Protein Modeling C

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TheWiseGirl
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Re: Protein Modeling C

Postby TheWiseGirl » February 14th, 2012, 10:36 pm

I'm trying to model the hydrophobic regions of my protein; I used tissue paper last year, but it took forever and was extremely difficult to put on (at least in my opinion, but then again, I'm a paranoid perfectionist...). Is there a type of paint that I can use on my toober, that doesn't smear very much? I understand that it's difficult to find a paint that won't smear on the porous material (if you rub it while working with the toober after the paint has dried), but I just want one that does the job.
My friend suggested a thick oil-based paint, one used for model cars, etc.
Could you use tape? You could always paint over the tape to make it smooth or change the color, since tape is probably a friendlier surface than toober.[/quote]

Several people have suggested this to me, but the thing about tape is that when the hydrophobic region is an amino acid that is a turn, the tape doesn't want to stick on the toober completely (it's kind of hard to explain; it won't cover the surface smoothly, if that makes sense, although I'm pretty sure I'm not making sense... :?) I guess a better way to put it, is it's a little too rigid for my taste (But thank you for your feedback! :) )
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Re: Protein Modeling C

Postby Starapollo1 » February 15th, 2012, 11:02 am

I'm trying to model the hydrophobic regions of my protein; I used tissue paper last year, but it took forever and was extremely difficult to put on (at least in my opinion, but then again, I'm a paranoid perfectionist...). Is there a type of paint that I can use on my toober, that doesn't smear very much? I understand that it's difficult to find a paint that won't smear on the porous material (if you rub it while working with the toober after the paint has dried), but I just want one that does the job.
My friend suggested a thick oil-based paint, one used for model cars, etc.
Could you use tape? You could always paint over the tape to make it smooth or change the color, since tape is probably a friendlier surface than toober.
Several people have suggested this to me, but the thing about tape is that when the hydrophobic region is an amino acid that is a turn, the tape doesn't want to stick on the toober completely (it's kind of hard to explain; it won't cover the surface smoothly, if that makes sense, although I'm pretty sure I'm not making sense... :?) I guess a better way to put it, is it's a little too rigid for my taste (But thank you for your feedback! :) )[/quote]

Totally get what your saying. Last year I tried painting my protein... compelte fail. I then used tape... more of a fail. In the end I used pipe cleaners and tied them around. You can also use twisty-ties, or even yarn/string.

Hope this helps!
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

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Re: Protein Modeling C

Postby Phenylethylamine » February 15th, 2012, 3:41 pm

I'm trying to model the hydrophobic regions of my protein; I used tissue paper last year, but it took forever and was extremely difficult to put on (at least in my opinion, but then again, I'm a paranoid perfectionist...). Is there a type of paint that I can use on my toober, that doesn't smear very much? I understand that it's difficult to find a paint that won't smear on the porous material (if you rub it while working with the toober after the paint has dried), but I just want one that does the job.
My friend suggested a thick oil-based paint, one used for model cars, etc.
Acrylic paint. Use a thin layer, and it will dry very quickly. It will not smear, although it could rub off somewhat with heavy handling – but in that case, you just retouch it before competition.
Would it be a good idea to include chain c as well in the model as one of the additions? I'm not really sure why we only had to do chains a and b, besides that's what they told us to do.
The reason we were told to only do chains A and B is that together, they represent one "asymmetrical unit" of caspase-3 – meaning that while chains A + B PLUS chains C + D is the way caspase-3 is found in the body (as a heterotetramer), A and C are identical and B and D are identical, so you can get a good idea of the functional shape of the protein by just looking at one heterodimer.

Like I said, the "biological unit" of caspase-3 – the way it's found in the body – does include all four chains A through D, so that could be one reason to show the other two chains as a creative addition (yes, the result would be huge, like Dragonshark suggested – even just the required part is already gigantic this year – but it could be useful).

Chains E and F are also identical to each other, and both represent XIAP. You could represent one, both, or neither as a creative addition; I mean, in order to totally inhibit the caspase-3 tetramer, you'd need two molecules of XIAP, but you can show how it binds on your model with only one, should you so desire.
Totally get what your saying. Last year I tried painting my protein... compelte fail. I then used tape... more of a fail. In the end I used pipe cleaners and tied them around. You can also use twisty-ties, or even yarn/string.
I used masking tape in my 2010 hemagglutinin prebuild (to show the fusion peptide, if anyone remembers that), and after a couple layers, it actually looked relatively neat. It was not easy, however. I've never actually painted my prebuild, but I've gotten acrylics on my Toober in the process of painting other things, and they seem to stick.

I use Sharpie to mark my protein fairly regularly, and it definitely rubs off – both over time and by scratching off with a nail/the edge of a piece of heavy paper/a blunt scissor. I tend to think of this as a feature rather than a bug, though: it lets me change things fairly easily between competitions if I change my mind about what to display.
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Re: Protein Modeling C

Postby TheWiseGirl » February 15th, 2012, 4:37 pm

I'm trying to model the hydrophobic regions of my protein; I used tissue paper last year, but it took forever and was extremely difficult to put on (at least in my opinion, but then again, I'm a paranoid perfectionist...). Is there a type of paint that I can use on my toober, that doesn't smear very much? I understand that it's difficult to find a paint that won't smear on the porous material (if you rub it while working with the toober after the paint has dried), but I just want one that does the job.
My friend suggested a thick oil-based paint, one used for model cars, etc.
Acrylic paint. Use a thin layer, and it will dry very quickly. It will not smear, although it could rub off somewhat with heavy handling – but in that case, you just retouch it before competition.
Would it be a good idea to include chain c as well in the model as one of the additions? I'm not really sure why we only had to do chains a and b, besides that's what they told us to do.
The reason we were told to only do chains A and B is that together, they represent one "asymmetrical unit" of caspase-3 – meaning that while chains A + B PLUS chains C + D is the way caspase-3 is found in the body (as a heterotetramer), A and C are identical and B and D are identical, so you can get a good idea of the functional shape of the protein by just looking at one heterodimer.

Like I said, the "biological unit" of caspase-3 – the way it's found in the body – does include all four chains A through D, so that could be one reason to show the other two chains as a creative addition (yes, the result would be huge, like Dragonshark suggested – even just the required part is already gigantic this year – but it could be useful).

Chains E and F are also identical to each other, and both represent XIAP. You could represent one, both, or neither as a creative addition; I mean, in order to totally inhibit the caspase-3 tetramer, you'd need two molecules of XIAP, but you can show how it binds on your model with only one, should you so desire.
Totally get what your saying. Last year I tried painting my protein... compelte fail. I then used tape... more of a fail. In the end I used pipe cleaners and tied them around. You can also use twisty-ties, or even yarn/string.
I used masking tape in my 2010 hemagglutinin prebuild (to show the fusion peptide, if anyone remembers that), and after a couple layers, it actually looked relatively neat. It was not easy, however. I've never actually painted my prebuild, but I've gotten acrylics on my Toober in the process of painting other things, and they seem to stick.

I use Sharpie to mark my protein fairly regularly, and it definitely rubs off – both over time and by scratching off with a nail/the edge of a piece of heavy paper/a blunt scissor. I tend to think of this as a feature rather than a bug, though: it lets me change things fairly easily between competitions if I change my mind about what to display.
Thank You!!!!!! :)
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Re: Protein Modeling C

Postby drummerdude13903 » February 16th, 2012, 1:50 pm

So we received an evaluation of our protein after our regionals event (pre-build didn't count, it was graded for our benefit only). The grader pointed out several errors we made regarding the appropriate length of our alpha helices. The lengths he told we should have do not correspond with the Jmol Pre-Build Environment, but rather seem to be lined up with the DSSP version of the 1i3o protein structure. The pre-build environment seems to be based off of the Author Sec. Struc. Secondary Structure version of the protein shown on the RCSB PBD, yet we were given comments that suggested our alpha helices should line up instead with the DSSP version. Has anyone else encountered this problem? What version are we supposed to use for competition?

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Re: Protein Modeling C

Postby Phenylethylamine » February 16th, 2012, 4:02 pm

So we received an evaluation of our protein after our regionals event (pre-build didn't count, it was graded for our benefit only). The grader pointed out several errors we made regarding the appropriate length of our alpha helices. The lengths he told we should have do not correspond with the Jmol Pre-Build Environment, but rather seem to be lined up with the DSSP version of the 1i3o protein structure. The pre-build environment seems to be based off of the Author Sec. Struc. Secondary Structure version of the protein shown on the RCSB PBD, yet we were given comments that suggested our alpha helices should line up instead with the DSSP version. Has anyone else encountered this problem? What version are we supposed to use for competition?
A National clarification has suggested that everything should be modeled as it appears in the Jmol file, but the DSSP secondary structure assignments are actually more accurate – so while you'll probably be fine at most competitions using what appears in Jmol, it's not entirely surprising that an event supervisor who has familiarity with protein structure independent of this event would prefer to grade based on DSSP.
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Re: Protein Modeling C

Postby Agggron » February 19th, 2012, 8:55 am

I've been a lurker on this thread for several months now, but I just wanted to post here to thank everybody for their questions and insightful information! They helped me win regionals against some tough Silicon Valley schools...and it was really helpful to find active sites, know how XIAP affects caspase-3, etc. So thanks again! :)

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Re: Protein Modeling C

Postby zatanna » February 19th, 2012, 8:01 pm

I also want to post a thank you. This board helped get 2nd place at regionals, and defeat 3 teams from Thomas Jefferson High School for Science and Technology (who practice every day), with only about a month of studying. I'll be going for the gold at states. :D
2012 Events
-Gravity Vehicle
-Protein Modeling
-Towers
-Thermodynamics

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Re: Protein Modeling C

Postby pabalan » February 20th, 2012, 2:30 pm

hi, so i'm kind of new to scioly.org (as well as science olympiad in general), and i don't really know how to efficiently use the informational forums... all I know is that this is a forum having to deal with something that i need help with, so I figured I'd post my question in here! I apologize for general newness to how everything works here, but here goes my question: will judges count you off if your model has lines marking up your tubers every two centimeters? if they do, i'd like to know so before i do anything i regret with a sharpie, but if they don't, they would make building a lot more convenient. thank you very much for your help! :)

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Re: Protein Modeling C

Postby FullMetalMaple » February 20th, 2012, 3:01 pm

hi, so i'm kind of new to scioly.org (as well as science olympiad in general), and i don't really know how to efficiently use the informational forums... all I know is that this is a forum having to deal with something that i need help with, so I figured I'd post my question in here! I apologize for general newness to how everything works here, but here goes my question: will judges count you off if your model has lines marking up your tubers every two centimeters? if they do, i'd like to know so before i do anything i regret with a sharpie, but if they don't, they would make building a lot more convenient. thank you very much for your help! :)
Welcome to the site! (:

Judges won't count off if you mark up your Toober. Marking the amino acids is encouraged, as far as I know. It helped our grader at my invitational, I think.

If nothing else, I've been able to rub off Sharpie on my model.


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