Protein Modeling C

[Allinea]

I am confused about how you determine which ends the blue cap and red cap go on. Can somebody explain this to me?

The way I figure it in Jmol:
color group

After that, hover over one end to figure out the amino acid number and the cap of the same color on that end, other cap on the other end. Sometimes the chain ends before both red and blue are present, and you just have to go on whatever color is there (red or blue)... unless I've been doing it wrong all season.

[bloopy]

I don't think there are any disulfide bonds in the pre-build. If there were, it would be a very important addition, though.

No, there are no disulfide bonds in the pre-build. Here's a good way to check, in general:

restrict *a or *b // Only look at the relevant chains
color white
select cys and sidechain // Select all the cysteine sidechains
wireframe 200 // Make them visible
color red // Make them really visible

Now look for any two cysteines where the ends are nearly touching, with nothing else in between them (the main thing likely to be between two close cysteines is a zinc ion; you can use "select zn" and then "spacefill 400" to check if there's a zinc in there). That is most likely a disulfide bond.
The PDB used to show disulfide bonds with green dotted lines on its sequence summary pages, but it doesn't seem to anymore, for whatever reason. Maybe they decided it looked too cluttered. It was useful, but I haven't found any way of turning that back on.

As for using disulfide bonds as creative additions, in general (not that it's really relevant this year): yes, it's good to show disulfide bonds, because they're important to maintaining the protein's structure. But unless you know how each disulfide bond's contribution to the protein's structure is important to its function, simply showing the disulfide bonds does not demonstrate "the relationship between structure and function" in the protein, which is the point of the creative additions.

Oh alright, thank you so much! I thought there were disulfide bonds in the structure since I read somewhere that there was... but I went back and reread my sources and I've realized what a stupid mistake I made since it was MHC that had the disulfide bonds, not Caspase 3.

In that case, if anyone is willing to offer some information, are there any important bonds in Caspase 3? I've got a lot of "within the cell as a whole" addons (such as the other proteins involved in the immune system) but nothing specific to the structure within Caspase 3.

[Phenylethylamine]

I am confused about how you determine which ends the blue cap and red cap go on. Can somebody explain this to me?

The blue cap goes on the amino terminus: the low-numbered end. The red cap goes on the carboxy terminus: the high-numbered end.

Here's an easy mnemonic to remember this: In alphabetical order, you go from blue to red, so the blue one goes at the beginning (low number), and the red one goes at the end (high number). This also works for remembering which end is amino and which is carboxy; amino comes before carboxy alphabetically, so the amino terminus is the end with the lower number and the carboxy terminus is the end with the higher number.

To find them in Jmol, you can just look at the little info box on the side of the online competition environment (or the sheet that came with the Toobers, or the CBM site, or any of the various other places that mention this) and use the numbers it says (e.g., this year's prebuild says 148-296 for chain A, and 310-401 for chain B, so you'd use 148 and 296 as the ends for A and 310 and 401 as the ends for B).

Then use the commands:
select *a and 148
color blue
select *a and 296
color red
select *b and 310
color blue
select *b and 401
color red

That will show you where the ends are in the 3D structure, and will also make them the right colors.

The way I figure it in Jmol:
color group

After that, hover over one end to figure out the amino acid number and the cap of the same color on that end, other cap on the other end. Sometimes the chain ends before both red and blue are present, and you just have to go on whatever color is there (red or blue)... unless I've been doing it wrong all season.

That's a perfectly fine way of doing it, too, but this way doesn't involve the guesswork of making sure you've found the end and that you're interpreting the colors correctly (especially since sometimes neither red nor blue is present, particularly when you're looking at a fragment of a protein rather than a whole one). "color group" could still be the easiest way if you didn't know what the numbers of the ends of the chains were.

I have done some heavy research and it says that there should be two zinc ions on Chain E and F?
But Phenylethylamine said there should be one?

There are two zinc ions if you count chain E and chain F together, because there is one zinc ion in each. If you don't believe me, you can try this in Jmol:

select zn (you should get the message "2 atoms selected")
spacefill 400
color red (to make them more visible)
You should then see one bright red zinc ion in chain E, and one bright red zinc ion in chain F.

Oh alright, thank you so much! I thought there were disulfide bonds in the structure since I read somewhere that there was... but I went back and reread my sources and I've realized what a stupid mistake I made since it was MHC that had the disulfide bonds, not Caspase 3.

In that case, if anyone is willing to offer some information, are there any important bonds in Caspase 3? I've got a lot of "within the cell as a whole" addons (such as the other proteins involved in the immune system) but nothing specific to the structure within Caspase 3.

Before you get into looking at specific bonds, I recommend going for important sidechains – in particular, the active site machinery of the protein. There have been some posts about it before in this thread, but you can also look at the Wikipedia article on caspase-3, which specifically mentions the most important active site residues.

[springer]

How could you show this as a creative addition?

most contacts to caspase-3 originate from the N-terminal extension

[Phenylethylamine]

How could you show this as a creative addition?

most contacts to caspase-3 originate from the N-terminal extension

I assume this is in reference to contacts between caspase-3 and the "N-terminal extension" of XIAP. To show this in creative additions, you would have to find out exactly which residues in the N-terminal extension of XIAP make contacts with which residues of caspase-3.

The best source for this information would probably be the primary citation for the XIAP/caspase-3 structure.

[gsheni]

Thanks for the help so far everyone
I was wondering,
http://www.pdb.org/pdb/explore/biologyA ... ureId=1I3O
In the Protein Details section, it shows a list of GO IDs for Chains A and C.
Are those ID corresponding to amino acids, which then is corresponding to a definition?

[Phenylethylamine]

Thanks for the help so far everyone
I was wondering,
http://www.pdb.org/pdb/explore/biologyA ... ureId=1I3O
In the Protein Details section, it shows a list of GO IDs for Chains A and C.
Are those ID corresponding to amino acids, which then is corresponding to a definition?

Not quite. Those IDs correspond to entries in the Gene Ontology database, which is basically a glossary of gene/protein terms; they're each a term that is relevant to this protein structure.

[gsheni]

Thanks for the help so far everyone
I was wondering,
http://www.pdb.org/pdb/explore/biologyA ... ureId=1I3O
In the Protein Details section, it shows a list of GO IDs for Chains A and C.
Are those ID corresponding to amino acids, which then is corresponding to a definition?

Not quite. Those IDs correspond to entries in the Gene Ontology database, which is basically a glossary of gene/protein terms; they're each a term that is relevant to this protein structure.

So they don specifically tell the function of each amino acid, they just tell functions of the whole chain A and C.
I was wondering where nucleophile came on the regional test and it seems that it came from that page.
You think its worth memorizing those things or having on the note sheet?

[Rackis]

Is the Wikipedia article accurate for the active site? Because on the PDB it says that the residue at 185 is Ala. I've also seen other sources that say the active site Cysteine is Cys163 and the PDB says there's a Gly at 163. Is anyone able to shine some light on this?

[FullMetalMaple]

Is the Wikipedia article accurate for the active site? Because on the PDB it says that the residue at 185 is Ala. I've also seen other sources that say the active site Cysteine is Cys163 and the PDB says there's a Gly at 163. Is anyone able to shine some light on this?

The active site residue is Cys285. The alanine is there for crystallization purposes for research; it's really a cysteine. The reason it's numbered 285 instead of 163 is because 285 comes from caspase-1 numbering, I believe. It's the same residue, though.