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rkoopma2 wrote:Is there a molecular story for capase-3?
all I can find is the one for XIAP

There's the PDB Molecule of the Month feature on caspases; that might be helpful. The CBM site does not have its own caspase-3 "molecular story", however.

Hi everybody,
Does anybody who's done Protein Modeling before remember for the on-site build, if there was a link available to a JMol commands reference sheet?

AlmightyBob wrote:Hi everybody,
Does anybody who's done Protein Modeling before remember for the on-site build, if there was a link available to a JMol commands reference sheet?

Yes, if I recall correctly, the Jmol quick reference sheet link is there in the on-site build environment just like it's there in the prebuild environment.

Phenylethylamine wrote:

Faustina wrote:For those of you experienced with Jmol:

I've read that Cys-285 is part of the active site for Caspase-3, the prebuild model, so I want to include its sidechain in the prebuild. However, when I try to select "285" in Jmol, it comes up with Ala, not Cys. Why don't the numbers match up? Has anyone else noticed this?

EASTstroudsburg13 wrote:It is possible that it is a typo, because I'm pretty confident it's a cysteine. Also, they could have mixed up the sulfur for a carbon. However, it is a good point to bring up, since it's definitely important to the protein's function. Perhaps we should submit a clarification on this.

Yes, it's absolutely supposed to be a cysteine, and yes, that cysteine is very important to the protein's function. The numbers do match up; the alanine is just in the spot where the cysteine is supposed to be.

Look at the sequence summary on the PDB: see that red A at 285? If you hover over the red A, it says "ALA 285 (mismatch to CYS in UniProtKB)". UniProtKB is the Protein Knowledgebase, which has the sequences of basically all the proteins being studied (and variants thereof).

The most likely reason that this PDB file has an alanine there instead of a cysteine is that the x-ray diffraction interpretation software didn't see enough electron density there, so it assigned the small bit of the sidechain that it did see as an alanine. This is a reasonably common occurrence in protein structure determination. If that explanation doesn't help, don't worry about it; the important part is that there is a cysteine at that spot in the protein, always, and the PDB knows that; this is just an error in this particular file.

Of course, that doesn't really tell us what to do about it, so yes, I think a clarification would be in order. Previous clarifications have basically said that the protein as it appears in Jmol is the final authority, but in this case, that doesn't make any sense: that cysteine really is vital to the protein's function.

On the 1i3o page on the Protein Data Bank is also says that there is a mutation C285A. I'm not exactly sure what this means, but it maybe it is saying that there is a mutation that changed the 285 Cysteine to an Alanine.

http://www.rcsb.org/pdb/explore/biology ... ureId=1I3O Polymeric Molecules --> Chain A,C --> Mutation.

I still don't understand the functionally relevant features. could these be the amino acid residues involved in hydrogen bonds?

Mithrandir wrote:On the 1i3o page on the Protein Data Bank is also says that there is a mutation C285A. I'm not exactly sure what this means, but it maybe it is saying that there is a mutation that changed the 285 Cysteine to an Alanine.

http://www.rcsb.org/pdb/explore/biology ... ureId=1I3O Polymeric Molecules --> Chain A,C --> Mutation.

Thanks, I didn't see that before. Looking back at the paper for this structure, under their methods, it does mention that they crystallized C285A mutant caspase-3 in complex with the XIAP BIR2 domain, so it was not an x-ray diffraction assignment error, as I guessed earlier.

They seem to have also mutated out a couple of cysteines in the XIAP chain... I don't know what the reason for this is; I couldn't find an explanation in the paper. My best guess is that these cysteines were bonding in unwanted ways when they tried to crystallize the wild-type protein, and they weren't relevant to the mechanism being studied, so they just mutated them out. It's a little frustrating for us, though, given that C285 is pretty important to the normal function of caspase-3.

rkoopma2 wrote:I still don't understand the functionally relevant features. could these be the amino acid residues involved in hydrogen bonds?

They could be (for example, last year we had a DNA transcription factor as our pre-build, and one creative addition was to show the sidechains that were hydrogen bonding with the DNA bases), but there will be many, many more residues involved in hydrogen bonding than just the relevant ones (for example, all secondary structures – e.g., helices and beta-sheets – are formed by hydrogen bonding between residues, but that doesn't mean you should particularly showcase every residue involved in a helix or sheet).

The best things to show are 1. the most important amino acid residues to the protein's function (for example, the residues found in the active site that particularly carry out the protein's action on its substrate) and 2. the features of the protein's environment that are relevant to its function (e.g., if the protein acts upon a particular cell structure, you could create a schematic model of that cell structure to show the protein acting upon it).

I read that the amino acid residue cysteine is very important in caspase-3, but how do I know if all of the cysteines in caspase-3 are important or if only just some of them are? Wikipedia says that cys285, his237, and gly 238 are important, but I cannot find a cys285 in caspase 3. is there a reason for this discrepancy?

rkoopma2 wrote:I read that the amino acid residue cysteine is very important in caspase-3, but how do I know if all of the cysteines in caspase-3 are important or if only just some of them are? Wikipedia says that cys285, his237, and gly 238 are important, but I cannot find a cys285 in caspase 3. is there a reason for this discrepancy?

nevermind, I should have read the posts above.
Does this mean that ala-285 is correct, and that it is just mutated, or that ala-285 should be cys-285
thanks!

rkoopma2 wrote:

rkoopma2 wrote:I read that the amino acid residue cysteine is very important in caspase-3, but how do I know if all of the cysteines in caspase-3 are important or if only just some of them are? Wikipedia says that cys285, his237, and gly 238 are important, but I cannot find a cys285 in caspase 3. is there a reason for this discrepancy?

nevermind, I should have read the posts above.
Does this mean that ala-285 is correct, and that it is just mutated, or that ala-285 should be cys-285
thanks!

Well, in caspase-3, position 285 is usually a cysteine. As you've probably gathered from this thread, that cysteine is relevant to the function of caspase-3 in a pretty major way. If you want to showcase that part of the function of caspase-3 as a creative addition on your model, then you should probably display CYS285. However, if you decided to, for example, display this particular mutation as a creative addition (which wouldn't be completely unreasonable – the researchers made that mutation for a reason, after all – but it might or might not be the best way to show the "molecular story" of caspase-3), then it would make sense to show ALA285 instead.

What you should show depends on what the goal of your model is.

Uh, did anyone compete in this event yet? On the exam (in regards to this year's topic), what questions did they generally ask? I know the mechanisms/signals of apoptosis will be on there, but I'm not sure about bone marrow transplants, as it says on the rules (kind of late, but thanks to anyone who answered my previous question).