Protein Modeling C

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Re: Protein Modeling C

Postby rfscoach » September 3rd, 2011, 6:07 am

Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?
It is not in the judging rubric, so, no.
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Re: Protein Modeling C

Postby butter side up » September 4th, 2011, 5:46 pm

Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?
It is not in the judging rubric, so, no.
No- we don't have it as a contributing part of our model, just to help keep it structurally sound. When we went to impound it, we would prop it up with skewers stuck in the base (which was decorated with things having to do with the protein) and then we could do things like make final adjustments to any deformations that may have happened en route, such as bending of the structure and the amino acids being pushed towards the wrong direction. With it supported, we could be sure that everything would remain as we wanted until the judges got to inspect it.
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Re: Protein Modeling C

Postby XXGeneration » September 6th, 2011, 6:07 pm

Hello all, as I am completely new to this event and everything seems so daunting, from the wiki to the test exchange to the threads, does anyone know any good websites or resources to introduce me to protein modeling?

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Re: Protein Modeling C

Postby Phenylethylamine » September 7th, 2011, 11:25 am

Hello all, as I am completely new to this event and everything seems so daunting, from the wiki to the test exchange to the threads, does anyone know any good websites or resources to introduce me to protein modeling?
The Center for Biomolecular Modeling at MSOE has a great site that's specific to SciO protein modeling: http://cbm.msoe.edu/stupro/so/index.html. That's a good place to start; it's got an overview of the event as well as a lot of more specific information.
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Re: Protein Modeling C

Postby XXGeneration » September 7th, 2011, 5:20 pm

How would I begin to study for the written portion of the test?

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Re: Protein Modeling C

Postby butter side up » September 9th, 2011, 11:23 am

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

Postby XXGeneration » September 13th, 2011, 6:58 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)?

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Re: Protein Modeling C

Postby Phenylethylamine » September 15th, 2011, 5:53 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.
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Re: Protein Modeling C

Postby gigaboo » September 16th, 2011, 10:24 am

I'm still not exactly sure what creative additions would be useful. Any help?

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Re: Protein Modeling C

Postby butter side up » September 16th, 2011, 12:12 pm

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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