<P> Trypsin - like proteases cleave peptide bonds following a positively charged amino acid (lysine or arginine). This specificity is driven by the residue which lies at the base of the enzyme's S1 pocket (generally a negatively charged aspartic acid or glutamic acid). </P> <P> The S1 pocket of chymotrypsin - like enzymes is more hydrophobic than in trypsin - like proteases . This results in a specificity for medium to large sized hydrophobic residues, such as tyrosine, phenylalanine and tryptophan . </P> <P> These include thrombin, tissue activating plasminogen and plasmin . They have been found to have roles in coagulation and digestion as well as in the pathophysiology of neurodegenerative disorders such as Alzheimer's and Parkinson's induced dementia . </P> <P> Elastase - like proteases have a much smaller S1 cleft than either trypsin - or chymotrypsin - like proteases . Consequently, residues such as alanine, glycine and valine tend to be preferred . </P>

The substrate specificity of serine proteases is primarily due to