Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

Hydrolase enzymes are involved in breaking different chemical bonds in diverse substrates of different sizes and complexity such as proteins, carbohydrates, lipids, and nucleic acids. This work presents a systematic analysis of the kinetic, structural, and biological information on hydrolases, taking into account the presence of different cofactors, the number of chains (i.e., oligomerization state), the number of amino acid residues, and the physicochemical properties of the substrates. Specific trends related to the catalytic activity of this large and rather diverse class of enzymes, including activation free energies, binding free energies, and enzyme efficiencies are revealed and rationalized. The results show that despite the diversity of hydrolases, their substrates, and reactions, hydrolases have quite characteristic activation free energies, substrate binding free energies, and enzyme efficiencies. Different subclasses of hydrolases employ different strategies to achieve these values, including the use of cofactors, different numbers of chains, and numbers of amino acid residues. The large structural and physicochemical diversity of the substrates acted by hydrolases is heavily neutralized by the hydrolases, resulting in activation free energies, binding free energies and enzyme efficiencies that are, in general, nearly independent of the diversity of the substrates.