Protein Modeling C

[amk578]

Hi Everyone!
I've discovered a dilemma. Ok, so the prebuild is 5keg.pdb, right? It's residues 31-145. That means there are 115 residues (including the first one, 145-31= 114, plus one is 115). That means, at the standard scale of 2cm per amino acid, I should need 230 cm. However, the kit is only 228 cm. What should be done?

It's 2 cm in between the residues, and what you are counting is a 2 cm gap after residue 145 which is unneeded.

[cbrant554]

Hi Everyone!
I've discovered a dilemma. Ok, so the prebuild is 5keg.pdb, right? It's residues 31-145. That means there are 115 residues (including the first one, 145-31= 114, plus one is 115). That means, at the standard scale of 2cm per amino acid, I should need 230 cm. However, the kit is only 228 cm. What should be done?

I was wondering this aswell, are we just supposed to leave off the first or last residue?

[naddruf]

Hi Everyone!
I've discovered a dilemma. Ok, so the prebuild is 5keg.pdb, right? It's residues 31-145. That means there are 115 residues (including the first one, 145-31= 114, plus one is 115). That means, at the standard scale of 2cm per amino acid, I should need 230 cm. However, the kit is only 228 cm. What should be done?

I was wondering this aswell, are we just supposed to leave off the first or last residue?

The kinks in the toober are the residues, so the first and last residue are the endpoints of the toober.

[meierfra]

Hi Everyone!
I've discovered a dilemma. Ok, so the prebuild is 5keg.pdb, right? It's residues 31-145. That means there are 115 residues (including the first one, 145-31= 114, plus one is 115). That means, at the standard scale of 2cm per amino acid, I should need 230 cm. However, the kit is only 228 cm. What should be done?

228 is correct. Read the MSOE page on building your model and they explain it. http://cbm.msoe.edu/scienceOlympiad/participant3.php

[Tailsfan101]

Hi Everyone!
I've discovered a dilemma. Ok, so the prebuild is 5keg.pdb, right? It's residues 31-145. That means there are 115 residues (including the first one, 145-31= 114, plus one is 115). That means, at the standard scale of 2cm per amino acid, I should need 230 cm. However, the kit is only 228 cm. What should be done?

Please watch this video from CBM.

When using a Mini-Toober or other similar tool as a backbone, the N- and C-termini are shortened to 1cm each. Therefore, with 115 residues, one can essentially not count one residue to allow for this.

[exla23]

Could anyone explain what is expected for the nationals specific addition to the prebuild? My partners and I were confused as to what is actually meant by a "schematic representation" as it says in the rules for the fusion protein model.

[MacintoshJosh]

How would one find the amount of hydrogen bonds in a protein structure on Jmol? I try 'hbonds on' but nothing happens.

[exla23]

How would one find the amount of hydrogen bonds in a protein structure on Jmol? I try 'hbonds on' but nothing happens.

Try using ‘calculate hbonds’ instead.

[Anomaly]

Piggybacking off of the question that was asked earlier, when building the model, how does the space taken up by the end caps also affect how the protein is built, if it does at all?

I know the video recommended that we label the amino acids on the toober, every two cm, but how would you label which amino acid number is which when there are also the end caps and the 1cm that are cut off by each terminus?

[jdoes179]

Since we don't have to put functionally relevant features for regionals, what should we put on the notecard?