Protein Modeling C

[Dragonshark]

Is the pre-build the same protein for the state competition as it was for the regional competition? Are we still building caspase-3 for state? If not, where do I find the new protein?

The prebuild protein does not change as the competition level increases. However, at States, more points will be assigned to creative additions than at regionals.

[Lily Essence]

I haven't really been around the pmod thread (I'm a heavy helicopters lurker), but I finally came round to reading...

Whew, I just read a marathon through this whole thread, and I have to say, there was great information from many people, especially you, Phenylethylamine. I'd love to meet you someday!

I will do the best I can at Nationals with this arsenal of information from ya'll! Thanks for answering so many questions I had, that I really didn't know I had until they were answered! ;P

[TheWiseGirl]

Just to make sure I'm assuming correctly, we're modeling MHC II at nationals, right?

*Edit: Nevermind! I was wrong, it's MHC I we're modeling.

[grump]

Has anyone accessed the primary citation for the MHC pdb file yet?
The file links to the abstract (http://www.ncbi.nlm.nih.gov/pubmed/1525 ... t=Abstract)
Is is just not available for free public viewing yet?

[Phenylethylamine]

Has anyone accessed the primary citation for the MHC pdb file yet?
The file links to the abstract (http://www.ncbi.nlm.nih.gov/pubmed/1525 ... t=Abstract)
Is is just not available for free public viewing yet?

In this case, it's not an issue of "yet" – this article was published in 1992. This article was published in a journal that doesn't seem to release its articles for public viewing (at least, not in any reasonable timespan).

My only recommendation is that you ask at your high school if they have a subscription to ScienceDirect or any other journal access service – which is fairly unlikely, as few high schools do – or find a student or faculty member at your nearest university and ask them really nicely to download it for you (as most universities will have a subscription to ScienceDirect). I haven't read it yet (yay for AP exams + senioritis?), but I'll be getting it from the nearby university where I'm co-enrolled/working in a research lab.

[Steelfoam]

does anyone have the numbers for amino acids that are involved in hydrogen bonds between the dimers?

[Phenylethylamine]

does anyone have the numbers for amino acids that are involved in hydrogen bonds between the dimers?

If you know how hydrogen bonding works, you should be able to figure out where the hydrogen bonds are by looking at the protein in Jmol. Just display all the sidechains near the dimer interface, and look for nitrogens and oxygens near each other where at least one of them has a hydrogen on it (the hydrogens do not appear in the PDB file, but if you have an amino acid reference sheet handy, you should be able to figure out where hydrogens should be).

[TheWiseGirl]

What does the P mean in P12, P17, etc? Is it just a way of differing between different monomers?

And adding to my question, what's the difference between 2 protein chains and 2 monomers forming a dimeric structure?

[EastStroudsburg13]

The numbers refer to the mass of each monomer is kilodaltons (kDa). You are correct in that they're a way to differentiate the monomers.

[TheWiseGirl]

The numbers refer to the mass of each monomer is kilodaltons (kDa). You are correct in that they're a way to differentiate the monomers.

Thank you! Also, thanks for sharing pictures of your prebuild!
And now for another question, this one having to do with XIAP. Does anyone know what Arginine 233 does? I read something where Asp.148 of XIAP bonds to Arginine 233; does this just keep the structure of the protein?