Mining versatile feruloyl esterases: phylogenetic classification, structural features, and deep learning model

Feruloyl esterases (FEs, EC 3.1.1.73) play a crucial role in biological synthesis and metabolism. However, the identification of versatile FEs, capable of catalyzing a wide range of substrates, remains a challenge. In this study, we obtained 2085 FE sequences from the BRENDA database and initiated with an enzyme similarity network analysis, revealing three main clusters (1-3). Notably, both cluster 1 and cluster 3 included the characterized FEs, which exhibited significant differences in sequence length. Subsequent phylogenetic analysis of these clusters unveiled a correlation between phylogenetic classification and substrate promiscuity, and enzymes with broad substrate scope tended to locate within specific branches of the phylogenetic tree. Further, molecular dynamics simulations and dynamical cross-correlation matrix analysis were employed to explore structural dynamics differences between promiscuous and substrate-specific FEs. Finally, to expand the repertoire of versatile FEs, we employed deep learning models to predict potentially promiscuous enzymes and identified 38 and 75 potential versatile FEs from cluster 1 and cluster 3 with a probability score exceeding 90%. Our findings underscore the utility of integrating phylogenetic and structural features with deep learning approaches for mining versatile FEs, shedding light on unexplored enzymatic diversity and expanding the repertoire of biocatalysts for synthetic applications.