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.
Automating calculations: pKa predictions - I want to compute the standard free energy difference for proton exchange between heliotridane and a molecule which I'll call compound 1 (comp1) heliotrida...
1 day ago