Protein Modeling C

[picats3141]

A lot of you are saying to restrict the model to chain A only, but could you possibly get extra credit for also including the monomer that this one pairs up with the portion we are modeling to form the dimer? I found a rubric from back in 2012, which stated that points were awarded if you represented both parts (because the protein they modeled that year, caspase-3, also functions as a dimer.)

Also, if I wanted to attach DNA to my model, where would it be relative to the protein? Just on the outside of the protein? (in the context of the whole 2fok protein, not just anywhere on the outside of the modeled domain)

In addition, what is the sequence of DNA that 2fok cleaves (just as EcoRI cleaves GAATCA, etc.)? The PubMed abstract says "FokI is a member an unusual class of restriction enzymes that recognize a specific DNA sequence and cleave nonspecifically a short distance away from that sequence." The only problem is, it doesn't say what the "specific DNA sequence" is anywhere that I could find.

[Gemma W]

A lot of you are saying to restrict the model to chain A only, but could you possibly get extra credit for also including the monomer that this one pairs up with the portion we are modeling to form the dimer? I found a rubric from back in 2012, which stated that points were awarded if you represented both parts (because the protein they modeled that year, caspase-3, also functions as a dimer.)

Also, if I wanted to attach DNA to my model, where would it be relative to the protein? Just on the outside of the protein? (in the context of the whole 2fok protein, not just anywhere on the outside of the modeled domain)

In addition, what is the sequence of DNA that 2fok cleaves (just as EcoRI cleaves GAATCA, etc.)? The PubMed abstract says "FokI is a member an unusual class of restriction enzymes that recognize a specific DNA sequence and cleave nonspecifically a short distance away from that sequence." The only problem is, it doesn't say what the "specific DNA sequence" is anywhere that I could find.

I believe that modeling the dimer could count as a creative addition, assuming you show their interactions and explain clearly in your index card. There may also be other ways of signifying this dimer interface besides folding a new monomer.
You should place DNA in the area of the protein that interacts with the DNA, which you can do a bit of research on. However, the tertiary structure of the 2fok PDB file is based on the conformation of FokI when not bound to DNA, so you would have to be careful about attaching it to DNA, as its conformation does change in reality.
The FokI recognition and cleavage site is mentioned specifically on the CBM website, so it shouldn't take much digging to find.

[annaphase]

Hey! Does anyone know how the time is split at the NY state competition? At our regional, we had a morning impound and then the 50 min window to both complete the test and fold the additional model; however, at the state competition the written test seems to happen concurrently with our impound on the friday afternoon, and then we have to self schedule the modeling part. I was wondering how they split the 50 minutes across these two separate sections

[tylarthefarmer]

Hi guys,
If I wanted to model the DNA-binding domain of the FokI protein for use as a creative addition, what amino acid sequence would I isolate in Jmol in order to model said domain?

[annaphase]

Hi guys,
If I wanted to model the DNA-binding domain of the FokI protein for use as a creative addition, what amino acid sequence would I isolate in Jmol in order to model said domain?

Ahaha I'll give you a hint: it's out there. Read journal articles, read databases, and you will find everything you need to know. Trust me, a few weeks ago I was banging my head on the wall because, as far as I could tell, no one gave a **** about the protein and there was no information on it but when you do the research and when you find it all out it's really, really awesome. Use the protein modeling website from the event sponsor, and they have all the information about the different domains, but it's no fun if you don't do the research yourself It's not hard to find, I promise. A carefully worded google search and some patience will do the trick.

[Gemma W]

Hey! Does anyone know how the time is split at the NY state competition? At our regional, we had a morning impound and then the 50 min window to both complete the test and fold the additional model; however, at the state competition the written test seems to happen concurrently with our impound on the friday afternoon, and then we have to self schedule the modeling part. I was wondering how they split the 50 minutes across these two separate sections

Yeah, I was wondering that myself. It seems like an odd way to run the event, since test questions are often significantly related to the onsite build. It also says walk-in, so it's unclear that people will even be starting and finishing at the same time. And the build time slots are the same length as usual. However they do it, it's certainly going to mess up our M.O....3 people working on the test for shortened time and then three people working on the build is not quite the same as we've prepared for.

[teaforterry]

When modeling sidechains, does it matter how specific they look? For example, is using a pushpin for a specific amino acid and then saying what amino acid it represents be the same as using the foam amino acids that you can buy?

[fozendog]

When modeling sidechains, does it matter how specific they look? For example, is using a pushpin for a specific amino acid and then saying what amino acid it represents be the same as using the foam amino acids that you can buy?

I honestly don't think it matters, but you need to make sure that they are positioned correctly, and that may be difficult to do with a pushpin.

[Gemma W]

When modeling sidechains, does it matter how specific they look? For example, is using a pushpin for a specific amino acid and then saying what amino acid it represents be the same as using the foam amino acids that you can buy?

I honestly don't think it matters, but you need to make sure that they are positioned correctly, and that may be difficult to do with a pushpin.

You get points for modeling features "creatively", so ideally sidechains would be shown with the features that contribute to their functions - even something as simple as color-coding for charge, hydrophobicity, and acidity, but also more specific things like important individual atoms and general shape. There's no need to buy them, though, you can just as easily make your own out of pipecleaners or wire and beads.

[jkatz16]

Does anyone know what the restriction numbers are for the onsite build for states, the TAL effectors? Thanks