Protein Modeling C

[FullMetalMaple]

And what is hetero?

What's it referring to?

Also, does the prebuild (klf4) have 2 zinc fingers or 3? There are 3 zinc atoms, but the last third of the protein has a shorter alpha helix and loop than the other 2 zinc fingers, making me think that it isn't a zinc finger.

Actually, I looked it up to make sure, and it does have three.

[The Eviscerator]

And what is hetero?

What's it referring to?

Also, does the prebuild (klf4) have 2 zinc fingers or 3? There are 3 zinc atoms, but the last third of the protein has a shorter alpha helix and loop than the other 2 zinc fingers, making me think that it isn't a zinc finger.

Actually, I looked it up to make sure, and it does have three.

As in what does hetero do if you type it into the command line? Or can you explain how to use it (I have no idea what it does or is supposed to do)?

Okay, thanks for clarifying the 3 zinc fingers thing.

*EDIT: Can we use more than 6 of the crosslink things on the prebuild or are we limited to just 6? Also, I'm having trouble discerning where klf4 bonds to the dna. Can someone help?

[TheWiseGirl]

*EDIT: Can we use more than 6 of the crosslink things on the prebuild or are we limited to just 6? Also, I'm having trouble discerning where klf4 bonds to the dna. Can someone help?

You can probably use more. In our model we didn't use any. As mentioned in earlier conversations I don't think they are actually used for anything significant unless you label it to be that way; otherwise it is just included to make your model more stable and to keep the shape. In our model it just got in the way, so now they are abandoned with no where else to go.

[The Eviscerator]

*EDIT: Can we use more than 6 of the crosslink things on the prebuild or are we limited to just 6? Also, I'm having trouble discerning where klf4 bonds to the dna. Can someone help?

You can probably use more. In our model we didn't use any. As mentioned in earlier conversations I don't think they are actually used for anything significant unless you label it to be that way; otherwise it is just included to make your model more stable and to keep the shape. In our model it just got in the way, so now they are abandoned with no where else to go.

I'm going to cut them in half and then use them to make a stand thing for my prebuild, which is currently sitting in a cardboard box on top of a piece of wood. >_>
I'm also using them to connect the protein model to the dna model, once I figure out where the protein bonds to the dna...

[TheWiseGirl]

*EDIT: Can we use more than 6 of the crosslink things on the prebuild or are we limited to just 6? Also, I'm having trouble discerning where klf4 bonds to the dna. Can someone help?

You can probably use more. In our model we didn't use any. As mentioned in earlier conversations I don't think they are actually used for anything significant unless you label it to be that way; otherwise it is just included to make your model more stable and to keep the shape. In our model it just got in the way, so now they are abandoned with no where else to go.

I'm going to cut them in half and then use them to make a stand thing for my prebuild, which is currently sitting in a cardboard box on top of a piece of wood. >_>
I'm also using them to connect the protein model to the dna model, once I figure out where the protein bonds to the dna...

Oh have fun. I'm glad my teammates and I got that over with. Just kidding, it wasn't all that bad, putting the protein and DNA together We just like to bicker a lot...

On another note, I vaguely remember someone mentioning that people done with the SO season could post pictures of their prebuild now? Where exactly can I find said pictures?

And on yet another note, how are you/ how would you suggest to study for nationals (Eviscerator and others)? I'm reading through a protein textbook right now, but I don't think I'll be getting through all of it...

[The Eviscerator]

On another note, I vaguely remember someone mentioning that people done with the SO season could post pictures of their prebuild now? Where exactly can I find said pictures?

And on yet another note, how are you/ how would you suggest to study for nationals (Eviscerator and others)? I'm reading through a protein textbook right now, but I don't think I'll be getting through all of it...

The pictures are here: http://gallery.scioly.org/categories.ph ... 36156fd726 So far there are only 2 sets of pictures.
I'm not really sure how to study for nationals though... Protein Modeling isn't an event in NC and we just had states last week, so I just began really working on it. I suggest knowing general protein basics (primary, secondary, tertiary, quaternary structure; amino acids; types of bonds; etc.) and then in depth knowledge on iPSC's and the transcription factors.
Somebody else that has experience can add to that short list.

[Phenylethylamine]

So how do you make disulfide bonds show up[...]?

Disulfide bonds are always between cysteines, so if you just display all the cysteines ("select cys and sidechain", "wireframe 200"), any disulfide bonds in the protein will be visible (the cysteines will appear to "merge" if they're disulfide bonded).

And what is hetero?

The term "hetero" refers to anything that isn't protein or DNA.

This includes ligands like the zinc ions in Klf4, other associated molecules (e.g., last year's influenza hemagglutinin was a glycoprotein, meaning that it had pieces of carbohydrate attached to the outside- those would also fall under "hetero"), and water (pretty much every protein crystal structure is in water).

If you display all heteroatoms, you'll end up with all the water molecules visible, which you rarely want (for the purpose of this event, never). Instead, you can type "select hetero and not hoh" to select only the non-water heteroatoms. In the case of Klf4, the zinc ions are the only non-water heteroatoms, so this is one way to select the zinc ions.

I'm going to cut them in half and then use them to make a stand thing for my prebuild

That's what I did. It worked wonderfully for me, although you can ask kwijiborjt if it was helpful on the judging end of things.

I suggest knowing general protein basics (primary, secondary, tertiary, quaternary structure; amino acids; types of bonds; etc.) and then in depth knowledge on iPSC's and the transcription factors.
Somebody else that has experience can add to that short list.

Know details about the protein for the national on-site build (in this case, c-Myc). If the state tests are any indication, there will be many in-depth questions about it. There will also likely be detailed questions about the pre-build protein, Klf4.

Know your bond strength order; know how hydrogen bonding works; know about retroviral, lentiviral, and adenoviral vectors as mechanisms for gene integration (how they work, pros and cons); know all about Yamanaka's methodology, since the event seems to be based specifically on his work with iPSCs.

[The Eviscerator]

How do you figure out where klf4 binds to DNA? I tried googling it, but didn't get much, and whenever I show the hydrogen bonds on jmol, none between the DNA and klf4 are shown.

*EDIT:On the websites I've looked at, they say that klf4 binds to the DNA sequence CACCC, but in jmol this nucleotide sequence is not shown. Does anybody know why?
Also, when amino acids interact with DNA, do they usually interact with the nitrogenous base or the sugar-phosphate backbone?

[FullMetalMaple]

How do you figure out where klf4 binds to DNA? I tried googling it, but didn't get much, and whenever I show the hydrogen bonds on jmol, none between the DNA and klf4 are shown.

I just know the zinc fingers are involved - they bind to the major groove of the DNA.

*EDIT:On the websites I've looked at, they say that klf4 binds to the DNA sequence CACCC, but in jmol this nucleotide sequence is not shown. Does anybody know why?
Also, when amino acids interact with DNA, do they usually interact with the nitrogenous base or the sugar-phosphate backbone?

That's correct. I modeled this sequence in my pre-build. I don't know why it's not in jmol, but I do know that amino acids interact with the backbone.

Know details about the protein for the national on-site build (in this case, c-Myc). If the state tests are any indication, there will be many in-depth questions about it. There will also likely be detailed questions about the pre-build protein, Klf4.

Know your bond strength order; know how hydrogen bonding works; know about retroviral, lentiviral, and adenoviral vectors as mechanisms for gene integration (how they work, pros and cons); know all about Yamanaka's methodology, since the event seems to be based specifically on his work with iPSCs.

To add to this already awesome and helpful list (no, really), I suggest definitely knowing your amino acid properties (polar, non-polar, etc). I had a list of them in my notes for state; I found it very helpful for application-like questions (specifically about the role of certain sidechains in the on-site protein).

I wish I could compete in this event for nats. /sigh

[The Eviscerator]

How do you figure out where klf4 binds to DNA? I tried googling it, but didn't get much, and whenever I show the hydrogen bonds on jmol, none between the DNA and klf4 are shown.

I just know the zinc fingers are involved - they bind to the major groove of the DNA.

What's the major groove?

*EDIT:About how many places did people find that there were hydrogen bonds between the DNA and klf4? I've found about 5 so far. If you have more than 5, what residues are they?