The concept of irreducible complexity/video workshop

Figure 4 - ribozyme activity

An animated ribozyme. The video needs to illustrate motion in the structure of the ribozyme during substrate binding/unbinding and during catalysis. The video will show movement of a substrate into and out of the active site of the ribozyme.

A decision has to be made about the level of structural detail in the molecules. Maybe there should be a preliminary video that illustrates both a detailed molecular structure of a ribozyme and a more diagrammatic structural model. During the "ribozyme activity" video it might be useful to have a "zoom in" part that shows more detail during the actual chemical reaction.

substrate: a choice needs to be made for the exact substrate to use for the initial ribozyme "R". The choice should make a useful point about a type of reaction that would be useful in the RNA world.

Figure 5 - amino acid binding

So what peptide/amino acids should be used to illustrate allosteric regulation of ribozyme "R"? How much molecular detail is needed to show that binding of the amino acids can couple to conformational change at the active site? Can the animation just show faster catalysis? Is it useful to show both an original, slow, non-amino acid-binding ribozyme and a newly evolved, faster version of the ribozyme that does bind amino acids?

Are there other ways that amino acid binding to 'R" could be beneficial besides an allosteric enhancement of enzyme activity? Maybe just protection from destruction of the ribozyme? Any evidence that amino acid/peptide binding can stabilize ribozmes?

There might be some useful results and theory about positively-charged amino acids that bind non-covalently to the phosphate backbones of RNA molecules. ribonuclease P as a model system? Also, there may be a relevant type of covalent amino acid-RNA interaction. (ADP-ribosylation? uridylylation?)

Nuclear ADP-Ribosylation Reactions in Mammalian Cells: Where Are We Today and Where Are We Going?

Does the non-biological origin of amino acids need to be illustrated? Would cells have biosynthesized amino acids before having a translation system?