Protein Modeling C

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Protein Modeling C

Postby Jim_R » August 10th, 2014, 10:47 am

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Re: Protein Modeling C

Postby Gearbox » September 3rd, 2014, 6:05 pm

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!
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Re: Protein Modeling C

Postby EastStroudsburg13 » September 5th, 2014, 6:48 pm

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.
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Re: Protein Modeling C

Postby colorado mtn science » September 12th, 2014, 10:16 am

EastStroudsburg13 wrote: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?

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Re: Protein Modeling C

Postby EastStroudsburg13 » September 12th, 2014, 11:23 am

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.
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Re: Protein Modeling C

Postby colorado mtn science » September 19th, 2014, 1:27 pm

Where can we find out what proteins we're modeling for the on site builds?

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Re: Protein Modeling C

Postby alwaysmatts » September 19th, 2014, 3:56 pm

hey anyone knows where can we study this event?

also, is this event more of a chemistry event, or biology event?
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Re: Protein Modeling C

Postby fantasyfan » September 20th, 2014, 12:45 pm

colorado mtn science wrote: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
Looking forward to anatomy, protein, fossils, and optics (NYS trial) this year!

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Re: Protein Modeling C

Postby JonB » September 22nd, 2014, 1:57 pm

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!

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Re: Protein Modeling C

Postby fantasyfan » September 22nd, 2014, 2:09 pm

JonB wrote: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"
Looking forward to anatomy, protein, fossils, and optics (NYS trial) this year!

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Re: Protein Modeling C

Postby JonB » September 22nd, 2014, 2:44 pm

fantasyfan wrote:
JonB wrote: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"



Thanks!

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Re: Protein Modeling C

Postby Tony116 » October 3rd, 2014, 2:23 pm

I'm a bit confused about the protein we're supposed to model for the pre-build. The criteria says that we are including amino acids 421-560, and based on this, there are 140 amino acids, not 139 like the rule book says. So there is a one amino acid difference. Has anyone else noticed this? Clarification would be appreciated.

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Re: Protein Modeling C

Postby bernard » October 3rd, 2014, 7:24 pm

Tony116 wrote:I'm a bit confused about the protein we're supposed to model for the pre-build. The criteria says that we are including amino acids 421-560, and based on this, there are 140 amino acids, not 139 like the rule book says. So there is a one amino acid difference. Has anyone else noticed this? Clarification would be appreciated.

In which section does it mention 139? I don't see it.
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Re: Protein Modeling C

Postby Tony116 » October 4th, 2014, 2:36 pm

bernard wrote:
Tony116 wrote:I'm a bit confused about the protein we're supposed to model for the pre-build. The criteria says that we are including amino acids 421-560, and based on this, there are 140 amino acids, not 139 like the rule book says. So there is a one amino acid difference. Has anyone else noticed this? Clarification would be appreciated.

In which section does it mention 139? I don't see it.


Oh sorry i guess it's not mentioned in the rule book. I saw it on the pre-build visualization site, it literally said this: "This section is 139 amino acids long and will require a toober that is 278cm long at the scale of 1 amino acid = 2cm."

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Re: Protein Modeling C

Postby EastStroudsburg13 » October 5th, 2014, 6:01 am

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.
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