Protein Modeling C

[Mithrandir]

A question regarding the onsite build, here. It may be stupidly obvious and I just can't figure it out, but it can't hurt to ask.

In the jmol program, how do you view where the add-ons are located? Is there a way of knowing by looking at the basic structure(which I ended up building fine), or is there something in the program that will show them?

Like I said, probably a stupid question, but one that would be really useful to know, so I don't have to lose out on half of the points of that section again. Thanks in advance, though.

So usually they'll say something like Glycine [58]. This will mean you put the side chain magnet on number 58. If you want to see the trace/cartoon style with the one side chain it is a little difficult. You have to right click, set picking atom. Then select number 58. Then change style to what you want like space fill. Then show the whole protein again. You can also do this in the console which is much faster, but a little tricky to use.

[Mithrandir]

My model is all supported by 22-gauge jewelry wire

At an invitational my school went to, one of our teams was docked points because our protein was held up by wood stakes (attached to the Styrofoam base) and the judges told us that they must be able to pick up the protein and move it around. Is suspending it from a "ceiling" with wire legal? I do not think there is anything in the rules about this (and it was only an invitational, so the judges may have been in the wrong).
Our DNA part of the model will probably be supported from underneath by wooden stakes (or suspended) because that has not been a problem, I think the issue was that the protein could not be separated from the rest of the display.
What are your thoughts on this? I'm concerned this will be sprung on all of us at competition, and anyone supporting their model with attachments will be second-tiered.

If you look on the online scoring rubric from last year they have to do things like compare the locations of two parts of the protein. Then decide if the protein is in the correct shape. This is difficult to do if the protein is mounted onto something with wooden stakes. You're so lucky that you invitationals has protein. My school's invitational only had like half the events.

[TheGenius]

Any reason why the Primary Structure section of the Protein Modeling wiki has "TL;DR" in it?

[Cheerwine]

1. Has anyone tried to invest in the magnetic sidechains to use them in the pre-build? I'm curious if they could make the model look a bit more professional.
2. Is there any place where I could find a sample of the official scoring rubric used for proteins (at any level) last year?
3. Finally, would showing the bonding within secondary structures be considered a purposeful addition to the Klf4? Or does it have to be more directly related to the function in iPSCs?

[Kokonilly]

How can I model DNA? Specifically, angle of ascent for the double-helix and space between the sugar phosphates vertically?

(Note: This isn't me, just a stressed team member.)

[Phenylethylamine]

Does anybody know if we should include the side chains that they included in their example of a Zinc finger? They gave an example of a Znf in their video on how to construct a protein. Also I was reading about how there are primarily four different kinds of Znf, does anybody know which one we have to model? Did anybody show some of the side chains of DNA?

I haven't watched that video lately, but if I recall correctly, the one they show is a Cys2/His2 zinc finger, which is the same as the ones in Klf4. As for whether you should include them, well, the zinc fingers are pretty vital to the protein's function, so...

In the jmol program, how do you view where the add-ons are located? Is there a way of knowing by looking at the basic structure(which I ended up building fine), or is there something in the program that will show them?

I assume you're referring to the on-site build, where you'll be using the pre-set-up competition environment with the backbone structure originally visible. You can show the sidechain "add-ons" using menus, but if you're serious about this event, you should learn how to use the console. You'll need to type "select [residue] and sidechain" (replacing [residue] with the number of the residue- that is, amino acid- that you're showing) and click "Execute", and then delete that and type "wireframe" and click "Execute" again (note: if you're using standalone Jmol or RasMol, which they might give you at some competitions, you don't need to click "Execute" or delete the previous line- just hit enter after each command). You can also use "wireframe 200", or some other number, where the number is the radius of the wireframe. Making it larger than just a single line (which is the default) can make it easier to see (the default backbone is also just a line; you can "select all" and then "backbone 300" to make it a more visible width).

My model is all supported by 22-gauge jewelry wire

At an invitational my school went to, one of our teams was docked points because our protein was held up by wood stakes (attached to the Styrofoam base) and the judges told us that they must be able to pick up the protein and move it around. Is suspending it from a "ceiling" with wire legal? I do not think there is anything in the rules about this (and it was only an invitational, so the judges may have been in the wrong).
Our DNA part of the model will probably be supported from underneath by wooden stakes (or suspended) because that has not been a problem, I think the issue was that the protein could not be separated from the rest of the display.
What are your thoughts on this? I'm concerned this will be sprung on all of us at competition, and anyone supporting their model with attachments will be second-tiered.

Nowhere in the rules does it say this kind of support isn't allowed, but as Mithrandir said, if they can't turn it around, busy judges may not try very hard to see if your model fits the requirements. Jewelry wire has two advantages: 1. it's flexible, so they can move it around a bit if necessary; 2. it's quite thin, so they can still see all sides of the protein, because the wire supports don't block their view.

Any reason why the Primary Structure section of the Protein Modeling wiki has "TL;DR" in it?

I wrote essentially all of the Protein Modeling wiki page; I put in the TL;DR there in case anyone was looking for quick tips or clarifications and didn't want to read through a full explanation of what primary structure is. That's all- no deep meaning behind it. (On the off chance that someone doesn't know, "TL;DR" stands for "too long; didn't read" and is used to mark short summaries of long paragraphs).

1. Has anyone tried to invest in the magnetic sidechains to use them in the pre-build? I'm curious if they could make the model look a bit more professional.
2. Is there any place where I could find a sample of the official scoring rubric used for proteins (at any level) last year?
3. Finally, would showing the bonding within secondary structures be considered a purposeful addition to the Klf4? Or does it have to be more directly related to the function in iPSCs?

1. I haven't, and I wouldn't recommend it. While it might make your model look more professional, judges aren't looking for "professional". Even though it technically shouldn't affect your score, it's better to have your model look as if it were made by students- just bright students. Also, it's not very practical- if you've built any of the on-sites, you know how easily those fall off.
2. They have the 2010 National event and rubrics here.
3. Showing the bonding of all secondary structures (e.g., the hydrogen bonds within every alpha helix) probably wouldn't help you much, as those bonds are there in every protein that has those secondary structures, but showing bonds, for example, between the protein and DNA might be helpful. Stick to things related to the protein's function one way or another, and if you can, specifically in iPSCs.

How can I model DNA? Specifically, angle of ascent for the double-helix and space between the sugar phosphates vertically?

I'm sure Wikipedia has that information, but I also sincerely doubt any judge will measure your DNA that carefully- not to mention that the DNA isn't directly part of the protein you're modeling, so it's a creative addition; you can make it schematic if you want. It doesn't even have to be super-accurate, as long as it's recognizable and accurate enough to illustrate whatever point you're making by including it.

[Mithrandir]

Does anybody know how to view regions of polar and nonpolar on the protein? I couldn't figure out how to do this in Jmol and I think it would be a good creative addition.

[TheGenius]

Does anybody know how to view regions of polar and nonpolar on the protein? I couldn't figure out how to do this in Jmol and I think it would be a good creative addition.

Display polar
Display not polar

Or

Hide not polar
Hide polar

Or

Restrict polar
Restrict not polar

The first two sets are functionally identical and can be reversed using display all or undo. The last set can only be reversed using undo.

[EastStroudsburg13]

My model is all supported by 22-gauge jewelry wire

At an invitational my school went to, one of our teams was docked points because our protein was held up by wood stakes (attached to the Styrofoam base) and the judges told us that they must be able to pick up the protein and move it around. Is suspending it from a "ceiling" with wire legal? I do not think there is anything in the rules about this (and it was only an invitational, so the judges may have been in the wrong).
Our DNA part of the model will probably be supported from underneath by wooden stakes (or suspended) because that has not been a problem, I think the issue was that the protein could not be separated from the rest of the display.
What are your thoughts on this? I'm concerned this will be sprung on all of us at competition, and anyone supporting their model with attachments will be second-tiered.

If you look on the online scoring rubric from last year they have to do things like compare the locations of two parts of the protein. Then decide if the protein is in the correct shape. This is difficult to do if the protein is mounted onto something with wooden stakes. You're so lucky that you invitationals has protein. My school's invitational only had like half the events.

What I'm probably going to do is place it on wooden stakes so it's stabilized, but make it so that the model can be removed. Hopefully the judges can figure out how to put the model back onto the support.

Should I color-code the helices and beta sheets on my Toober, and then label the respective colors on the note card? I'm not sure how well the colors would show up and the rubric didn't have anything about coloring the secondary structures. Will the judges assume where the structures are or do I have to show them?

[Phenylethylamine]

Should I color-code the helices and beta sheets on my Toober, and then label the respective colors on the note card? I'm not sure how well the colors would show up and the rubric didn't have anything about coloring the secondary structures. Will the judges assume where the structures are or do I have to show them?

If your alpha helices are correctly twisted and your beta sheets appropriately kinked, the judges should be able to figure out what's what, and you don't have to specifically color the secondary structures. That being said, I can't think of any particular reason why you couldn't color them; it might serve as insurance to make sure the judges know that's supposed to be a beta sheet if the structures get a little squished or aren't folded quite clearly enough. On the other hand, they might say that just coloring them isn't enough, so if they can't clearly see the folds you don't get credit anyway. Based on last year's national prebuild rubric, it seems like they're pretty strict about the secondary structures being folded exactly.

TL;DR You can color the secondary structures or not color them, but make sure you've folded them accurately either way.

Does anybody know how to view regions of polar and nonpolar on the protein? I couldn't figure out how to do this in Jmol and I think it would be a good creative addition.

Display polar
Display not polar

Or

Hide not polar
Hide polar

Or

Restrict polar
Restrict not polar

The first two sets are functionally identical and can be reversed using display all or undo. The last set can only be reversed using undo.

These all work, but they cause everything else to disappear. If you want to display polar/nonpolar sidechains without affecting the rest of your model, try:

select polar and sidechain
wireframe [number]

The number is the radius of the wireframe; I usually use 200. If you don't put in a number, the sidechains will show up as thin lines.