Protein Modeling C

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TheWiseGirl
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Re: Protein Modeling C

Postby TheWiseGirl » February 21st, 2012, 11:58 pm

I'm new on the forum and the team leader on my school's Science Olympiad Protein Modelling team. In preparation for our regional tournament, I had our team study the online resources from the CBM website made for the event as well as outside resources on apoptosis, caspase-3 and bone marrow transplants to prepare for the written tests. However, when we got to the test we encountered vocabulary and information that we had not seen in our research and were not as prepared as I would have liked. After speaking with other teams at the tournament, I am curious to know what other Protein Modelers might suggest for studying for the test on this event. Do some of you use textbooks? If so, could you suggest any? Are there any other specific sites you may suggest?
Thanks.
Nobody really uses a textbook; we use Google! And Wikipedia! :D Haha, but I would suggest really knowing your protein basics, like Amino Acids and Secondary structure. And make sure to find answers to your questions! I've had questions before or I didn't understand something, and simply brushed it aside because I figured we wouldn't need to know it for the test, but low and behold, there it was.
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Re: Protein Modeling C

Postby Phenylethylamine » February 23rd, 2012, 10:11 am

First, just a friendly reminder, since there seem to be a lot of new people posting in this thread:
Please read the entire thread before asking your questions. Many similar questions have already been addressed in detail.
And from what I've read on the forum it seems like a lot of people are confused about which ones the 3/10 helices are. But if you look at the protein on jmol on the PDB website and color by secondary structure the 3/10 helices show up as a purple color. Am I missing something? It just seems like a lot of people are super confused, which makes me wonder if I've got something wrong... :?
3/10 helices show up as a darker, more purple color in newer versions of Jmol, like what you'd find on the PDB website, or what you'd get if you downloaded standalone Jmol now.

However, in older versions of Jmol, like what they're using in the online prebuild competition environment, 3/10 helices show up as the same color as alpha helices. This is presumably the source of the confusion.

If you are using the online prebuild environment and you are confused about where the 3/10 helices are, try looking at the protein on the PDB site instead.

As for what 3/10 helices are: they're just another kind of helix, which is vastly less common than the alpha-helix. They have three residues per turn instead of 3.6 residues per turn, which makes them tighter than alpha-helices, not looser. All the 3/10 helices in this protein are exactly three residues in length, and therefore should be exactly one turn.

If you use colors to label your secondary structures, it might make sense to differentiate between alpha-helices and 3/10-helices; however, if you rely on the accuracy of your folding to identify your secondary structures, the tighter helix should make the difference clear.
1) What's a beta bridge? How is it different from a beta sheet?
A beta bridge is an isolated residue that forms hydrogen bonds with its neighbors in a way similar to how beta sheet residues bond to each other. We do not have to show beta bridges in our model – their only function is to slightly increase the stability of the structure, and they don't look like much.
2) Why is chain C of Caspase (which is identical to chain A) apparently 144 amino acids versus 143? That's what the sequence map on PDB said at least.
The ends of chains can be hard to resolve via x-ray diffraction, because they're typically more mobile than the rest of the protein – so all that happened here is that they managed to resolve 144 residues of chain C, but only 143 of chain A. In reality, the two chains are identical.
3) On the sequence map for chain A (and others) there are some SNP's. Do they affect the structure/function of the protein in any way, or is it just there to show people that there have been mutations there before?
The particular single nucleotide polymorphisms (SNPs) that you see on the sequence map don't really affect the structure or function of the protein; they just mean that some percentage of the population has a different residue at that position, which still maintains the functionality of the protein.

However, another SNP is pretty important to the event this year: Nic Volker's disease was caused by a very, very rare SNP in his XIAP gene, which rendered his XIAP proteins non-functional. Note that because this SNP is not common, it does not appear in the sequence summary for XIAP (chain E) at all; you can read about it on the CBM site.
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Re: Protein Modeling C

Postby NinjaKim » February 23rd, 2012, 7:37 pm

Hello. This is my first time participating in this event, and there were some difficulties in getting some things, so now the model building was placed upon me, a high school freshman with no idea how to even start. I need a tip or two before tomorrow arrives.

I looked at this (http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html) and it didn't yield much help. Any help?

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Re: Protein Modeling C

Postby gsheni » February 23rd, 2012, 9:40 pm

um, do these commands
restrict *a or *b
backbone 300
that should set up to see what the final protein should look like, to model each protein individually use this
restrict*a
backbone 300
//////////
restrict*b
backbone 300
/////////

For the creative additions, just look on the site provided and do some messing around in jmol. Phenylethylamine can probably give you more direction on that.

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Re: Protein Modeling C

Postby pabalan » February 24th, 2012, 10:04 am

how do you color a chain? I've finished modeling both chains, and am currently working on combining the two together. I'm having trouble seeing exactly how to place them together, so i figured that coloring them would make it easier. can anyone on here kindly explain it to me in an understandable way, or post a helpful link that could help? thank you!

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Re: Protein Modeling C

Postby eJewell » February 24th, 2012, 11:27 am

how do you color a chain? I've finished modeling both chains, and am currently working on combining the two together. I'm having trouble seeing exactly how to place them together, so i figured that coloring them would make it easier. can anyone on here kindly explain it to me in an understandable way, or post a helpful link that could help? thank you!
If you want to see both chains on the same screen of Jmol in different colors these are the commands i would use (even though they are a bit tedious as others have pointed out)
select* a
backbone 200
color red
(or any other color you want it)
select* b
backbone 200
color yellow

This will give you a red chain a and yellow chain b which allows you to see the two different structures and how they fit together.

I would also like to say that i spent 2 and a half hours going through this wiki as suggested by other users and it answered all of my questions and helped me learn so much about Caspase and the event. I recommend reading all of the forum to anyone out there who is confused. :)

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Re: Protein Modeling C

Postby Phenylethylamine » February 25th, 2012, 7:34 am

Hello. This is my first time participating in this event, and there were some difficulties in getting some things, so now the model building was placed upon me, a high school freshman with no idea how to even start. I need a tip or two before tomorrow arrives.

I looked at this (http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html) and it didn't yield much help. Any help?
I recommend reading through the Protein Modeling Wiki – in addition to a lot of other helpful information, it includes a link to the CBM's model-folding tutorial videos, which are quite useful.

If you are looking for information about what creative additions to include, I recommend reading all the information on the CBM site, as well as the Wikipedia article on caspase-3. Reading the entirety of this thread would probably also be helpful :-)
how do you color a chain? I've finished modeling both chains, and am currently working on combining the two together. I'm having trouble seeing exactly how to place them together, so i figured that coloring them would make it easier. can anyone on here kindly explain it to me in an understandable way, or post a helpful link that could help? thank you!
If you want to see both chains on the same screen of Jmol in different colors these are the commands i would use (even though they are a bit tedious as others have pointed out)
select* a
backbone 200
color red
(or any other color you want it)
select* b
backbone 200
color yellow

This will give you a red chain a and yellow chain b which allows you to see the two different structures and how they fit together.
This is essentially the simplest method. If you already have the protein displayed in backbone (I usually use backbone 300, but that's just a matter of personal preference, you can use whatever size you like best), you don't need to include the backbone commands again: you can just use

select *a
color [color]
select *b
color [other color]

A couple more potentially useful things:

color structure
select *a and not (helix or sheet)
color [color]
select *b and not (helix or sheet)
color [other color]

will give you the advantages of "color structure" (i.e., shows you where helices and sheets are) while also showing you which chain is which.

select *a
color translucent

will maintain whatever previous coloring of chain A you had, but makes it a little bit see-through. It's a good way of distinguishing between chains when you want to fold them one at a time, or are trying to figure out how they fit together, but still want to keep the colors you had before.
I would also like to say that i spent 2 and a half hours going through this wiki as suggested by other users and it answered all of my questions and helped me learn so much about Caspase and the event. I recommend reading all of the forum to anyone out there who is confused. :)
Thank you!
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Re: Protein Modeling C

Postby gsheni » February 25th, 2012, 8:26 am

On the regional test, one of the questions on the regional test had to do with Cys203 and Arg233.
It asked for the importance of these amino acids to XIAP.

How do you deal with these questions, what commands do you do?
I know they are bound to come up during states.

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Re: Protein Modeling C

Postby Allinea » February 25th, 2012, 9:08 am

On the regional test, one of the questions on the regional test had to do with Cys203 and Arg233.
It asked for the importance of these amino acids to XIAP.

How do you deal with these questions, what commands do you do?
I know they are bound to come up during states.
I've been wondering that same thing. The River Falls invite gave us paperclips to put on the on-site model where those were, but I had no idea where to put them, or how to turn them on in Jmol.
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Re: Protein Modeling C

Postby EastStroudsburg13 » February 25th, 2012, 10:01 am

To turn on specific residues, type in "select 203", or whatever number amino acid it is, and then "spacefill 1.0", or whatever size you want. It may also help to color them a different color than the rest of the protein so it's more visible.
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