Protein Modeling C

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EastStroudsburg13
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Re: Protein Modeling C

Post by EastStroudsburg13 » October 30th, 2014, 11:08 am

That's probably the better way to represent it, however I'm not sure how many supervisors out there will actually realize this. There may be some who just look at it, see that you're omitting an amino acid, and take off points regardless.

In terms of the Toober model may be better to think of the space between marks as the peptide bond connecting the two amino acids. Even though it's not as correct as the visualization mentioned above, it will at least result in the right length for the Toober (since you wouldn't be representing the peptide bonds connecting 420-421 and 560-561). Just realize there's more to the protein than sidechains and peptide bonds, haha.

Of course, if you use your own materials, you can make it whatever length you want! ;)
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Re: Protein Modeling C

Post by JonB » October 30th, 2014, 2:39 pm

EastStroudsburg13 wrote:
Of course, if you use your own materials, you can make it whatever length you want! ;)

Could you clarify this statement? I did not think it mattered what material you used- each AA must be 2cm?

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Re: Protein Modeling C

Post by EastStroudsburg13 » October 30th, 2014, 7:57 pm

Yes, this is true. I only meant that if you use your own material, you can change the length slightly, as long as each amino acid is represented by 2 cm. So if you want to make it 280 cm, you'd be free to. So you're not allowed any length, but you've got a little more freedom.
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Re: Protein Modeling C

Post by JonB » October 31st, 2014, 4:31 am

EastStroudsburg13 wrote:Yes, this is true. I only meant that if you use your own material, you can change the length slightly, as long as each amino acid is represented by 2 cm. So if you want to make it 280 cm, you'd be free to. So you're not allowed any length, but you've got a little more freedom.

Got it, thank you!

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Re: Protein Modeling C

Post by picats3141 » November 1st, 2014, 10:53 am

Hey, I'm new to this forum.

So I've gotten pretty decent at using Jmol/the command line to edit the appearance of the molecule. What settings do you guys think are optimal for modeling this protein? And which peptides are important/ should be modeled in more detail? Thanks in advance.

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Re: Protein Modeling C

Post by Dhruvster » November 2nd, 2014, 6:46 pm

I've been using cartoon off and backbone set to 0.9 so far and its been pretty useful so far as it makes jmol look pretty much like the model we're making. I actually had a similar question to you, I imagine just doing amino acids that are pertinent to the tertiary structure or are on the active site. But I was wondering how are you guys representing the different side chains going off the amino acids?

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Re: Protein Modeling C

Post by mrericsully » November 5th, 2014, 6:31 am

I understand the basics of modelling and sidechains, but I am having trouble finding information about what side chains are important. Where should I be looking? Also, if anyone is looking to 3D print a model for comparison purposes, I have made so 3D printer files of just the backbone structure and would be willing to share them after I print them and verify that they do print well.

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Re: Protein Modeling C

Post by actionpotential » November 10th, 2014, 2:21 pm

Yeah that's a good question. Does anyone have suggestions for finding out which amino acids/sidechains are important to the protein's structure? I have googled all about endonuclease and specifically 2fok but cannot seem to locate specific amino acids that were important.

Thanks

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Re: Protein Modeling C

Post by 18liuj_stoga » November 10th, 2014, 6:39 pm

The minitoober has space for 139 Amino Acids (AAs). Thus, the 140 AAs cant fit on. This is because only the alpha carbons of structures are counted(the inner carbon). On the side, however, the Amine group will have to be cut off and the Carboxyl group on the other side will have to be cut off.

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Re: Protein Modeling C

Post by hscmom » November 13th, 2014, 5:08 pm

actionpotential wrote:Yeah that's a good question. Does anyone have suggestions for finding out which amino acids/sidechains are important to the protein's structure? I have googled all about endonuclease and specifically 2fok but cannot seem to locate specific amino acids that were important.

Thanks
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