Intramolecular interactions, enzyme activity and models

The specificity of protein binding and the specificity-catalysis relationship in enzymes are analysed. Many enzymes use extended binding sites to achieve specificity and to create special environments which activate chemical groups on both the substrate and the enzyme itself. Aside from this effect, which is not adequately available in model compounds, the use of models is exemplified for several possibly separable effects in enzyme-substrate reactions. These include proximity (entropy loss on binding), locking into a productive binding mode, desolvation, electrostatic effects, changes of pKa by local environments, geometric strain, acid-base catalysis, and formation of other intermediates.