Enzymes
Summary
Enzymes are protein catalysts that accelerate the vast majority of chemical transformations in living systems by lowering activation barriers without being consumed. They achieve remarkable rate enhancements—often by more than 10^8-fold—through exquisitely organised active sites that bind substrates with high specificity and stabilise transition states. Dynamic conformational changes in enzymes enable induced-fit interactions, cooperative effects and allosteric regulation, thereby allowing fine-tuned control of metabolic fluxes. Catalytic parameters such as the turnover number (kcat) and the Michaelis constant (Km) quantify enzyme efficiency and substrate affinity, while the ratio kcat/Km provides a measure of catalytic prowess under physiological conditions. Advances in structural biology, biophysics and computational modelling continue to reveal how enzyme architecture, dynamics and chemical microenvironments underpin catalytic function, with implications for drug discovery, industrial biocatalysis and understanding the origin and evolution of biological catalysts.
Research from Nature Portfolio
Structural and mechanistic studies of glycoside hydrolase family 87 (GH87) α-1,3-glucanases have defined their potential as precise biofilm disruptors. A collated analysis of an enzyme from Flavobacterium sp. EK-14 revealed a multipartite domain architecture—comprising immunoglobulin-like and lectin-like modules—that recruits and cleaves fungal cell-wall α-1,3-glucan under physiological conditions. Complementary crystallography of the Bacillus circulans Agl-KA core unit at 1.8 Å resolution uncovered tandem galactose-binding-like and β-helix domains, with conserved aspartate residues lining a closed-end catalytic cleft that explains product specificity. In parallel, a unified computational framework has been introduced to predict key kinetic parameters (kcat, Km and kcat/Km) directly from protein sequence and substrate structure. By incorporating environmental factors such as pH and temperature and by employing re-weighting strategies to refine high-value predictions, this approach enables rapid in silico screening for enzyme discovery and directed evolution efforts.
Enzymes publication trend
The graph below shows the total number of articles in enzymes across all publications each year (not limited to Nature Index journals).
Technical terms
Active site: The specialised region of an enzyme where substrates bind and chemical transformation occurs.
Turnover number (kcat): The maximum number of substrate molecules converted to product per enzyme molecule per second at saturation.
Michaelis constant (Km): The substrate concentration at which the reaction rate reaches half of its maximum (Vmax), reflecting enzyme–substrate affinity.
Catalytic efficiency: The ratio kcat/Km, indicating how effectively an enzyme processes substrate at low concentrations.
GH87 α-1,3-glucanase: A family 87 glycoside hydrolase that specifically cleaves α-1,3-linked glucan polymers in microbial biofilms.
Partial reversible inhibition: A mode of enzyme inhibition where the enzyme–inhibitor complex retains residual catalytic activity.
References
- α-1,3-Glucanase from the gram-negative bacterium Flavobacterium sp. EK-14 hydrolyzes fungal cell wall α-1,3-glucan. Scientific Reports (2023).
- Crystal structure of the catalytic unit of GH 87-type α-1,3-glucanase Agl-KA from Bacillus circulans. Scientific Reports (2019).
- UniKP: a unified framework for the prediction of enzyme kinetic parameters. Nature Communications (2023).
- Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein–Ligand Binding and Competitive Binding. Journal of Chemical Information and Modeling (2024).
- Partial Reversible Inhibition of Enzymes and Its Metabolic and Pharmaco-Toxicological Implications. International Journal of Molecular Sciences (2023).
About these summaries
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