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Condenzymes: Biomolecular condensates with inherent catalytic activities
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Condenzymes: Biomolecular condensates with inherent catalytic activities

Michael W. Chen, Xiao Guo, Mina Farag +14 more
May 2025
 ·
bioRxiv
 ·
DOI 
10.1101/2024.07.06.602359
94
%
Reproducible
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It ranks in the top 1% of preprints assessed in Biophysics this quarter.
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Why this is interesting

By demonstrating that protein condensates catalyze hydrolysis via emergent interfacial electrochemistry—without enzymatic active sites—this work overturns the passive-hub paradigm and establishes phase separation itself as a programmable catalytic mechanism in cells.

QED claims analysis

Summary

Biomolecular condensates formed by intrinsically disordered proteins possess inherent catalytic activities that emerge from their sequence-dependent electrochemical microenvironments and interfacial electric fields, enabling them to function as programmable mesoscale catalysts ("condenzymes") that can hydrolyze diverse cellular substrates including complete ATP decomposition to adenine, with catalytic behaviors controllable through rational sequence design and functional in living cells where they modulate ATP levels, activate transcription pathways, and drive synthetic gene circuits.

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Main Claim 1 –

IDP Condensates Catalyze Hydrolysis Without Intrinsic Enzymatic Activity

Supporting evidence

  • Condensates Catalyze Diverse Substrate Hydrolysis with Substrate-Dependent Rates
  • Condensate-Scale Electric Fields Lower Hydrolysis Activation Free Energy
  • Charged Dense-Phase Chemistry Required for Condensate Hydrolysis Catalysis
  • Highly Charged Natural IDP Condensates Are Catalytic; Low-Charge Are Not
  • Condensates Hydrolyze Disaccharides, Peptides, NTPs, and Nucleic Acids
Main Claim 2 –

Programming Condensate Interfacial Electric Fields via IDP Sequence Design

Supporting evidence

  • Single N-Terminus Mutations Tune Interfacial Fields Over Fivefold
  • Catalytic Activity Scales with Interfacial Electric Field Across Variants
  • Condensate Interfaces Are Required for Maximal Catalytic Activity
  • Sequence-Dependent Interfacial Water Structure Drives Programmable Catalysis
Main Claim 3 –

Condensates Fully Decompose ATP to Adenine and Carbohydrates

Main Claim 4 –

Synthetic Condensates Catalyze Reactions in Cells, Altering ATP and Transcription

Supporting evidence

  • Condensate ATP Depletion Activates PhoB/PhoP Phosphate-Response Transcription
  • Condensates Hydrolyze Fluorogenic Probes in Cells with 100-Fold Signals
  • Condensate Catalysis Activates Synthetic Gene Circuits and Intercellular Signaling

Abstract

We report the discovery that chemical reactions can be catalyzed by condensates formed by intrinsically disordered proteins (IDPs). The proteins themselves lack any catalytic activities. Catalytic functions of condensates emerge as a consequence of sequence-dependent mesoscale electrochemical microenvironments created by phase separation. Stimulated Raman spectroscopy suggests that the catalytic behaviors of condensates are attributable to the spatial variations of water activities across condensate interiors and interfaces. We show that condensates are capable of catalyzing diverse cellularly relevant hydrolysis reactions. Through sequence design, the electrochemical properties of condensates can be programmed to exert control over catalytic behaviors. Incorporation of synthetic condensates into live cells alters transcription profiles and enables the activation of gene circuits that depend on products of hydrolysis reactions catalyzed by condensates. Our discovery of suggests that condensates, depending on their composition-dependent electrochemical properties, can be “Condenzymes”, which contribute unexpected emergent chemical functions in cells.

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