For me when I look in Jmol, those alpha helices are located at 221-225 (A); 270-274 (A); and 314-318 (B). So for me twisting them wasn't as big a problem since they weren't two residue alpha helices - but I'm not sure how those helices show up in another program.In the model for caspase-3, would we have to show the helices in chain A for residues 224-226 and 271-273, and in chain B for 315-317?
Protein Modeling C
- Agggron
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Re: Protein Modeling C
Hmm...out of the three possible 3/10 helices you stated earlier:
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Re: Protein Modeling C
On the sequence charts at:
http://www.pdb.org/pdb/explore/remediat ... ureId=1I3O
It shows the 3/10 helices as light pink and always 3 amino acids long... that's what I went with, but now with Jmol I'm not so sure anymore
http://www.pdb.org/pdb/explore/remediat ... ureId=1I3O
It shows the 3/10 helices as light pink and always 3 amino acids long... that's what I went with, but now with Jmol I'm not so sure anymore
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Re: Protein Modeling C
Don't you mean Chain E? (since that one is a domain of XIAP, which inhibits caspase-3). Based on its function, including XIAP is pretty much guaranteed to get you creative points, though it doesn't need to be perfectly accurate in structure (just show the overall shape of the protein, a long fishing-pole-esque line above the active site of caspase-3, connected to the globular BIR2 domain which is located away from caspase-3). I used toobers to display XIAP on my model, mainly because it was the easiest method available and also because XIAP was the regionals onsite, though you don't need to use toobers to display XIAP.Dragonshark wrote:zatanna wrote:Would it be a good idea to include chain c as well in the model as one of the additions? I'm not really sure why we only had to do chains a and b, besides that's what they told us to do.
hey, new here.
So, is chain e or chain c is the inhibitor of caspase-3? i think it would help puting that info on the index card.
- TheWiseGirl
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Re: Protein Modeling C
Chain C is part of the second monomer of caspase-3. It is identical to chain A.sci-man wrote:Don't you mean Chain E? (since that one is a domain of XIAP, which inhibits caspase-3). Based on its function, including XIAP is pretty much guaranteed to get you creative points, though it doesn't need to be perfectly accurate in structure (just show the overall shape of the protein, a long fishing-pole-esque line above the active site of caspase-3, connected to the globular BIR2 domain which is located away from caspase-3). I used toobers to display XIAP on my model, mainly because it was the easiest method available and also because XIAP was the regionals onsite, though you don't need to use toobers to display XIAP.Dragonshark wrote:zatanna wrote:Would it be a good idea to include chain c as well in the model as one of the additions? I'm not really sure why we only had to do chains a and b, besides that's what they told us to do.
hey, new here.
So, is chain e or chain c is the inhibitor of caspase-3? i think it would help puting that info on the index card.
I guess Chain E and F are what make up XIAP? Not sure if one of those are different...
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Re: Protein Modeling C
In jmol aren't the 3/10 helices a purple color? If you go to the RCSB website, and use jmol on there and chose the dropdown option for secondary structure it should show beta sheets in yellow, alpha helices in pink, and 3/10 helices in purple...theyankee wrote:On the sequence charts at:
http://www.pdb.org/pdb/explore/remediat ... ureId=1I3O
It shows the 3/10 helices as light pink and always 3 amino acids long... that's what I went with, but now with Jmol I'm not so sure anymore
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Re: Protein Modeling C
Visually and structurally, whats the difference between 3-10 helices and normal helices.
Do we make 3-10 more "looser" that normal helices? Do we also tag them as "3-10 helix" and "normal helix"
When i made my model, i didnt make a distinction between norm and 3-10 because i didnt see any difference in jmol
Do we make 3-10 more "looser" that normal helices? Do we also tag them as "3-10 helix" and "normal helix"
When i made my model, i didnt make a distinction between norm and 3-10 because i didnt see any difference in jmol
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Re: Protein Modeling C
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.
Thanks.
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Re: Protein Modeling C
So, I have finished the backbone of my pre-build and I was wandering if anyone could give me their insight on how to find out which amino acids are important to the structure and function of the two chains we built of capsase-3?
- Agggron
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Re: Protein Modeling C
Yeah, Chain C and Chain D are identical in structure to Chain A and Chain B, respectively. Additionally, while Chain E represents XIAP with respect to Chains A and B, Chain F also represents a second XIAP that inhibits Chains C and D. From what the regional judges told me, either showing Chain E (XIAP) and/or showing Chains C and D (the second dimer) will get you creative addition points. Your model will be really big, but still.TheWiseGirl wrote:Chain C is part of the second monomer of caspase-3. It is identical to chain A.
I guess Chain E and F are what make up XIAP? Not sure if one of those are different...
(Oh, and sorry for massive quote hashing. ) EDIT: Lol, looks like I can only embed 3 quotes inside one another anyways.
I don't think you have to tag them as two separate types of helices, as long as the difference in structures themselves is notable. I didn't mark them differently and at regionals they didn't harp on it, but who knows at higher levels. Like you said, there isn't a difference in color in the online Jmol environment, though the structure there is notably different. And yeah, earlier in this thread it was stated that 3/10 helices have 3 residues per turn whereas normal helices have ~3.6 helices per turn - so 3/10 ones will be "looser."sci-man wrote:Visually and structurally, whats the difference between 3-10 helices and normal helices.
Do we make 3-10 more "looser" that normal helices? Do we also tag them as "3-10 helix" and "normal helix"
When i made my model, i didnt make a distinction between norm and 3-10 because i didnt see any difference in jmol
Good luck with the event!aomdahl wrote: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.
I'll say that in my opinion, everything that was on the test was located in the resources that MSOE provided to us. I mean, definitely what our team could have studied more was the role of caspase in general in apoptosis, since I feel we were so focused on caspase-3 specifically and its mechanism that we forgot to look at the big picture. Anyways, I guess I would also study the chemical mechanism that caspase-3's active site (or XIAP/PARP/MHC's active sites) undergo, since that falls under the category of basic biochemistry. If anybody has any other ideas please add!
The first thing I did after finishing the backbone was look at Wikipedia for information on the active site of caspase-3; there's definitely a lot you can do just from wiki alone. (I recommend clicking some of the links for citations at the bottom of the Wiki article for more important amino acids than just those in the active site! ) Good luck!jmb04 wrote:So, I have finished the backbone of my pre-build and I was wandering if anyone could give me their insight on how to find out which amino acids are important to the structure and function of the two chains we built of capsase-3?
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Re: Protein Modeling C
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...
Okay, I have a huge stack of questions here. Hopefully somebody will be able to answer some of them!
1) What's a beta bridge? How is it different from a beta sheet?
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.
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?
Sequence map link: http://www.pdb.org/pdb/explore/remediat ... 500&page=2
And @Agggron: Thanks!
Okay, I have a huge stack of questions here. Hopefully somebody will be able to answer some of them!
1) What's a beta bridge? How is it different from a beta sheet?
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.
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?
Sequence map link: http://www.pdb.org/pdb/explore/remediat ... 500&page=2
And @Agggron: Thanks!
I'm quirky like a quark.
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