Enzymatic metabolon improves kinetic efficiency of reaction-limited enzyme pathways
bioRxiv (Cold Spring Harbor Laboratory)(2023)
摘要
In this work, we investigate how the spatial proximity of enzymes belonging to the same pathway (metabolon) affects metabolic flux. Using off-lattice Langevin Dynamics (LD) simulations in tandem with a stochastic reaction-diffusion protocol and a semi-analytical reaction-diffusion model, we systematically explored how the strength of protein-protein interactions, catalytic efficiency, and protein-ligand interactions affect metabolic flux through the metabolon. Formation of a metabolon leads to a greater speed up for longer pathways and especially for reaction-limited enzymes while for fully optimized diffusion-limited enzymes the effect is negligible. Notably, specific cluster architectures are not a prerequisite for enhancing reaction flux. Simulations uncover the crucial role of optimal non-specific protein-ligand interactions in enhancing the catalytic efficiency of a metabolon. Our theory implies that bioinformatics analysis confirms that longer catalytic pathways are enriched in less optimal enzymes while most diffusion-limited enzymes populate shorter pathways. Our findings point towards a plausible evolutionary strategy where enzymes compensate for less-than-optimal efficiency by increasing their local concentration in the clustered state.
### Competing Interest Statement
The authors have declared no competing interest.
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关键词
enzymatic metabolon,enzyme,kinetic efficiency,reaction-limited
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