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Sticky Enzymes: Increased Metabolic Efficiency via Substrate-Dependent Enzyme Clustering

Alejandro Martínez-Calvo1,2,3,*, Jello Zhou3, Yaojun Zhang4,5, and Ned S. Wingreen1,6,7,†

  • *Contact author: amcalvo@princeton.edu
  • †Contact author: wingreen@princeton.edu
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PRX Life 3, 033011 – Published 12 August, 2025

DOI: https://doi.org/10.1103/99bt-4ss4

Abstract

Coclustering of subsequent enzymes in a pathway can accelerate the processing of metabolic intermediates, with benefits including increased pathway fluxes, reduced toxicity, and sensitive branch-point regulation. While the optimal organization of such clusters has been explored theoretically, little is known about how to achieve such organization inside cells. Here we propose that phase-separating enzymes can self-organize into nearly optimally sized and spaced clusters, provided that their “stickiness” is regulated by local substrate availability. In a nutshell, enzyme clusters only form when and where they are needed to process substrate. We study a mathematical model that implements this scheme for simple metabolic pathways, including all thermodynamic constraints. We find that pathway fluxes can be increased by 50- to 1000-fold and toxic metabolites can be decreased by 10- to 100-fold at realistic enzyme densities. Finally, we discuss how enzyme “stickiness” could be allosterically regulated. This study presents a self-organization strategy that goes beyond current paradigms for natural and engineered enzyme clusters and thus represents a motivating challenge to the fields of synthetic biology and metabolic engineering.

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PRX Life 3, 033011– Published 12 August, 2025
  • Received 13 January 2025
  • Accepted 16 July 2025
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