Protein Modeling C

User avatar
rfscoach
Coach
Coach
Posts: 604
Joined: July 7th, 2008, 4:58 pm
Division: B
State: GA
Has thanked: 4 times
Been thanked: 9 times

Re: Protein Modeling C

Post by rfscoach »

starpug wrote: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.
I am the Lorax. I speak for the trees. I speak for the trees, for the trees have no tongues.
User avatar
butter side up
Member
Member
Posts: 136
Joined: January 6th, 2011, 9:52 am
Division: Grad
State: PA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by butter side up »

rfscoach wrote:
starpug wrote: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.
I am the one called "TARDIS Hat Girl," and am known as such by all.
2013: Anatomy, Experimental Design, Genetics, Forestry, Disease Detectives
XXGeneration
Member
Member
Posts: 96
Joined: February 23rd, 2011, 4:39 pm
Division: C
State: NJ
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by XXGeneration »

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?
User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by Phenylethylamine »

XXGeneration wrote: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.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
XXGeneration
Member
Member
Posts: 96
Joined: February 23rd, 2011, 4:39 pm
Division: C
State: NJ
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by XXGeneration »

How would I begin to study for the written portion of the test?
User avatar
butter side up
Member
Member
Posts: 136
Joined: January 6th, 2011, 9:52 am
Division: Grad
State: PA
Has thanked: 0
Been thanked: 0

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.
I am the one called "TARDIS Hat Girl," and am known as such by all.
2013: Anatomy, Experimental Design, Genetics, Forestry, Disease Detectives
XXGeneration
Member
Member
Posts: 96
Joined: February 23rd, 2011, 4:39 pm
Division: C
State: NJ
Has thanked: 0
Been thanked: 0

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)?
User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Has thanked: 0
Been thanked: 0

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.
Protein Modeling Event Supervisor 2015
MA State Science Olympiad Tournament
MIT Invitational Tournament
--
Ward Melville High School Science Olympiad 2010-2012
Paul J Gelinas JHS Science Olympiad 2007-2009
gigaboo
Member
Member
Posts: 64
Joined: February 23rd, 2011, 9:46 pm
Division: C
State: UT
Has thanked: 0
Been thanked: 0

Re: Protein Modeling C

Post by gigaboo »

I'm still not exactly sure what creative additions would be useful. Any help?
User avatar
butter side up
Member
Member
Posts: 136
Joined: January 6th, 2011, 9:52 am
Division: Grad
State: PA
Has thanked: 0
Been thanked: 0

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.
I am the one called "TARDIS Hat Girl," and am known as such by all.
2013: Anatomy, Experimental Design, Genetics, Forestry, Disease Detectives
Locked

Return to “2012 Lab Events”

Who is online

Users browsing this forum: No registered users and 2 guests