Protein Modeling C

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Re: Protein Modeling C

Post by butter side up »

XXGeneration wrote:How would I begin to study for the written portion of the test?
The websites that the Science Olympiad environment of CBM link to will give you good information specific to the protein. Some genetics information will be really helpful- transcription, translation, and terminology are very frequently on tests. Studying the general topic of which the protein functions as (for example, last year klf4 was related to the state of stem cells, so information about the different stages of stem cells, like toti- and pluripotent, and how stem cells were made artificially). This year learning about apoptosis, such as how it works, and what happens when it doesn't work correctly. Looking at previous tests will be helpful for the general information not specific to this year's protein.
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Re: Protein Modeling C

Post by XXGeneration »

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)?
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Re: Protein Modeling C

Post by Phenylethylamine »

XXGeneration wrote: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.
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Re: Protein Modeling C

Post by gigaboo »

I'm still not exactly sure what creative additions would be useful. Any help?
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Re: Protein Modeling C

Post by butter side up »

gigaboo wrote:I'm still not exactly sure what creative additions would be useful. Any help?
Creative addtions are anything besides the original protein that you add, that are helpful.
For example, last year we made the DNA the protein coiled around, and put it in the space where it was. Also, instead of using the provided amino acids, we made them out of the small glass beads and wire. (Plus they were pretty!) Adding in the things floating around (last year it was zinc ions- haven't checked to see what would be useful this year) that interact with the protein are also good additions, as long as you explain them on your notecard.
Marking relevant structures with pipe cleaners, ribbons, etc is also a good way to earn points.
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Re: Protein Modeling C

Post by XXGeneration »

Phenylethylamine wrote:
XXGeneration wrote: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

Post by GCXC »

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

Post by Starapollo1 »

GCXC wrote: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

Post by FullMetalMaple »

XXGeneration wrote: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...
GCXC wrote: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

Post by GCXC »

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