Thursday, June 7, 2012

DNA Binding Proteins

I've been tweaking my Ultimaker a lot lately so I haven't done many protein prints. I did do a couple recently and I think they came out pretty good:

Once again I've been making structures with DNA in them because it looks so cool.

Here's Topoisomerase:

Notice that DNA strand running up the middle. This model is definately a lot better in person.
Topoisomerase is an enzyme that untwists DNA so it doesn't get broken by being too twisted. Have you ever tried to untangle a rope? Ever wished that the rope would just pass through itself to remove knots, and unwind itself to remove twist? Well DNA is a magical rope that does all those things, so whenever our cells need to divide they can easily untangle that mess and sort it out. This particular model is from pdb structure 1A31 (thing). It's a human type I topoisomerase, meaning this molecule is responsible for relaxing twisting stresses on the DNA. What it does is it cuts one strand of the DNA double helix, allows it to twist around the uncut strand, then reanneals the cut strand to make sure the DNA stays intact.
  As you can imagine it's pretty crucial that topoisomerase reanneals the strands exactly how they were. For type II topoisomerases the task is even harder; type IIs cut BOTH STRANDS of the DNA double helix and allow another double helix to pass through the cut. These are your typical knot-dissolvers, and for them its even more crucial to make sure the double helix goes back to the way it was. A single cut in the double helix can be fixed by DNA ligase. A double cut is much harder, because the two ends can diffuse away and information will be lost.

And here's Catabolite Gene Activator Protein (CAP):

CAP is a transcription factor from E. Coli (1CGP) (thing) that functions to turn on the lac operon and other alternative nutrition pathways when glucose levels are low. What a transcription factor does is activate or inhibit RNA polymerase from transcribing certain genes into mRNA. Almost everything that a cell does is controlled by what genes are being expressed, aka, which regions of the genome are being transcribed. A single transcription factor molecule (or a dimer, as in the case of CAP), can result in the production of a single strand of mRNA. That mRNA in turn can produce many proteins, and each one of those proteins can have a huge number of individual interactions with other proteins or small molecules. So the action of each transcription factor has a huge outcome for the rest of the cell.
   CAP binds two molecules of cAMP, one in each monomer, and the binding increases CAP's affinity to DNA. When CAP binds DNA it bends the double helix almost 90 degrees, and turns the adjacent gene on by activating RNA transcription. In that sense it is a bit rare because most bacterial genes are on by default, and require the binding of a transcription factor to turn them off. The bend in DNA is thought to be required for activating transcription, possibly by opening the DNA up to RNA polymerase binding.

Oh and another thing I've been working on is making a protein model kit, similar to chemistry model kits. I'm still working on the right way for the pieces to interact with each other but here's what I have so far:


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  3. Hi, this area fascinated me, but I have no tools to build with. I have visualised working models using differently charged polimers at the appropriate sites on the proteins suspending them in solutions applying a charge and watching them go. Please let me know how far you have got.