The Eviscerator wrote:Just to clarify: other residue sidechains (say for example tyrosine, a non-charged hydrophillic amino acid) besides arginine interact with dna, right?
I see one tyrosine that could be interacting with the DNA backbone based on its position, and possibly a couple serines (one by the backbone, another by one of the bases), but apart from those, I'm only seeing positively charged sidechains (i.e., arginine, lysine, and histidine*) involved with the DNA.
*Histidine is not always positively charged, and most charts show it as uncharged polar. However, there are a few cases when it becomes positively charged, and when it's involved in hydrogen bonds is one of them.
The Eviscerator wrote:I looked at 1nkp (c-myc the nationals on-site build) and the rcsb site says there are 8 chains, but in the jmol on the rcsb site, there were only 4. Can someone explain?
I can see two different ways you could have counted only four chains in that file: either you're not counting the DNA (which makes up four of the eight named chains in 1NKP), or you're not counting the duplicates (there's two copies of each chain in 1NKP). If you use the command "color chain", you should see eight different colors indicating the eight different chains.
butter side up wrote:My coach has proctered several protein modeling competitions and says that as a rule, judges actually prefer the notecard to be typed whenever possible. Our notecard has explinations about the function of the protein and the important structures (hydrophobic cores, zincs, alpha helices and beta sheets, etc.) typed on the back and small samples of all our materials with handwritten labels. We also usually tape two notecards together so we don't have to redo the sample part every time we redo the explanation part (which is often.)
I also typically type my notecards, including the key (for which I also use small samples of my materials, partly because it's the easiest way to identify what's what and partly because it just looks cool), and leave spaces to glue the bits of materials afterward.
I usually do my notecard at the last minute before competition, and not just because of procrastination: I don't want to redo it multiple times, because it's a fairly effort-intensive process (especially gluing all those little pieces of pipe cleaner onto the card >.<), so I want to make sure the model is finished and contains everything it's going to contain before I try to make the card.
Edited for errors.