Protein Modeling C

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » December 22nd, 2010, 11:46 am

(Also, you can give me any hints you'd like; I'm from a TINY homeschooling team in north Alabama that will not make it past the first level of competition!)
People keep saying things like this. I'm not particularly concerned with who I give hints to– even if I told you everything I could think of about the topic, I'm pretty sure I'd still understand it better than the person I explained it to. The same goes for others: if they explain something to me, they presumably still know it better than I do. Unless you have some really revolutionary idea that puts you way ahead of everyone else, there's not much to worry about in sharing information with the community, because chances are the original will turn out better than its derivatives anyway.

(Also, you're very welcome.)
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

mmanders
Member
Member
Posts: 2
Joined: November 8th, 2008, 4:19 pm

Re: Protein Modeling C

Postby mmanders » January 25th, 2011, 6:28 pm

I have not been able to figure out what the crosslinkers are for in the pre-build kit. Does Klf4 have any disulfide bonds?

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » January 26th, 2011, 9:00 am

I have not been able to figure out what the crosslinkers are for in the pre-build kit. Does Klf4 have any disulfide bonds?
No, Klf4 does not have any disulfide bonds (they would show up as green dotted lines between cysteines on the Klf4 sequence summary page in the PDB), but the crosslinkers don't have to represent a part of the protein structure; they can just be used to hold your model together and keep it from getting bent out of shape.
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

User avatar
EastStroudsburg13
Administrator
Administrator
Posts: 3045
Joined: January 17th, 2009, 7:32 am
Division: Grad
State: MD
Location: At work trying to be a real adult
Contact:

Re: Protein Modeling C

Postby EastStroudsburg13 » January 29th, 2011, 6:20 am

While marking my model, I noticed that I end up with 86 marks, including the end caps, when they are spaced apart 2 cm, but there are only 85 amino acids. Did I do something wrong marking it? Is one of the caps included as an amino acid and the other not? I don't want to mess up this model making marks I shouldn't.
East Stroudsburg South Class of 2012, Alumnus of JT Lambert, Drexel University Class of 2017

Helpful Links
Wiki
Wiki Pages that Need Work
FAQ and SciOly FAQ Wiki
Chat (See IRC Wiki for more info)
BBCode Wiki


So long, and thanks for all the Future Dictator titles!

Starapollo1
Member
Member
Posts: 244
Joined: January 16th, 2010, 1:55 pm
Division: Grad
State: IN

Re: Protein Modeling C

Postby Starapollo1 » January 29th, 2011, 7:17 am

Another question . . .

What exactly do you DO to model the proteins??? Do you stick tacks in the toobers for molecules? Are we representing the molecular structure? And how exactly can you build such a complex Klf4 protein from the image on the computer? Any tips??? (Sorry, I'm new to this event.)
www.soinc.org has some AMAZING resources. Here is the Protein Modeling link: http://www.soinc.org/protein_modeling_c
Once you follow that link, follow the •Event Supervisor Tips, Notes and Video! link. It is fairly user friendly and will help you understood what you are doing better (and what you'll graded on). Futhermore if you go to the prebuild's jmol: http://cbm.msoe.edu/includes/jmol/SOJmo ... Build.html you can then go to the quick reference sheet. The reference sheet is a little more confusing but it's still an option.
2009: Protein Modeling (4th) overall 7th
2010: Cell Bio (11), Write it Do it (10), overall 5th
2011: Disease (4), Microbe (10), Protein Modeling (5), Sounds of Music (2), overall 1st, nats 21
2012: Disease (4), Forestry (5), Microbe (-), Protein Modeling (6), Sounds of Music (7), TPS (7) overall 4th

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » January 30th, 2011, 4:27 pm

While marking my model, I noticed that I end up with 86 marks, including the end caps, when they are spaced apart 2 cm, but there are only 85 amino acids. Did I do something wrong marking it? Is one of the caps included as an amino acid and the other not? I don't want to mess up this model making marks I shouldn't.
The Mini-Toober may be a little longer than necessary, or you may have marked slightly closer than 2 cm together, just enough to add up to a total of 2 cm over the entire thing. It's pretty common, and it's not a problem unless you're way off (2 cm isn't "way off")– just ignore the last marking, or rub it off, or cover it with the end cap. You won't be penalized for having an extra marking. Just don't get confused and think that it's a residue that isn't there (I recommend numbering your markings with the residue numbers- not every one, but maybe every five- just so you can keep your bearings when folding and adding sidechains or other additions).
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

User avatar
EastStroudsburg13
Administrator
Administrator
Posts: 3045
Joined: January 17th, 2009, 7:32 am
Division: Grad
State: MD
Location: At work trying to be a real adult
Contact:

Re: Protein Modeling C

Postby EastStroudsburg13 » January 31st, 2011, 1:48 pm

Okay, I just wanted to make sure it wasn't too big of a deal. I'm pretty sure that, assuming that the residues are marked correctly and the Toober is the correct length, there will be 86 counting the ends since you have to count an extra one at the end if you just divide by 2. I'm not too concerned anymore, my model's turning out quite nicely. :)
East Stroudsburg South Class of 2012, Alumnus of JT Lambert, Drexel University Class of 2017

Helpful Links
Wiki
Wiki Pages that Need Work
FAQ and SciOly FAQ Wiki
Chat (See IRC Wiki for more info)
BBCode Wiki


So long, and thanks for all the Future Dictator titles!

GCXC
Member
Member
Posts: 44
Joined: April 19th, 2010, 6:16 pm
Division: C
State: TX
Location: C-W

Re: Protein Modeling C

Postby GCXC » February 5th, 2011, 8:54 am

has anyone found any good websites to use for the prebuild portion of this event besides the cbm website?
2012 State:
1st Robot Arm
2nd Protein Modeling
3rd Microbe Mission

User avatar
Phenylethylamine
Exalted Member
Exalted Member
Posts: 1075
Joined: January 8th, 2009, 4:47 pm
Division: Grad
State: MA
Location: Harvard University

Re: Protein Modeling C

Postby Phenylethylamine » February 5th, 2011, 11:23 am

has anyone found any good websites to use for the prebuild portion of this event besides the cbm website?
There's not that much information about it out there... I even found an article that said something about Klf4 being less well understood than the rest of the factors. There's a little bit more information on the Protein Modeling Wiki now, though.
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

jsg2007
Member
Member
Posts: 1
Joined: February 14th, 2011, 3:59 pm
Division: C
State: IL

Re: Protein Modeling C

Postby jsg2007 » February 14th, 2011, 4:05 pm

2 Questions:
1 - What is the exact section of the 2GT0.pdb protein to be made on-site
2 - How do you open the 2G20.pdb file on jmol
Replies are appreciated.


Return to “2011 Lab Events”

Who is online

Users browsing this forum: No registered users and 2 guests

cron