I am doing biochemical characteristics of 2 cysteine proteases (A and B). However, the substrate specificity of enzyme B is very different (Enzyme A worked as I expected but B showed different substrate specificity). I tried enzyme assay with several conditions (pH, temperatures), but got the same results. So I wonder is there any possibility of some key residues that affect to protein conformation or structure, consequently resulting in the difference of substrate-binding specificity between two enzymes? If possible, how can I predict of identify those residues?
Actually I tried modeling 2 proteins and predicted some potential residues but It did not work as I expected.
Can anyone help me to serve this problem? Thank you for your suggestion.