Protein Modeling C

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Re: Protein Modeling C

Postby XXGeneration » December 5th, 2011, 12:15 pm

Shh, don't kill his pride! :D

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Re: Protein Modeling C

Postby EastStroudsburg13 » December 5th, 2011, 3:23 pm

I'm aware that chain B is easier. >.> My pride is unscathed, though.

My FAQ has been answered! Thank you very much to whoever answered it. :D
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Re: Protein Modeling C

Postby Flavorflav » December 6th, 2011, 2:30 am

I am quite surprised by the answer. I would have said go with the PDB, since that is the original data. I suppose this does make it easier for event supervisors, though.

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Re: Protein Modeling C

Postby quizbowl » December 9th, 2011, 2:29 pm

Hey guys,

Just wondering, what are the exact numbers of residues for chains A and B in Caspace-3.

There are so descrepancies with the numbers listed on the Center for Biomolecular Modeling sheet sent in with the prebuild kit (Chain A=92aa, Chain B=149aa), the PDB bank sequence (Chain A=175aa, 110aa), and jmol counts (Chain A= 148aa, Chain B=91aa).

Can anyone clear this up for us? (Or point out where we're going wrong)

Thanks!
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Re: Protein Modeling C

Postby Luo » December 9th, 2011, 2:45 pm

Hey guys,

Just wondering, what are the exact numbers of residues for chains A and B in Caspace-3.

There are so descrepancies with the numbers listed on the Center for Biomolecular Modeling sheet sent in with the prebuild kit (Chain A=92aa, Chain B=149aa), the PDB bank sequence (Chain A=175aa, 110aa), and jmol counts (Chain A= 148aa, Chain B=91aa).

Can anyone clear this up for us? (Or point out where we're going wrong)

Thanks!
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Re: Protein Modeling C

Postby EastStroudsburg13 » December 9th, 2011, 6:14 pm

The numberings for Caspase-3 are 148-296 for Chain A, and 310-401 for Chain B.

In the Jmol Vizualization, you can select or restrict the specific chains by doing "select *A". There are chains from A through F, so you have to isolate the two you need. Also, if you look on the side, they give you a nice numbering map.

I'm not sure where you're getting those numbers from. They look vaguely familiar... perhaps they're from last year? :?

EDIT: I don't think they're last years'. For some reason they look familiar, but I can't determine from where.
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Re: Protein Modeling C

Postby njjonas » December 10th, 2011, 10:41 am

How do you find active sites in chain A and Chain B???

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Re: Protein Modeling C

Postby brobo » December 12th, 2011, 7:11 am

Question about something that came up at an invites:
If a protein is made up mostly of Alanine, Valine and Isoleucine, how would the R groups be arranged on the protein and where might this protein be found in a cell:
a. R groups on the inside of the protein's tertiary structure as the protein spans the plasma membrane
b. R groups on the outside of the protein's tertiary structure as the protein spans the plasma membrane
c. R groups on the outside of the protein's tertiary structure while the protein is in the cytoplasm
d. R group positioning is not affected by the local environment
The correct answer is B, but we put A since all those amino acids have hydrophopic sidechains. If they're hydrophobic, then why are the sidechains on the outside of the tetiary structure?
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Re: Protein Modeling C

Postby Phenylethylamine » December 12th, 2011, 7:44 pm

Question about something that came up at an invites:
If a protein is made up mostly of Alanine, Valine and Isoleucine, how would the R groups be arranged on the protein and where might this protein be found in a cell:
a. R groups on the inside of the protein's tertiary structure as the protein spans the plasma membrane
b. R groups on the outside of the protein's tertiary structure as the protein spans the plasma membrane
c. R groups on the outside of the protein's tertiary structure while the protein is in the cytoplasm
d. R group positioning is not affected by the local environment
The correct answer is B, but we put A since all those amino acids have hydrophopic sidechains. If they're hydrophobic, then why are the sidechains on the outside of the tetiary structure?
In the part of the protein spanning the membrane, it is more favorable for hydrophobic groups to be outside, because the phospholipid plasma membrane is, well, lipid – and therefore hydrophobic (nonpolar), so the hydrophobic sidechains want to be in contact with the membrane surroundings.
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Re: Protein Modeling C

Postby Allinea » December 18th, 2011, 10:33 am

I was at the Boyceville invite, and as we were impounding, I saw one model with a portion of DNA on it. I can't seem to find any sort of DNA in Jmol, unless I can't seem to turn it on right?

So my question is in two parts:
-How do you turn the DNA on in Jmol, if there is any around chains A and B and,
-Anyone have any good ideas for creative additions yet? I'm stumped besides coloring the helices and sheets differently.
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