Protein Modeling C

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Protein Modeling C

Postby pikachu4919 » June 30th, 2018, 11:56 am

Protein Modeling C: Students will use computer visualization and online resources to construct physical models of the CRISPR Cas9 protein that is being engineered to edit plant and animal cell genomes, and answer a series of questions about the chemistry of protein folding and the interaction of structure and function for model proteins.

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Re: Protein Modeling C

Postby luanne » September 4th, 2018, 10:00 pm

Only first day after rules come out and I already have questions.. :roll:
so here they come:
1. In Jmol if I enter "restrict 1-85" I get around 4 distinct backbones. Is this correct?
2. How should I research and find which secondary structures are important to the function of the protein?
and lastly:
3. In jmol I would do the "select structures" and realize that one of the dna strands is also a beta sheet. So when I build my model, should I say that it is dna or a beta sheet?
(If you can't tell I am very lost)
Thanks :)
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Re: Protein Modeling C

Postby pikachu4919 » September 5th, 2018, 9:02 pm

luanne wrote:Only first day after rules come out and I already have questions.. :roll:
so here they come:
1. In Jmol if I enter "restrict 1-85" I get around 4 distinct backbones. Is this correct?
2. How should I research and find which secondary structures are important to the function of the protein?
and lastly:
3. In jmol I would do the "select structures" and realize that one of the dna strands is also a beta sheet. So when I build my model, should I say that it is dna or a beta sheet?
(If you can't tell I am very lost)
Thanks :)


1. When I opened it and played around with it, I saw four beta pleated strands and one long alpha helix.
2. The cbm msoe website will upload lots of resources for that part, however, the name of the paper accompanies the PDB file info on RCSB, with that title you could probably search it on the web. If it doesn't grant you access, see if you can log in through your school's library system to get to it.
3. "select structures" is a pretty general command. Most of the time, you would do "select" and then your more specific kind of structure like "helix," "sheet," "dna," "rna," etc. then you can use Boolean operators to select multiple kinds of structures at once. I'm not entirely sure what you did that made it appear that way since the two are biochemically very different. But no, if it does not have amino acid structures, then it cannot be a beta sheet.
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Re: Protein Modeling C

Postby Creationist127 » September 6th, 2018, 7:06 am

Do we need to model all four of the strands? If so, how? If not, which one do we need to model? :?:
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Re: Protein Modeling C

Postby nervoussenior1 » September 6th, 2018, 1:05 pm

pikachu4919 wrote:
luanne wrote:Only first day after rules come out and I already have questions.. :roll:
so here they come:
1. In Jmol if I enter "restrict 1-85" I get around 4 distinct backbones. Is this correct?
2. How should I research and find which secondary structures are important to the function of the protein?
and lastly:
3. In jmol I would do the "select structures" and realize that one of the dna strands is also a beta sheet. So when I build my model, should I say that it is dna or a beta sheet?
(If you can't tell I am very lost)
Thanks :)


1. When I opened it and played around with it, I saw four beta pleated strands and one long alpha helix.
2. The cbm msoe website will upload lots of resources for that part, however, the name of the paper accompanies the PDB file info on RCSB, with that title you could probably search it on the web. If it doesn't grant you access, see if you can log in through your school's library system to get to it.
3. "select structures" is a pretty general command. Most of the time, you would do "select" and then your more specific kind of structure like "helix," "sheet," "dna," "rna," etc. then you can use Boolean operators to select multiple kinds of structures at once. I'm not entirely sure what you did that made it appear that way since the two are biochemically very different. But no, if it does not have amino acid structures, then it cannot be a beta sheet.


Hm When i played around, i got 5 sheets. I think we have to restrict the chain to B (?). They still haven't updated the prebuild link that's on the event description.

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Re: Protein Modeling C

Postby luanne » September 6th, 2018, 3:58 pm

nervoussenior1 wrote:
Hm When i played around, i got 5 sheets. I think we have to restrict the chain to B (?). They still haven't updated the prebuild link that's on the event description.


in the rules it just said residue 1-85?
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Re: Protein Modeling C

Postby nervoussenior1 » September 6th, 2018, 6:46 pm

luanne wrote:
nervoussenior1 wrote:
Hm When i played around, i got 5 sheets. I think we have to restrict the chain to B (?). They still haven't updated the prebuild link that's on the event description.


in the rules it just said residue 1-85?


Like on the rcsb website it says that chain B is the protein and chain A C D are nucleic acids/hybrids. And the description says to model residues 1-85 of the PROTEIN, so I just assumed that we restrict it to B. I may be wrong because it's my first time doing protein modeling.

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Re: Protein Modeling C

Postby nervoussenior1 » September 6th, 2018, 6:47 pm

luanne wrote:
nervoussenior1 wrote:
Hm When i played around, i got 5 sheets. I think we have to restrict the chain to B (?). They still haven't updated the prebuild link that's on the event description.


in the rules it just said residue 1-85?


Like on the rcsb website it says that chain B is the protein and chain A C D are nucleic acids/hybrids. And the description says to model residues 1-85 of the PROTEIN, so I just assumed that we restrict it to B. I may be wrong because it's my first time doing protein modeling.

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Re: Protein Modeling C

Postby luanne » September 6th, 2018, 6:56 pm

hmm, I guess we are going to have to wait until msoe uploads their work.. and its my first time too, but I was pretty sure if it was just chain 'b' it would say "Residue 1-85 of chain B"
I could be totally wrong tho :)
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Re: Protein Modeling C

Postby luanne » September 6th, 2018, 6:58 pm

Also, rcsb hasn't updated their science Olympiad page? It is still on influenza from last year.
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Re: Protein Modeling C

Postby luanne » September 6th, 2018, 7:00 pm

Creationist127 wrote:Do we need to model all four of the strands? If so, how? If not, which one do we need to model? :?:

Right now, I'm assuming so. MSOE has great resources how to fold your pre build model and is a great start point :)
here:http://cbm.msoe.edu/scienceOlympiad/participant3.php
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Re: Protein Modeling C

Postby EastStroudsburg13 » September 7th, 2018, 4:57 am

nervoussenior1 wrote:
luanne wrote:
nervoussenior1 wrote:
Hm When i played around, i got 5 sheets. I think we have to restrict the chain to B (?). They still haven't updated the prebuild link that's on the event description.


in the rules it just said residue 1-85?


Like on the rcsb website it says that chain B is the protein and chain A C D are nucleic acids/hybrids. And the description says to model residues 1-85 of the PROTEIN, so I just assumed that we restrict it to B. I may be wrong because it's my first time doing protein modeling.

This would be correct; the required segment of protein should only be one chain.
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Re: Protein Modeling C

Postby nervoussenior1 » September 7th, 2018, 9:19 am

EastStroudsburg13 wrote:
nervoussenior1 wrote:
luanne wrote:
in the rules it just said residue 1-85?


Like on the rcsb website it says that chain B is the protein and chain A C D are nucleic acids/hybrids. And the description says to model residues 1-85 of the PROTEIN, so I just assumed that we restrict it to B. I may be wrong because it's my first time doing protein modeling.

This would be correct; the required segment of protein should only be one chain.


Except the problem is that when I restrict to chain B, the chain starts at residue 4 not 1..... so I’m sort of confused. I don’t know enough about JMOL to know why that’s happening :(

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Re: Protein Modeling C

Postby JonB » September 7th, 2018, 1:37 pm

nervoussenior1 wrote:
EastStroudsburg13 wrote:
nervoussenior1 wrote:
Like on the rcsb website it says that chain B is the protein and chain A C D are nucleic acids/hybrids. And the description says to model residues 1-85 of the PROTEIN, so I just assumed that we restrict it to B. I may be wrong because it's my first time doing protein modeling.

This would be correct; the required segment of protein should only be one chain.


Except the problem is that when I restrict to chain B, the chain starts at residue 4 not 1..... so I’m sort of confused. I don’t know enough about JMOL to know why that’s happening :(



The PDB file is a bit wonky. If you compare the beginning of FASTA sequences found on PDB versus Uniprot you find:

PDB:
>4UN3:B|PDBID|CHAIN|SEQUENCE
GAASMDKKYSIGLDIG..............

Uniprot:
>sp|Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease
MDKKYSIGLDIGT...............

Is the first residue that is showing up the "K" immediately before the "Y"? That is what is showing up even in PyMol. I am not convinced that the first three residues are included in the PDB file that can be downloaded.

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Re: Protein Modeling C

Postby luanne » September 7th, 2018, 3:50 pm

officially confused.
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