people at States this year).
Hey, I'm just studying PARP-1 based off of 3OD8 and I see that they're a few ligands/amino acids (not sure what they are), but on proteopedia it calls them MSE can someone explain to me what exactly it is and if it has anything to do with the function of PARP...Thanks
They are modified amino acids called selenomethionine
(MSE being the three-letter code they use for this particular modified residue). This means that the sulfur normally in the methionine residue has been replaced with a selenium atom.
They are not normally present in PARP; this is a modification that the crystallographers made so they could do some kind of imaging based on the position of the selenium atoms (I'm not sure why selenium, but this was in the original citation for 3OD8, albeit somewhat buried in the Materials and Methods section). So sadly, no, they are not relevant to the function of PARP; it's another one of those changes (like taking out some of the cysteines in caspase-3 in 1I3O) that the researchers made to make it easier to get the correct structure.
Rackis wrote:What's the difference between the beta-buldge and the standard beta strand and how would one show this on a model? Thanks.
As far as this event is concerned, beta bulges don't exist. A beta bulge is just a localized disruption of "normal" backbone structure that has hydrogen bonding roughly similar to what you find in a beta strand, but it really doesn't look that different from the rest of the backbone, and it doesn't appear in Jmol. They're interesting – you can read the Wikipedia article
, which is pretty concise – but not relevant to the event.
In short, fold your beta strands as usual; don't worry about beta bulges at all.