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Protein Modeling C

Posted: August 10th, 2014, 10:47 am
by Jim_R

Re: Protein Modeling C

Posted: September 3rd, 2014, 6:05 pm
by Gearbox
Hello All, I first want to say how excited I am this year for this event. Anyway, I have a question regarding side chains. What are they and how will we model them on our protein? Thanks!

Re: Protein Modeling C

Posted: September 5th, 2014, 6:48 pm
by EastStroudsburg13
Sidechains are the part of amino acids that vary, depending on which amino acid you are talking about. Every amino acid has a similar structure, so the sidechain is what differentiates them. The diagram below shows the structure of every amino acid, with "R" representing the sidechain that varies.
Image

This website shows the sidechains pretty well. In the diagrams on the left, all the sidechains are colored in red.

Typically, most sidechains are not modeled on your proteins, since not all sidechains will have a function. However, certain sidechains will be important to the function of the protein, so it would be important to model those sidechains. For example, in 2012, the pre-build was caspase-3. The active site for this protein has a cysteine and a histidine, so it was a good idea to model those particular sidechains in their correct locations on the pre-build.

Too often people get caught up in trying to put as much information on their build, and they lose sight of the fact that the build's main purpose is to show the FUNCTION of the protein. Since only a few sidechains actually contribute to the protein's function, these are the only sidechains you should worry about modeling.

Re: Protein Modeling C

Posted: September 12th, 2014, 10:16 am
by colorado mtn science
Sidechains are the part of amino acids that vary, depending on which amino acid you are talking about. Every amino acid has a similar structure, so the sidechain is what differentiates them. The diagram below shows the structure of every amino acid, with "R" representing the sidechain that varies.
Image

This website shows the sidechains pretty well. In the diagrams on the left, all the sidechains are colored in red.

Typically, most sidechains are not modeled on your proteins, since not all sidechains will have a function. However, certain sidechains will be important to the function of the protein, so it would be important to model those sidechains. For example, in 2012, the pre-build was caspase-3. The active site for this protein has a cysteine and a histidine, so it was a good idea to model those particular sidechains in their correct locations on the pre-build.

Too often people get caught up in trying to put as much information on their build, and they lose sight of the fact that the build's main purpose is to show the FUNCTION of the protein. Since only a few sidechains actually contribute to the protein's function, these are the only sidechains you should worry about modeling.
Isn't the carboxyl group COO- and not COOH? Also, isn't the amino group H3N+ and not H2N?

Re: Protein Modeling C

Posted: September 12th, 2014, 11:23 am
by EastStroudsburg13
Typically the general structure is drawn without charges on any functional groups. You can represent it that way chemically though, since all you've really changed is removing the hydrogen from the carboxyl group and putting it on the amine. Normally a carboxyl group is represented by COOH, while a carboxylate ion is COO-. Either way, you still perform a dehydration synthesis reaction when linking two amino acids, it's just a matter of where the second hydrogen comes from.

Re: Protein Modeling C

Posted: September 19th, 2014, 1:27 pm
by colorado mtn science
Where can we find out what proteins we're modeling for the on site builds?

Re: Protein Modeling C

Posted: September 19th, 2014, 3:56 pm
by alwaysmatts
hey anyone knows where can we study this event?

also, is this event more of a chemistry event, or biology event?

Re: Protein Modeling C

Posted: September 20th, 2014, 12:45 pm
by fantasyfan
Where can we find out what proteins we're modeling for the on site builds?
They aren't available yet, but when they are, you will be able to find them at: http://cbm.msoe.edu/scienceOlympiad/participant4.php

Re: Protein Modeling C

Posted: September 22nd, 2014, 1:57 pm
by JonB
When the fokI endonuclease protein is loaded on jmol, first we use the console to eliminate all amino acids besides 421-560. Then, we are left with two biomolecules. At first they appeared to be the same, however, when selecting one of them to view, jmol displays biomolecule 2 as have 53 more atoms than biomolecule 1. Does anyone know which biomolecule we are supposed to be modeling our protein after? Thank you!

Re: Protein Modeling C

Posted: September 22nd, 2014, 2:09 pm
by fantasyfan
When the fokI endonuclease protein is loaded on jmol, first we use the console to eliminate all amino acids besides 421-560. Then, we are left with two biomolecules. At first they appeared to be the same, however, when selecting one of them to view, jmol displays biomolecule 2 as have 53 more atoms than biomolecule 1. Does anyone know which biomolecule we are supposed to be modeling our protein after? Thank you!
You need to specify that you want chain A,
Restrict *A
Don't forget to capitalize the "A"