This is the mechanism of peptide cleavage by chymotrpysin. It features the three amino acids shown in the last post. This time I went back to the standard approach for the visualisation. The main feature is that a proton can be passed back and forth between serine and aspartate with histidine in between. This way you always have a proton at hand without the need of a low pH. Chymotrypsin is not something strange that somehow works. It is an amazing nano machine.
I tried to model the steps of the mechanism at first but I do not really know how to do it. Including the whole protein wouldn't work on my laptop. I tried using only the side chains of these three amino acids with fixed Cα positions. It worked out to pass a proton from protonated serine to aspartate. That was pretty nice. But it did not work out well to do more.
Finding disordered residues in an NMR ensemble - Note to self: here's how you identified disordered residues in the NMR ensemble 2KCU.pdb 1. In Pymol: "fetch 2kcu" 2. Action > align > states (*/CA) 3. "...
5 days ago