Secondary and conformational specificities of trypsin and chymotrypsin

Specific and non-specific trypsin substrates of known structure have been examined for common features. This analysis suggests that trypsin has a specificity for a particular conformation near the scissile bond which I denote as a conformational specificity. This conformation is a bent left-handed helix at the third and fourth (P3 and P4) amino acid positions toward the amino terminus from the scissile bond which I denote as a conformational specificity. This conformation is a bent left-handed show a high frequency of proline and glycine at these positions consistent with the left-handed helical conformation. This apparent secondary specificity for a particular substrate residue other than that at the primary position is not related to the nature of the residues at the third and fourth positions. Rather, these residues determine the bend of left-handed helix which has the effect of exposing main chain hydrogen-bonding groups of the substrate peptide chain to hydrogen-bonding groups on the enzyme. Thus, the secondary specificity of trypsin is not sequence-specific, but is for peptide main chain in the third and fourth positions and is determined by the tertiary structure of the substrate. This hypothesis for conformational and secondary specificity in trypsin can be extended to chymotrypsin. It also provides a means for the regulation of certain processes in vivo catalyzed by other proteases.