Catalysis-Induced Phase Separation and Autoregulation of Enzymatic Activity

Enhanced Stability and Chaotic Condensates in Multispecies Nonreciprocal Mixtures

Random nonreciprocal interactions between a large number of conserved densities are shown to enhance the stability of the system toward pattern formation. The enhanced stability is an exact result when the number of species approaches infinity and is confirmed numerically by simulations of the multispecies nonreciprocal Cahn-Hilliard model. Furthermore, the diversity in dynamical patterns increases with an increasing number of components, and novel steady states such as pulsating or spatiotemporally chaotic condensates are observed. Our results may help to unravel the mechanisms by which living systems self-organize via metabolism.

Anomalous Fluctuations in a Droplet of Chemically Active Colloids or Enzymes

Chemically active colloids or enzymes cluster into dense droplets driven by their phoretic response to collectively generated chemical gradients. Employing Brownian dynamics simulation techniques, our study of the dynamics of such a chemically active droplet uncovers a rich variety of structures and dynamical properties, including the full range of fluidlike to solidlike behavior, and non-Gaussian positional fluctuations. Our work sheds light on the complex dynamics of the active constituents of metabolic clusters, which are the main drivers of nonequilibrium activity in living systems.

Enzyme-Mediated Temporal Control over the Conformational Disposition of a Condensed Protein in Macromolecular Crowded Media

Temporal regulation between input and output signals is one of the hallmarks of complex biological processes. Herein, we report that the conformational disposition of a protein in macromolecularly crowded media can be controlled with time using enzymes. First, we demonstrate the pH dependence of bovine serum albumin (BSA) condensation and conformational alteration in the presence of poly(ethylene glycol) as a crowder. However, by exploiting the strength of pH-modulatory enzymatic reactions (glucose oxidase and urease), the conversion time between the condensed and free forms can be tuned. Additionally, we demonstrate that the trapping of intermediate states with respect to the overall system at a particular α-helix or β-sheet composition and rotational mobility can be possible simply by altering the substrate concentration. Finally, we show that the intrinsic catalytic ability of BSA toward the Kemp elimination (KE) reaction is inhibited in the aggregated form but regained in the free form. In fact, the rate of KE reaction can also be actuated enzymatically in a temporal fashion, therefore demonstrating the programmability of a cascade of biochemical events in crowded media.

Network Effects Lead to Self-Organization in Metabolic Cycles of Self-Repelling Catalysts

Mixtures of particles that interact through phoretic effects are known to aggregate if they belong to species that exhibit attractive self-interactions. We study self-organization in a model metabolic cycle composed of three species of catalytically active particles that are chemotactic toward the chemicals that define their connectivity network. We find that the self-organization can be controlled by the network properties, as exemplified by a case where a collapse instability is achieved by design for self-repelling species. Our findings highlight a possibility for controlling the intricate functions of metabolic networks by taking advantage of the physics of phoretic active matter.

Self-organization of primitive metabolic cycles due to non-reciprocal interactions

One of the greatest mysteries concerning the origin of life is how it has emerged so quickly after the formation of the earth. In particular, it is not understood how metabolic cycles, which power the non-equilibrium activity of cells, have come into existence in the first instances. While it is generally expected that non-equilibrium conditions would have been necessary for the formation of primitive metabolic structures, the focus has so far been on externally imposed non-equilibrium conditions, such as temperature or proton gradients. Here, we propose an alternative paradigm in which naturally occurring non-reciprocal interactions between catalysts that can partner together in a cyclic reaction lead to their recruitment into self-organized functional structures. We uncover different classes of self-organized cycles that form through exponentially rapid coarsening processes, depending on the parity of the cycle and the nature of the interaction motifs, which are all generic but have readily tuneable features.