Protein Modeling C [NY Trial]

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Re: Protein Modeling C [NY Trial]

Postby skiblack331 » January 3rd, 2010, 10:28 am

I'm a little bit confused with this event. It says that we're supposed to add the side chains that are important to the protein's shape. How are we supposed to figure out which side chains are important?
I wasn't sure which ones are important, so while I was going through the steps, I went to one of the websites listed (http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html). Though it doesn't outright state the important side chains, the website gives the number of a few of the amino acids. I figured that these must be the important ones, so when I used Jmol, I input the specific protein numbers to view the specific amino acids. I found, however that according to the website above, amino acid #106 is histidine, but according to the protein database website, that amino acid is argine. Which website is right?
Also, the rules state we should build a model of Chain B, but there is not a chain listed as "B", but instead the letters "H" through "M". I used Chain M, is that the correct one to use?
I appreciate any insights anyone might have. Thanks.
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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » January 6th, 2010, 11:18 am

I'm a little bit confused with this event. It says that we're supposed to add the side chains that are important to the protein's shape. How are we supposed to figure out which side chains are important?
I wasn't sure which ones are important, so while I was going through the steps, I went to one of the websites listed (http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html). Though it doesn't outright state the important side chains, the website gives the number of a few of the amino acids. I figured that these must be the important ones, so when I used Jmol, I input the specific protein numbers to view the specific amino acids. I found, however that according to the website above, amino acid #106 is histidine, but according to the protein database website, that amino acid is argine. Which website is right?
Also, the rules state we should build a model of Chain B, but there is not a chain listed as "B", but instead the letters "H" through "M". I used Chain M, is that the correct one to use?
I appreciate any insights anyone might have. Thanks.
It actually says the side chains that are important to the protein's function. If you research the function of the protein, you'll probably find information about certain side chains that are specifically involved (I haven't done this research yet, but I did a similar project with a different protein, and a very little research quickly revealed which side chains were important. I'm talking Wikipedia research, and clicking a few of the links at the bottom of the page. Not too in-depth).

To find out what residue 106 actually is, select it in Jmol and look at its three-letter amino acid code. However, I'm thinking that since you're seeing a contradiction, it's possible that you've downloaded a different file than you intended?

When I downloaded the PDB file, there was definitely a Chain B. Do you have the exact link of what you downloaded?
If you haven't already, try using the commands "select*b" or "restrict*b". If you were using another command, you may have been selecting something else; those commands will definitely work in the case that there is a B chain. Jmol can be screwy sometimes, though, so you can always try closing the file and reopening it, or redownloading it.
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Re: Protein Modeling C [NY Trial]

Postby skiblack331 » January 8th, 2010, 7:27 pm

Thanks for the help. I realized that none of the chains in Jmol were actually chain B, but were labeled with different letters. I'm not sure what the problem is with the contradiction, but I don't think it matters because I don't think it's that important. I read the websites we were given, but I didn't see anything about important amino acids. We were given three crosslinks with the kit, so they must have a significance, so I'll check there first.
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Re: Protein Modeling C [NY Trial]

Postby batmankiller » January 19th, 2010, 8:33 pm

I too, am having troubles findign the important side chains, the helices and all that were easy by the important side chains is annoying to find.. lemme know if you guys find sites for the research because I've been looking and not having any luck (don't have to give me the exact amino acid #.. unless you don't mind =D.. just give me a place to look >.>)
Last edited by batmankiller on February 1st, 2010, 8:53 pm, edited 1 time in total.

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Re: Protein Modeling C [NY Trial]

Postby Flavorflav » February 1st, 2010, 6:06 am

I too, am having troubles findign the important side chains, the helices and all that were easy by the important side chains is annoying to find.. lemme know if you guys find sites for the research because I've been looking and not having any luck (don't have to give me the exact amino acid #.. unless you don't mind =D.. just give me a place to look >.>)

and do we have to know about dark energy/dark matter?
For protein modeling? I wouldn't think so.

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Re: Protein Modeling C [NY Trial]

Postby batmankiller » February 1st, 2010, 8:53 pm

lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?

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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » February 3rd, 2010, 5:22 pm

lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?
For the on-site build at the competition, they will tell you which side chains to show, and give you little foam representations of those side chains to use. You will not have to decide what's important.

I found various information about important side chains simply by following the links listed in the event rules; the MSOE site mentioned there has several helpful links, including one that provided me with most of my information about side chains important to the protein's function. Alternately, you could try googling "structure of influenza hemagglutinin", since that is the protein we're working with.
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Re: Protein Modeling C [NY Trial]

Postby ahage16 » March 9th, 2010, 1:22 pm

lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?
For the on-site build at the competition, they will tell you which side chains to show, and give you little foam representations of those side chains to use. You will not have to decide what's important.

I found various information about important side chains simply by following the links listed in the event rules; the MSOE site mentioned there has several helpful links, including one that provided me with most of my information about side chains important to the protein's function. Alternately, you could try googling "structure of influenza hemagglutinin", since that is the protein we're working with.
What exact links on the MSOE site did you use to find the information about the important sidechains?

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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » March 9th, 2010, 3:28 pm

lmao dunno why i wrote about dark matter here.. anyways... umm yeah anyone have any ideas on side chains this is depressing..how are we going to do the real build at the competition if it's so hard to look for them online with an unlimited amount of resources and 3 months?
For the on-site build at the competition, they will tell you which side chains to show, and give you little foam representations of those side chains to use. You will not have to decide what's important.

I found various information about important side chains simply by following the links listed in the event rules; the MSOE site mentioned there has several helpful links, including one that provided me with most of my information about side chains important to the protein's function. Alternately, you could try googling "structure of influenza hemagglutinin", since that is the protein we're working with.
What exact links on the MSOE site did you use to find the information about the important sidechains?
It says, "View David Marcey's Molecular Museum page", and links to http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html. That's the most helpful one.
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Re: Protein Modeling C [NY Trial]

Postby Phenylethylamine » March 10th, 2010, 5:51 pm

In Jmol, you can type "select sheets" and then color them to see the beta sheets, and "select helix" and then color to see the helices. The standard color for beta sheets is yellow, and for helices some type of red, but it's really irrelevant- as long as you choose a different color from the rest of your file, you'll be able to see exactly where they start and end.

The cross-linkers are for structural purposes only, so you can put them wherever you need them to stabilize your model.

To show important sidechains, you can use anything that will attach to the toober lol; it can represent the actual shape of the sidechain, but it doesn't have to. The shapes of the sidechains can be found at http://www.3dmoleculardesigns.com/AASK/ ... 20List.pdf, if you want your sidechains to actually represent the real shape. I've seen people use pushpins- just to show where the sidechains are, without the shape- model magic, pipe cleaners, ribbon (again, more for placement than shape), and tons of other things.

Yes, 1-160 refers to the amino acid numbers, and yes, blue goes at the starting point- the amino terminus- and red goes at the end point- the carboxy terminus.

When you put those sidechains on your computer model (for example, "select*b and his106 and sidechain", "wireframe 250"), you'll be able to see exactly where they are, and that the site (http://www.callutheran.edu/BioDev/omm/jmol/ha/ha.html) is accurate.
This is some advice I gave gsheni in answer to their questions, which I thought could be helpful to other people doing the event as well.
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