Protein Modeling C

[XXGeneration]

Correct me if I'm wrong, but isn't the Chain A supposed to be 298 cm? It's 2 cm per amino acid and I read that it was 149 amino acids.

[Phenylethylamine]

We started modeling with the longest chain, a and ran out of tuber, even with the 286 cm length...has anyone else had this problem?

Correct me if I'm wrong, but isn't the Chain A supposed to be 298 cm? It's 2 cm per amino acid and I read that it was 149 amino acids.

Although the first residue of chain A is 148 and the last is 296, the chain is only 143 amino acids in length– as the prebuild kit page explains, the numbering is not consecutive:

Please Note!

The numbering in the PDB file 1i3o is not consecutive. In the field of caspase research, scientists number caspase proteins based on the numbering of caspase-1. Researchers can then compared the sequences between the members of the caspase family to look for insertions/deletions.

They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.

[XXGeneration]

Thank you for the clarification; the link will be very helpful in numbering the toober hehe :3

[kwijiborjt]

Is suspending/building something to display the protein all that important? I mean yes it helps transport an keep the protein in a specific shape, but do you think judges view it as contributing to your model?

Winning teams usually have taken some effort to display their protein. I can give some examples from last year's NY competition to illustrate what is useful:

One team built a large sideless cube with a poster on the back with beautiful elaborate drawings. While they clearly put a lot of effort in, i couldn't give them creative addition points for their drawings because they had little to nothing to do with the relationship between the structure and function of Klf4.

My high school team used to use a very un-elaborate ring stand (think chemistry) as structural support and would clamp the protein to hold it in place. The ringstand was mounted on a painted wooden board which could be used to display extra items for creative additions as well as the note card.

Many teams make some sort of frame out of balsa wood or another material so that they have something to hang their protein from.

It's useful to have something to keep your protein fixed so that it won't get bent out of shape in transit or from you or the judges handling it. It also adds to the presentation value. While you don't get points specifically for presentation value, an attractive (=/= elaborate) display can positively influence the judges in their somewhat subjective evaluation process.

[bocahighscienceolypm]

They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.

Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?

[Phenylethylamine]

They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.

Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?

How are you finding that they "do not exist"? When I look at the pdb file, they are there.

Try opening the PDB in Jmol (or going to the online prebuild environment, I don't know what you prefer to use) and, before typing anything else, type "restrict *b and 310-401". Chain B – amino acids 310 through 401 – should appear.

If this doesn't work, there are a couple possibilities I've thought of: if you're using standalone Jmol on your computer and have downloaded the PDB file, I suppose it is possible that your download was cut short and you're missing part of the file... in which case you could try re-downloading the file. If you're using the online environment or are using standalone Jmol but are certain that all your downloads were complete, my best guess is that you used a command that caused chain B to be excluded (e.g., "restrict *a") and then afterwards tried to look at chain B. Try "select all", then "backbone" (or any other viewing command, just to get everything visible again), and then "restrict *b and 310-401".

[bocahighscienceolypm]

They have a link to a PDF that shows how the numbering actually goes (this information should also be on the PDB structure summary page, but I'm currently getting an error when I try to look at this or any other structure summary in the PDB). If you're trying to number your Toober from 148 straight through to 296, you'll run out of Toober; make sure you follow the actual numbering of the file.

Amino acids (for chain B) 310-401 do not exist in the pdb file. Can anyone help?

How are you finding that they "do not exist"? When I look at the pdb file, they are there.

Try opening the PDB in Jmol (or going to the online prebuild environment, I don't know what you prefer to use) and, before typing anything else, type "restrict *b and 310-401". Chain B – amino acids 310 through 401 – should appear.

If this doesn't work, there are a couple possibilities I've thought of: if you're using standalone Jmol on your computer and have downloaded the PDB file, I suppose it is possible that your download was cut short and you're missing part of the file... in which case you could try re-downloading the file. If you're using the online environment or are using standalone Jmol but are certain that all your downloads were complete, my best guess is that you used a command that caused chain B to be excluded (e.g., "restrict *a") and then afterwards tried to look at chain B. Try "select all", then "backbone" (or any other viewing command, just to get everything visible again), and then "restrict *b and 310-401".

It was something odd with the commands we were using, thanks for the advice.

[akatsuki9]

Hey,

At my first invitational, they gave us pipe cleaners for the on-site model. Will they give us a minitoober(s) for district? The pipe cleaners aren't that great for a protein model because they don't keep their shape as well.
Also, are there any good textbooks out there to study from for this event?

[Lily Essence]

I know this thread is not the place to complain about an event, but I am deeply disappointed in the amount of on-site builds this year (yet again).

Last year, as the first year this event came out, the only times I ever got to model were for state (nervous as heck since it was my first onsite build... AT STATE), and nationals, despite also going to regionals and two invitationals. The kits for the onsite builds were purchasable from the website. I passed this off as an unforeseen complication since the event was new, and asked the proctors at nationals about it. On the sheet asking about my experience, I commented on how there just wasn't enough onsite building experience available, whether the problem be price or something else.

This year, the kits are being sold at cost, and sadly both of the invitationals that my team is going to isn't offering a true "on-site build". One offered pipecleaners and an extremely simple protien, the other is telling competitors that there will be no onsite build a head of time. Hopefully, my regionals will offer a proper onsite build, but honestly, this isn't the way to run such a planned event.

What are you guys' experience with the whole on-site build portion of the exam? Is it really necessary to have 3 people for just a onsite test?

[akatsuki9]

I know this thread is not the place to complain about an event, but I am deeply disappointed in the amount of on-site builds this year (yet again).

Last year, as the first year this event came out, the only times I ever got to model were for state (nervous as heck since it was my first onsite build... AT STATE), and nationals, despite also going to regionals and two invitationals. The kits for the onsite builds were purchasable from the website. I passed this off as an unforeseen complication since the event was new, and asked the proctors at nationals about it. On the sheet asking about my experience, I commented on how there just wasn't enough onsite building experience available, whether the problem be price or something else.

This year, the kits are being sold at cost, and sadly both of the invitationals that my team is going to isn't offering a true "on-site build". One offered pipecleaners and an extremely simple protien, the other is telling competitors that there will be no onsite build a head of time. Hopefully, my regionals will offer a proper onsite build, but honestly, this isn't the way to run such a planned event.

What are you guys' experience with the whole on-site build portion of the exam? Is it really necessary to have 3 people for just a onsite test?

See my above post.