Protein Modeling C

[Faustina]

Flyingwatermelon,
1) No, not necessarily.
2) Yeah, just follow the backbone.
3) The pi helices have more turns per residue than a normal alpha helix.

[flyingwatermelon]

Ok, then last question. I'm probably color-blind but I'm not sure whether caspase has pi helices or 3/10 helices...a lot of people say 3/10 but does anyone know for sure?

[Dragonshark]

Ok, then last question. I'm probably color-blind but I'm not sure whether caspase has pi helices or 3/10 helices...a lot of people say 3/10 but does anyone know for sure?

Caspase-3 has 3/10 helices, which have 3 amino acids per turn. Pi helices have 4.1 amino acids per turn, at least according to Wikipedia.

Oh, and according to the national event supervisor, the rubric doesn't discriminate between alpha helices and the other types of helices, so just fold them the way you would normally fold alpha helices, though with the correct number of turns, since there is something about that on the rubric. (However, I'm not sure if individual judges will view them as the same.)

[TheGenius]

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.

[chalker]

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.

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.

[TheGenius]

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.

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.

[FullMetalMaple]

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.

Slightly different from what you're asking, but I'm also curious - what did you think of how Jmol was set up at state? I found it surprisingly difficult to work with and wondered if anyone else had the same problem. I couldn't get different views without a weird zoom effect, which I've never experienced before. It might have been better with the regular version.

[Dragonshark]

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.

Slightly different from what you're asking, but I'm also curious - what did you think of how Jmol was set up at state? I found it surprisingly difficult to work with and wondered if anyone else had the same problem. I couldn't get different views without a weird zoom effect, which I've never experienced before. It might have been better with the regular version.

The jmol at States was difficult to work with at times. I couldn't seem to center the display, unlike the jmol version I normally use, when I could click and hold to shift the display around without rotating it. Despite this being the same jmol version, this didn't seem to be a problem at Regionals.

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).

[GCXC]

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

[Rackis]

What's the difference between the beta-buldge and the standard beta strand and how would one show this on a model? Thanks.