A comparative conformational analysis of thimet oligopeptidase (EC 3.4.24.15) substrates

The specificity of thimet oligopeptidase (EC 3.4.24.15) (TOP 24.15) does not agree with theoretical models devised to explain the specificity characteristic of peptidases toward certain sequences of amino acid residues. According to previous studies peptide chains hydrolyzed by TOP 24.15 adopt similar main chain conformations, although with different and in some cases small probabilities of occurrence in aqueous solution. To determine specific structural features recognized by TOP 24.15, a conformational search including eight polypeptides with known susceptibilities for catalytic hydrolysis was executed and the distribution of each main chain conformation found in the search was tabulated. Two sets of main chain conformations were selected, those common to all peptides in the study and those common only to substrates of TOP 24.15. The former set is very small and includes mainly extended conformations. In contrast, the latter set is large and its conformations are coiled and exhibit sharp turns coincident with positions of hydrolysis by TOP 24.15. These results indicate a possible basis for the selectivity of TOP 24.15.