Protein Modeling C

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luanne
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Re: Protein Modeling C

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

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 :)
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Re: Protein Modeling C

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


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


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


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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Re: Protein Modeling C

Postby nervoussenior1 » September 8th, 2018, 12:22 am

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.
Hmm... then would that mean that residue 4 is actually residue 1? I guess we will just have to wait till MSOE updates their website.

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Re: Protein Modeling C

Postby platypusomelette » September 8th, 2018, 1:28 pm

I've been doing "display 1-85 and not dna" but I still end up with one DNA strand. Has anyone been able to isolate it yet?
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Re: Protein Modeling C

Postby freed2003 » September 9th, 2018, 12:53 am

Does anyone know if we still have to study general protein knowledge for the test? On the rules it just states the test will have questions specific to the onsite protein, CRISPR, and protein folding.
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Re: Protein Modeling C

Postby nicholasmaurer » September 9th, 2018, 7:53 am

Does anyone know if we still have to study general protein knowledge for the test? On the rules it just states the test will have questions specific to the onsite protein, CRISPR, and protein folding.
3.III.b.i does not limit itself to CRISPR Cas9
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Re: Protein Modeling C

Postby freed2003 » September 9th, 2018, 11:13 am

Does anyone know if we still have to study general protein knowledge for the test? On the rules it just states the test will have questions specific to the onsite protein, CRISPR, and protein folding.
3.III.b.i does not limit itself to CRISPR Cas9
But it does limit itself to protein folding(specifically the process that drive it) where past test contained more general protein questions(such as "what amino acid contains sulfur?")
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