Protein Modeling C

XXGeneration
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Re: Protein Modeling C

Postby XXGeneration » September 16th, 2011, 9:15 pm

I just noticed something while playing around with the jmol thing on this page: http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html

At the spot 285, wikipedia and the PDB diagram (http://www.rcsb.org/pdb/101/motm_disscu ... do?id=1pau) say that it should be a cysteine. However, on the pre-build model, it states that it is alanine. Could someone please help me confirm that it is a cysteine?

Edit: Also could I please check with someone, does it skip from the 247th amino acid (asparagine) to the 254th amino acid (glycine)?
I wish I had enough time to actually check now, but let me just say this: the file they assigned goes. Most of the files on the PDB are from X-ray crystallography; sometimes the crystal structure isn't perfect (parts may be missing), causing a larger sidechain to be registered as an alanine or glycine, or several residues to just... disappear. Unless it's a major error in the file that would cause the protein to lose function if it happened in real life (in this case, is the cysteine supposed to form a disulfide bond?), base your model on the file, not on information you find elsewhere. Chances are, any such discrepancies won't be in anything sufficiently vital to functionality that you'd be modeling it anyway.

Alternatively, sometimes researchers use a particular mutant of a given protein- that is, the protein with one or more sidechains mutated to different residues, added, or deleted- because it is easier to crystallize than the wild-type protein or more relevant for drug discovery/other research applications. This may not be clear from the heading of the PDB file, but that information would probably be in the original publication (which is cited on the PDB page). In that case, the mutated residues might well be relevant to the function, but you should still follow what's in the given file- if there are other crystal structures available, they chose that mutant for a reason (if no other crystal structures are available, it's probably because they can't crystallize the wild-type).

In a couple months I'll have time to start getting back into the details of this event, but in general, you should base your model on the sequence that actually appears in the file specified in the rules.
This cysteine is basically one of two active sites on the protein; I would assume that yes, it would cause the protein to lose function (off the top of my head I'm unsure but I think the cysteine cleaves another protein..).

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Re: Protein Modeling C

Postby GCXC » September 17th, 2011, 9:57 am

Well, I am not sure if anyone else has ordered/received their prebuild kits from CBM, but did anybody (if you have ordered/received) get an email from CBM telling them that the lengths of the toobers are wrong and that the chains and lengths that have been posted are incorrect?
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Re: Protein Modeling C

Postby Starapollo1 » September 19th, 2011, 7:40 pm

Well, I am not sure if anyone else has ordered/received their prebuild kits from CBM, but did anybody (if you have ordered/received) get an email from CBM telling them that the lengths of the toobers are wrong and that the chains and lengths that have been posted are incorrect?
I did not... keep me posted (via the forum) if you can... I definitely want to know if the numbers are wrong
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Re: Protein Modeling C

Postby FullMetalMaple » September 21st, 2011, 6:41 pm

This cysteine is basically one of two active sites on the protein; I would assume that yes, it would cause the protein to lose function (off the top of my head I'm unsure but I think the cysteine cleaves another protein..).
Cys-285 is one of the active sites, yes. From what I've read so far (which I suppose isn't incredibly in-depth, but I haven't had much time to research further yet), I understand that this cysteine cleaves a peptide bond and also works with Gly-238 to stabilize things through hydrogen bonding.

I did look up the possibility of not having this residue, and I believe I found that yes, there can be mutant forms in which the cysteine is alanine or serine instead. I'll look into that in greater detail if the file lacks Cys-285, I suppose...
Well, I am not sure if anyone else has ordered/received their prebuild kits from CBM, but did anybody (if you have ordered/received) get an email from CBM telling them that the lengths of the toobers are wrong and that the chains and lengths that have been posted are incorrect?
I actually still have last year's kit and planned to use that, but it'd be nice to know how this winds up.

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Re: Protein Modeling C

Postby GCXC » September 27th, 2011, 5:00 pm

2012 State:
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Re: Protein Modeling C

Postby XXGeneration » September 28th, 2011, 4:08 pm

Thank you! I didn't know they changed the proteins from regional to states to nationals :3

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Re: Protein Modeling C

Postby EastStroudsburg13 » October 3rd, 2011, 4:04 pm

I decided recently to look at the jmol for this year, and I can't view it on my computer. Whenever I try to view it, it comes up with a [url=res://ieframe.dll/acr_error.htm#msoe.edu,http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html]"Website restore error"[/url]. Anyone else experiencing this or is it just me? :?
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Re: Protein Modeling C

Postby Phenylethylamine » October 3rd, 2011, 5:30 pm

I decided recently to look at the jmol for this year, and I can't view it on my computer. Whenever I try to view it, it comes up with a [url=res://ieframe.dll/acr_error.htm#msoe.edu,http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html]"Website restore error"[/url]. Anyone else experiencing this or is it just me? :?
Nope, when I go to the online prebuild environment, it works just fine.

It took me a second to figure out what you meant by "the jmol for this year"... I use Jmol on my computer, so I didn't immediately realize that you meant the online prebuild environment.
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Re: Protein Modeling C

Postby amerikestrel » October 3rd, 2011, 5:42 pm

What are the advantages of using the standalone Jmol application instead of the web applet?
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Re: Protein Modeling C

Postby TheGenius » October 3rd, 2011, 7:19 pm

I decided recently to look at the jmol for this year, and I can't view it on my computer. Whenever I try to view it, it comes up with a [url=res://ieframe.dll/acr_error.htm#msoe.edu,http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html]"Website restore error"[/url]. Anyone else experiencing this or is it just me? :?
You need Java if you don't have it installed. If you're using IE, try compatibility view.
What are the advantages of using the standalone Jmol application instead of the web applet?
Undo and a history of commands are the biggest ones I can think of right now.
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