  Trypsin and chymotrypsin are both serine proteases with high sequence and
structural similarities, but with different substrate specificity. Previous
experiments have demonstrated the critical role of the two loops outside the
binding pocket in controlling the specificity of the two enzymes. To understand
the mechanism of such a control of specificity by distant loops, we have used
the Gaussian Network Model to study the dynamic properties of trypsin and
chymotrypsin and the roles played by the two loops. A clustering method was
introduced to analyze the correlated motions of residues. We have found that
trypsin and chymotrypsin have distinct dynamic signatures in the two loop
regions which are in turn highly correlated with motions of certain residues in
the binding pockets. Interestingly, replacing the two loops of trypsin with
those of chymotrypsin changes the motion style of trypsin to chymotrypsin-like,
whereas the same experimental replacement was shown necessary to make trypsin
have chymotrypsin's enzyme specificity and activity. These results suggest that
the cooperative motions of the two loops and the substrate-binding sites
contribute to the activity and substrate specificity of trypsin and
chymotrypsin.
