Chemical aspects of proteolysis and of substrate specificity

Without any knowledge of the spatial structure, the following evidence concerning the structure and the function of proteases can be learned: the organic chemical structure, the identity of some of the groups in the active site, the proximity of these groups, the length of the active site, the occurrence of non-productive binding, the prediction of certain K(, m) values and the occurrence of acylenzyme intermediates. For a precise understanding of substrate binding, for example in trypsin, chymotrypsin and elastase, the spatial structure is required. Papaine is cited as an example of how a combination of chemical studies, spectrometry, X-ray crystallography and quantum chemistry provides a picture of the catalytic mechanism. The latter mechanism is compared with those of the serine proteases and of carboxypeptidase: similarities and differences are discussed.