Protein Modeling C

MacintoshJosh
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Re: Protein Modeling C

Postby MacintoshJosh » November 29th, 2018, 12:13 pm

Just to clarify, 5vw1.pdb has 3 chains, not 2.
Last edited by MacintoshJosh on November 30th, 2018, 3:47 pm, edited 1 time in total.

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Re: Protein Modeling C

Postby ukhakimova3944 » November 29th, 2018, 8:11 pm

Hello!
Just to clarify, we are only building chain b? Looking at previous models the chain looks too small, so I am worried that we need to model the other chains. I read the previous posts, but being the anxious person that I am, I cannot help but ask.

Also, can the other chains be kept as functionally relevant parts if they are not part of the main build? I wanted to make them just in case and though I have not gotten to that, I may very well still model them and have the other members do so as practice.

Many thanks in advance.

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Re: Protein Modeling C

Postby juakk700 » November 30th, 2018, 2:46 pm

How do we figure out which terminal is which? I'm a bit confused.
Also, any general tips to start out?
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Re: Protein Modeling C

Postby MacintoshJosh » November 30th, 2018, 3:24 pm

ukhakimova3944 wrote:Hello!
Just to clarify, we are only building chain b? Looking at previous models the chain looks too small, so I am worried that we need to model the other chains. I read the previous posts, but being the anxious person that I am, I cannot help but ask.

Also, can the other chains be kept as functionally relevant parts if they are not part of the main build? I wanted to make them just in case and though I have not gotten to that, I may very well still model them and have the other members do so as practice.

Many thanks in advance.


Yes, you are correct, we are building only chain B of the protein complex shown on Jmol (5vw1.pdb file). http://www.rcsb.org/structure/5VW1
Here is the link to the protein complex from the Protein Data Bank if you haven't already checked it out.
(Chain B is the anti-CRISPR protein.)

Now for your other question,

It is definitely not required to build parts from other chains but the rules sheet does say that 'Participants will use materials of their own choosing to add functionally relevant features to their model.'

Functionally relevant features could include parts from different chains but it's really up to you if you want to add those parts and if you find they are 'functionally relevant' and highlight the significance of structure to function of the protein.

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Re: Protein Modeling C

Postby MacintoshJosh » November 30th, 2018, 3:47 pm

juakk700 wrote:How do we figure out which terminal is which? I'm a bit confused.
Also, any general tips to start out?

(Make sure you understand the event thoroughly, here's a good place to start: http://cbm.msoe.edu/scienceOlympiad/participantHome.php)

Research
I suggest first doing some research on proteins in general. Amino acids, levels of protein structure, sheets and helices, sidechains, hydrogen bonds, disulfide bonds, residues, peptide bonds, protein folding; these are all examples of some terms and concepts you should be familiar with before starting your model.

Once you understand everything about proteins, try researching on DNA. For example, genes, genomes, RNA, and specifically CRISPR and anti-CRISPR.

Jmol
Next, you need to be familiar with Jmol, which basically a program that allows you to view biological structures, in this case, the specified protein. http://cbm.msoe.edu/scienceOlympiad/designEnvironment/prebuild.html -- Link to Jmol and this year's protein. Practice the commands for Jmol with a reference sheet, located on the side of the Jmol model. Typing "restrict 1-85" then "restrict :B" will get you to the protein we are building this year (1-85 residues and B chain).

Building
CBM has some good videos on how to build your protein, I suggest checking them out.

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Re: Protein Modeling C

Postby SOS_pls » December 2nd, 2018, 12:44 pm

Are we allowed to bring in a double-sided notecard or a single sided notecard to accompany our prebuild model?

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Re: Protein Modeling C

Postby dnzsnr » December 2nd, 2018, 4:32 pm

Anyone know how to undo a command in the JSmol design environment? I've tried just typing "undo" or "undo <command>" but nothing seems to be working.

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Re: Protein Modeling C

Postby eagerlearner102 » December 3rd, 2018, 4:21 pm

Did any of you receive an orange strand for the protein modeling prebuild kit? The orange strand is longer than the blue strand. They said that it was because the blue strand wasn't the correct length. Did any of you get this?
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Re: Protein Modeling C

Postby KSSOISLIT » December 3rd, 2018, 7:03 pm

Are y'all bringing in 3 sheets of notes at your invitationals? We've been using only 1 sheet, but someone pointed out to me recently that the rules, similar to the Forensics rules this year, say "each participant" before mentioning the "one sheet" comment. Would this mean a team of 3 can bring 3 sheets? Thanks.
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Re: Protein Modeling C

Postby BanjoRodriguez » December 3rd, 2018, 7:05 pm

Hey all,

How much are the functional add ons weighted in the judging process? Also how many are recommended? The rules are quite ambiguous about it. :?:

I’ve been relatively successful with the event at the two invitationals I’ve been to, but I’m really trying to take my pre-build to the “next level” to remain competitive with some of the great teams in my region. Any suggestions? :D
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Re: Protein Modeling C

Postby CookiePie1 » December 3rd, 2018, 7:15 pm

KSSOISLIT wrote:Are y'all bringing in 3 sheets of notes at your invitationals? We've been using only 1 sheet, but someone pointed out to me recently that the rules, similar to the Forensics rules this year, say "each participant" before mentioning the "one sheet" comment. Would this mean a team of 3 can bring 3 sheets? Thanks.


Yes, that's correct. If you have a team of two, bring two sheets, etc.

BanjoRodriguez wrote:Hey all,

How much are the functional add ons weighted in the judging process? Also how many are recommended? The rules are quite ambiguous about it. :?:

I’ve been relatively successful with the event at the two invitationals I’ve been to, but I’m really trying to take my pre-build to the “next level” to remain competitive with some of the great teams in my region. Any suggestions? :D


As you go from regionals/invies to states and nats, there will be more and more weight placed on the added features. In general, you should add as many as you can that are functionally relavant to the protein. To further improve your model, you can spray paint your model to indicate the different secondary structures, and keep adding more add ons. You should also focus on the test to get as high a score as possible.
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Re: Protein Modeling C

Postby eagerlearner102 » December 4th, 2018, 4:55 pm

For those that had past experience, do any of you have suggestions on how to fold it? I watched the videos but I struggle with the 3D structure folding. It is so hard! :(
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Re: Protein Modeling C

Postby JoeyC » December 5th, 2018, 10:44 am

Practice. Keep on doing it til you can't function. Rinse repeat, and folding comes natural
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Re: Protein Modeling C

Postby tm-scioli » December 5th, 2018, 5:46 pm

Hello,
I am a bit confused as to add-ons. I have the main chain, end caps, and colored secondary structures, but I'm not sure what to add from here beyond putting in a hundred hydrogen bonds.
Thanks in advance!

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Re: Protein Modeling C

Postby CookiePie1 » December 5th, 2018, 6:05 pm

tm-scioli wrote:Hello,
I am a bit confused as to add-ons. I have the main chain, end caps, and colored secondary structures, but I'm not sure what to add from here beyond putting in a hundred hydrogen bonds.
Thanks in advance!


You should only add extra features that are functionally relevant to the protein. There's no use to adding so many hydrogen bonds because they aren't specific to the function of this particular protein.
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2019 Events: Thermodynamics, Protein Modeling, Mission Possible, Dynamic Planet

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anything you do.”
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