It would be great it we could find a way to use Alphafold to kindof reverse engineer proteins - like to specify the shape you want and then run Alphafold 'backwards' so that you're going from shape -> DNA instead of DNA -> shape
Rarely, there have been attempts to engineer entirely new folds, although it's not clear how necessary that is.
Fortunately, evolution already encoded robustness against this sort of problem into proteins and the vast majority of single point mutations are tolerated (the resulting enzymes are often nearly as active and stable as the originals).
Don't forget that you can replace the three residues in the serine protease catalytic triad and still see significant proteolytic activity. Everything we know about protein activity is wrong.