Protein Modeling C

emmadej
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Re: Protein Modeling C

Postby emmadej » October 23rd, 2014, 2:22 pm

Both caps count as one amino acid I believe. That way when you mark the 2 cm lengths you end up with 140 amino acids, even though you have only 278 cm to work with.

The pre-build visualization site includes both end amino acids 421 and 560. therefore including 140 amino acids.

The tuber is 278 cm, and if each amino acid is 2 cm then it will represent 139 amino acids. Each endcap is appoximately 2 cm long and therefore will cover a total of 4 cm when placed on the model, leaving 274 cm to work with. That is enough to represent 137 amino acids and the 2 end amino acids, which is 139. Yet the online visualization site includes 140 amino acids. Which end amino do we leave off?

http://cbm.msoe.edu/scienceOlympiad/des ... build.html - here is the prebuild visualization. Once you restrict everything, type in "select 421-560" and then "color red" and it colors the whole protein red.

Please help! :(

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Re: Protein Modeling C

Postby EastStroudsburg13 » October 23rd, 2014, 4:26 pm

The tuber is 278 cm, and if each amino acid is 2 cm then it will represent 139 amino acids. Each endcap is appoximately 2 cm long and therefore will cover a total of 4 cm when placed on the model, leaving 274 cm to work with. That is enough to represent 137 amino acids and the 2 end amino acids, which is 139. Yet the online visualization site includes 140 amino acids. Which end amino do we leave off?
The first and last amino acids are represented by the very ends of the Toober, the endcaps are just there to represent that. You should mark the locations of the amino acids first, and then put the endcaps on. I never had to leave off any amino acids in 2011 and 2012, so it should still work out okay now.
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Re: Protein Modeling C

Postby pikachu4919 » October 23rd, 2014, 5:05 pm

Hey, so this is what I did to select the section to be modeled. First, did I do it correctly? Second, how do you manipulate it to get it to display the amino acid numbers for the alpha helices, beta pleated sheets and key amino acids?
Capture2fok.JPG
(Although I'm a veteran competitor, this is my first time doing protein modeling since this is the first time it has appeared while I've been in SciOly...)
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Re: Protein Modeling C

Postby fantasyfan » October 23rd, 2014, 5:22 pm

Hey, so this is what I did to select the section to be modeled. First, did I do it correctly? Second, how do you manipulate it to get it to display the amino acid numbers for the alpha helices, beta pleated sheets and key amino acids?
Looks correct to me!

I don't believe that there is a specific function such that it gives you the starts and ends of the sheets and helices, but if you click on any atom it'll tell you which amino acid it belongs to.

Here is a quick reference sheet: http://cbm.msoe.edu/includes/jmol/SOJmo ... eSheet.pdf

(Also, as a side note, I personally don't like the cartoon structure that it defaults to. If you don't like it either, you can change it by typing "cartoon off" and then either "backbone on", "wireframe on", "space fill on", or "strands on".)
Looking forward to anatomy, protein, fossils, and optics (NYS trial) this year!

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Re: Protein Modeling C

Postby pikachu4919 » October 23rd, 2014, 6:19 pm

Hey, so this is what I did to select the section to be modeled. First, did I do it correctly? Second, how do you manipulate it to get it to display the amino acid numbers for the alpha helices, beta pleated sheets and key amino acids?
Looks correct to me!

I don't believe that there is a specific function such that it gives you the starts and ends of the sheets and helices, but if you click on any atom it'll tell you which amino acid it belongs to.

Here is a quick reference sheet: http://cbm.msoe.edu/includes/jmol/SOJmo ... eSheet.pdf

(Also, as a side note, I personally don't like the cartoon structure that it defaults to. If you don't like it either, you can change it by typing "cartoon off" and then either "backbone on", "wireframe on", "space fill on", or "strands on".)
Yeah, I (eventually) figured out how to change it to backbone, but thanks! :)
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Re: Protein Modeling C

Postby emmadej » October 24th, 2014, 6:03 pm

The tuber is 278 cm, and if each amino acid is 2 cm then it will represent 139 amino acids. Each endcap is appoximately 2 cm long and therefore will cover a total of 4 cm when placed on the model, leaving 274 cm to work with. That is enough to represent 137 amino acids and the 2 end amino acids, which is 139. Yet the online visualization site includes 140 amino acids. Which end amino do we leave off?
The first and last amino acids are represented by the very ends of the Toober, the endcaps are just there to represent that. You should mark the locations of the amino acids first, and then put the endcaps on. I never had to leave off any amino acids in 2011 and 2012, so it should still work out okay now.

Yeah I understand that! c:

I'm just confused because the tuber can represent 139 amino acids, but the online model represents 140. Which amino acid do we leave off? I might be having a blonde moment, but 560-421 is 140 amino acids, if you include both ends of the restriction :C

Sorry, I don't mean to be troublesome!

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Re: Protein Modeling C

Postby EastStroudsburg13 » October 25th, 2014, 11:07 am

Okay, let's say you want to represent two amino acids. It would look something like this (pardon the makeshift drawing):

Image

So for a two-amino acid chain, you would need 2 cm of Toober, since you have one amino acid on each end and they're separated by 2 cm.

Then, if you want to add another amino acid, you would need 2 additional cm, thus making a 3-acid chain have a length of 4 cm.

Notice there's a pattern here. For a protein with x number of sidechains, you need a corresponding Toober that's 2*(x-1) cm long. If you extend this out for a 140 amino acid chain, then, you'd need a Toober of length 2*(140-1) = 2*139 = 278 cm.

I think what you might be doing is considering the space between the markings as the amino acids. That space is merely the backbone of the protein that connects the individual amino acids. Each marking represents the individual amino acids, and that would be where you'd identify any sidechains important to the function of the protein.
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Re: Protein Modeling C

Postby fantasyfan » October 27th, 2014, 8:05 pm

I think what you might be doing is considering the space between the markings as the amino acids. That space is merely the backbone of the protein that connects the individual amino acids. Each marking represents the individual amino acids, and that would be where you'd identify any sidechains important to the function of the protein.
Thank you, this helps.
Also, when folding the beta-sheets, should the lines be at the kinks or in between the kinks?
Looking forward to anatomy, protein, fossils, and optics (NYS trial) this year!

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Re: Protein Modeling C

Postby Dhruvster » October 27th, 2014, 9:23 pm

According to the event supervisor video on the MSOE website, either should be acceptable I believe.

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Re: Protein Modeling C

Postby Phenylethylamine » October 30th, 2014, 6:39 am

Okay, let's say you want to represent two amino acids. It would look something like this (pardon the makeshift drawing):

Image

So for a two-amino acid chain, you would need 2 cm of Toober, since you have one amino acid on each end and they're separated by 2 cm.

Then, if you want to add another amino acid, you would need 2 additional cm, thus making a 3-acid chain have a length of 4 cm.

Notice there's a pattern here. For a protein with x number of sidechains, you need a corresponding Toober that's 2*(x-1) cm long. If you extend this out for a 140 amino acid chain, then, you'd need a Toober of length 2*(140-1) = 2*139 = 278 cm.

I think what you might be doing is considering the space between the markings as the amino acids. That space is merely the backbone of the protein that connects the individual amino acids. Each marking represents the individual amino acids, and that would be where you'd identify any sidechains important to the function of the protein.
While this seems to be what they're going for if they're trying to get you to represent a 140-aa protein with a 278-cm Toober, it's a basic misunderstanding of how proteins work. A protein is not made up of a backbone that "connects" individual amino acids; the backbone is part of the amino acids. Emmadej is entirely correct to be confused by this, because the 2 cm space of backbone SHOULD correspond to one amino acid residue, and if not, then MSOE is counting wrong. That said, do what works with the Toober you're given, but as Protein event supervisor for MA States and the MIT invitational, I would certainly not take off points from someone who decided to omit either 421 or 560 in order to be able to correctly represent every aa as having its own 2 cm of backbone.
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