Protein Modeling C

[Phenylethylamine]

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.

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.

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.

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.

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.

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.

[Rackis]

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.

Thanks Phenyl, but my state was today lol. Got first place anyhow though!

[Infinity Flat]

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.

I would assume that they are using selenium simply because it is directly below sulfur on the periodic table, and so is chemically very similar. There may be a little more subtlety to it, but that's the main gist of it.

[Phenylethylamine]

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.

I would assume that they are using selenium simply because it is directly below sulfur on the periodic table, and so is chemically very similar. There may be a little more subtlety to it, but that's the main gist of it.

Sorry, I understand why it's feasible to replace the sulfur with selenium; the part I'm not sure about is how they detect the position of the selenium atoms in particular. There's some structure determination method that uses the position of the selenium atoms – which apparently they can somehow determine more easily – to align the overall protein structure. I understand how they do the alignment once they have the positions of the selenium atoms, but I don't know what method they use to find those positions.

[GCXC]

Just want to thank Phenyl and everyone else that contributed to this forum, without y'all I highly doubt I would've placed 2nd at State, our team came in fourth overall so two spots out from Nats (from TX), but since this is my senior year it was a good run

[Steelfoam]

Were everyone's regionals tests from MSOE? or were all the state tests written by MSOE?

[FullMetalMaple]

MSOE writes invitational, regional, state, and national tests, but supervisors can choose whether to use them. My invitational and regional tests were not MSOE tests except for short answer questions. My state test, however, was the MSOE one.

It's nice to have a standard test written for the event, but then there's the unfortunate temptation to share questions and answers with teams in other states.

[3slh9]

Sometimes a regional event supervisor will write their own test due to they feel the MSOE one is too short (ie 10 MC questions and 3 short answer) or in our case, we had reason to believe a school had gotten ahold of a copy of the CD and thus seen the test. Since I was in charge of two different regions in this event, I just gave the same test to both regions.

[Steelfoam]

I guess this could be a serious problem in states with multiples regionals that do matter. In wisconsin, I dont think any of the tests were modified. The state supervisor was a hard grader though.

[kentuckyfan1001]

I guess this could be a serious problem in states with multiples regionals that do matter. In wisconsin, I dont think any of the tests were modified. The state supervisor was a hard grader though.

Isn't the state supervisor the national event supervisor in Wisconsin?