Protein Modeling C

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Phenylethylamine
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Re: Protein Modeling C

Postby Phenylethylamine » March 13th, 2011, 8:49 am

I was wondering... on the Jmol of 2wbu, what are the red sphere things? Are they hydrogen molecules or something? I looked up the structure and found the alpha helixes and sidechains, but I just can't figure out what the little spheres are. :?:
When you first open a file in Jmol, it shows you all the atoms of the protein in "ball-and-stick" format. The spheres are individual atoms; red ones are oxygen in the default color scheme.

Have you been using the menus in Jmol or the command prompt? (That is, have you been changing the way you view the molecule at all, and if so, how?)

For anyone new to the event, I recommend reading the Protein Modeling Wiki; if you have more questions after reading that (which you most probably will), come back and ask (this also helps us keep updating the wiki to make it as helpful as possible).
I've been using the menus to try to figure out what those (the molecules) are and which creative additions to add. I still don't really understand Jmol, so I'm trying to avoid messing around and confusing myself further, and we don't have our mini-toobers yet, so I can't really do much now, but I'm trying to start with figuring out the sidechains.
First, I recommend trying to use the command prompt. It's a little more difficult, but you have much more control over the display of your protein. If you're using Jmol online, the command line is right there under the display; if you have Jmol downloaded, you can access the command line by going to File -> Output Console.

Start by putting the entire protein in backbone mode by typing:

select all
backbone 250
wireframe off
spacefill off

Now you have essentially a clean slate, with none of the sidechains showing- just the protein and the DNA (you don't have to model the DNA, but it's a good creative addition, so it can be useful to know where it is). In order to display a certain sidechain, you have to select it, and then choose a viewing mode- typically wireframe:

select [residue #] and sidechain
wireframe 200

If you want to display all the sidechains of a given type, you can instead select the residue type; for example, if you wanted to select all the cysteines, you would use the commands:

select cys and sidechain
wireframe 200

If you're wondering which sidechains to model, try looking through the links at the bottom of the Protein Modeling Wiki. One of the useful links is broken at the moment, but I'm trying to get that figured out. There are still some good resources there, though.
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Megan95
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Re: Protein Modeling C

Postby Megan95 » March 13th, 2011, 10:00 am

First, I recommend trying to use the command prompt. It's a little more difficult, but you have much more control over the display of your protein. If you're using Jmol online, the command line is right there under the display; if you have Jmol downloaded, you can access the command line by going to File -> Output Console.

Start by putting the entire protein in backbone mode by typing:

select all
backbone 250
wireframe off
spacefill off

Now you have essentially a clean slate, with none of the sidechains showing- just the protein and the DNA (you don't have to model the DNA, but it's a good creative addition, so it can be useful to know where it is). In order to display a certain sidechain, you have to select it, and then choose a viewing mode- typically wireframe:

select [residue #] and sidechain
wireframe 200

If you want to display all the sidechains of a given type, you can instead select the residue type; for example, if you wanted to select all the cysteines, you would use the commands:

select cys and sidechain
wireframe 200

If you're wondering which sidechains to model, try looking through the links at the bottom of the Protein Modeling Wiki. One of the useful links is broken at the moment, but I'm trying to get that figured out. There are still some good resources there, though.
Thanks. I really appreciate all your help.

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Re: Protein Modeling C

Postby kwijiborjt » March 16th, 2011, 6:09 pm

Hi all,
I'm the NYS event coordinator, and a former competitor. If you have any questions between now and Friday, feel free to ask here. Due to some room issues, the event will be run in two time blocks from 5:30-6:20 (teams 2-32) and 6:30-7:20 (teams 33-54). Please try to impound your protein in Thayer 442 by 5:00 PM. More information will be provided to your coaches at registration.
NYS/Lower Hudson Valley Protein Modeling event supervisor
Entomology 2nd and 3rd in NY state
Rocks and Minerals 5th and 6th in NY state

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Re: Protein Modeling C

Postby paradoxgirl » March 16th, 2011, 6:56 pm

I have a question, although i'm not from New York and will not be at the competition, but I guess this applies to all state competitions.
Is the exam portion of the event written by MSOE? It seems that all tests were written by them at invitationals/regionals, and I was wondering if the exams are the same for all state competitions. Thinking about it though, just because they are written by MSOE won't mean that they are all the same...I was just curious
Thanks!
Harriton High School Science Olympiad

kwijiborjt
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Re: Protein Modeling C

Postby kwijiborjt » March 16th, 2011, 7:05 pm

To the best of my knowledge all states are given the same exam from MSOE, but it is within the discretion of the event coordinator to modify the exams.
NYS/Lower Hudson Valley Protein Modeling event supervisor
Entomology 2nd and 3rd in NY state
Rocks and Minerals 5th and 6th in NY state

gsheni
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Re: Protein Modeling C

Postby gsheni » March 17th, 2011, 1:53 am

How do you know which side chains to model? Do you go to each wikipedia page of, lets say histine, and look at its function? Then show the sidechains on your model? All I know is that i have to model the amino acids that look like they are nearby to the DNA in jmol? Anything else.

Also how do you model the zinc ion and the zinc fingers in the program? I dont see the two histine and two cysteine supposed to be at the c terminus but all i see is Phenylalanine.
I cant see the zinc ion you guys keep talking about, or even the zinc fingers in 2WBU.

Also what does this mean>?
http://upload.wikimedia.org/wikipedia/en/2/2e/Fig.2.jpg
Last edited by gsheni on March 17th, 2011, 9:04 pm, edited 1 time in total.

kwijiborjt
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Re: Protein Modeling C

Postby kwijiborjt » March 17th, 2011, 7:31 am

Sadly this is information you'll have to research for yourself, mostly. That's the point of the event!

I wouldn't worry about that link you showed me. The green boxes are highlighting the amino acids that make up the zinc finger domains. Comparison between klf4 and 5 isn't necessary. And i think ERK phosphorylation sites means potential areas where the proteins are phosphorylated by kinases in the endoplasmic reticulum. I'll let you look that up and make of that what you will, if you think that's a worthwhile creative addition.

Only model side chains that demonstrate an important connection between structure and function. You lose points if you model every side chain. But modeling any number of subsets of side chains that help the protein to serve certain functions would be good creative additions to your model.

If you want to find cysteine and histidine residues, i would suggest using the jmol program to select these residues by type and visualize them with the wireframe function.

You should be able to look up information about zinc finger structure very easily online.

That's a lot of help, i'm not giving any more for those questions!
NYS/Lower Hudson Valley Protein Modeling event supervisor
Entomology 2nd and 3rd in NY state
Rocks and Minerals 5th and 6th in NY state

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Phenylethylamine
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Re: Protein Modeling C

Postby Phenylethylamine » March 17th, 2011, 2:20 pm

Hi all,
I'm the NYS event coordinator, and a former competitor. If you have any questions between now and Friday, feel free to ask here. Due to some room issues, the event will be run in two time blocks from 5:30-6:20 (teams 2-32) and 6:30-7:20 (teams 33-54). Please try to impound your protein in Thayer 442 by 5:00 PM. More information will be provided to your coaches at registration.
Will we only be able to use the online Jmol competition environment, or will Jmol (or Rasmol/RasWin/comparable) be available locally on the computers as well?

The online environment is very inconvenient to use (because it's necessary to manually click "Execute" and delete the previous line after every command), so I prefer to use native Jmol whenever possible.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009

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Re: Protein Modeling C

Postby leoeckman » March 17th, 2011, 5:50 pm

Big Question!

Despite my frequent searches, I can't seem to find any information on which amino acid sidchains methylate the Cytosine in the DNA sequence. The closest I've come to is Leucine's double-branched methyl group. The problem though is that only one Leucine sidechain faces toward the actual DNA molecule because of the molecules polarity. Therefore I can't be certian that Leucine's sidechain is causing the reaction. So: which amino acids are important for DNA alteration?


TL;DR- Which amino acids function to methylate (enact upon) the DNA?

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Re: Protein Modeling C

Postby nanowhale » March 18th, 2011, 6:19 am

Does anyone know any good references for protein structures? I am still a young member of the team I haven't took any AP classes yet. Also, if anyone can tell me the commands to show sidechains and such it would be greatly appreciated because our team at state moved from "A" to "AA" so it is more competitive. Thanks! :)
2012 events:
Forensics
Protein Modeling
Thermodyanmics


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