Protein Modeling C

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akatsuki9
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Re: Protein Modeling C

Postby akatsuki9 » December 18th, 2011, 12:00 pm

There is no DNA in the Jmol.
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Re: Protein Modeling C

Postby Allinea » December 18th, 2011, 7:19 pm

There is no DNA in the Jmol.
Hnn... Ah well. There goes that hope for an addition :(
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Re: Protein Modeling C

Postby akatsuki9 » December 21st, 2011, 1:58 pm

Does anyone have ideas on how to do the active site for caspase-3?
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Re: Protein Modeling C

Postby kappakun » December 30th, 2011, 5:47 pm

After bending the toober excessively, I have found that our model has become wobbly. What do you guys do to keep the model stable?

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Re: Protein Modeling C

Postby Phenylethylamine » January 1st, 2012, 5:46 am

After bending the toober excessively, I have found that our model has become wobbly. What do you guys do to keep the model stable?
I use 22-gauge jewelry wire to make supports (in place of those connectors that come with the kit, because those cannot be adjusted in length). I just have it around, because I make jewelry, but it should be possible to find at Michael's or a similar craft store.

Basically, you can use it to connect any two points that you want to stay fixed at a particular distance. Putting in just a few of these supports will drastically increase the rigidity of your model. You can also use it for vertical supports to attach your model to a base, since the toober isn't very heavy – but I do recommend doubling up the wire in that case.
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Re: Protein Modeling C

Postby Faustina » January 3rd, 2012, 7:49 am

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?

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Re: Protein Modeling C

Postby EastStroudsburg13 » January 3rd, 2012, 8:08 am

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.
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Re: Protein Modeling C

Postby akatsuki9 » January 3rd, 2012, 5:19 pm

To who?
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Re: Protein Modeling C

Postby quizbowl » January 3rd, 2012, 5:21 pm

To who?
*To whom.

You can send a clarification to the national coordinator of Protein Modeling here -> http://soinc.org/node/289
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Re: Protein Modeling C

Postby Phenylethylamine » January 3rd, 2012, 5:31 pm

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?
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.
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