Measuring catalytic mechanism similarity – a new approach to study enzyme function and evolution

Similarity measures for protein sequence, structure and enzyme reactions have been essential tools for translating an abundance of experimental data about enzymes into biological insights. Enzymes with similar sequence and structure, for example, can be organised into evolutionary families, and within families, reaction similarity can highlight examples of conservation or divergent evolution. When it comes to reaction mechanisms, despite their importance in explaining the catalytic power of enzymes and their evolution, no similarity measures have been developed until now. We addressed this gap by developing a method to calculate mechanism similarity based on the bond changes and charge transfers occurring at each catalytic step, where we have the ability to adjust the size of the chemical environment surrounding the atoms directly involved in these transformations. Using this newly developed method, we performed a pairwise comparison of all the mechanisms stored in the Mechanism and Catalytic Site Atlas (M-CSA) database. This analysis illustrates how mechanism similarity can be a powerful tool to navigate the known catalytic space and to discover and characterise both convergent and divergent evolutionary relationships.