Ribeiro Antonio J M, Riziotis Ioannis G, Borkakoti Neera, Fernandes Pedro A, Ramos Maria J, Thornton Janet M
LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Portugal.
European Bioinformatics Institute, Cambridge, UK.
FEBS J. 2025 Aug;292(16):4200-4210. doi: 10.1111/febs.70106. Epub 2025 Apr 22.
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.
蛋白质序列、结构和酶反应的相似性度量一直是将大量关于酶的实验数据转化为生物学见解的重要工具。例如，具有相似序列和结构的酶可以被组织成进化家族，在家族内部，反应相似性可以突出保守或趋异进化的例子。当涉及到反应机制时，尽管它们在解释酶的催化能力及其进化方面很重要，但到目前为止还没有开发出相似性度量方法。我们通过开发一种基于每个催化步骤中发生的键变化和电荷转移来计算机制相似性的方法来填补这一空白，在该方法中我们能够直接调整直接参与这些转化的原子周围化学环境的大小。使用这种新开发的方法，我们对存储在机制与催化位点图谱（M-CSA）数据库中的所有机制进行了成对比较。该分析说明了机制相似性如何能够成为一个强大的工具，用于探索已知的催化空间以及发现和表征趋同和趋异的进化关系。
