Collective catalysis under spatial constraints: Phase separation and size-scaling effects on mass action kinetics

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F23%3A00577944" target="_blank" >RIV/61388963:_____/23:00577944 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.1103/PhysRevE.108.044410" target="_blank" >https://doi.org/10.1103/PhysRevE.108.044410</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1103/PhysRevE.108.044410" target="_blank" >10.1103/PhysRevE.108.044410</a>

Result language

angličtina

Original language name

Collective catalysis under spatial constraints: Phase separation and size-scaling effects on mass action kinetics

Original language description

Chemical reactions are usually studied under the assumption that both substrates and catalysts are well-mixed (WM) throughout the system. Although this is often applicable to test-tube experimental conditions, it is not realistic in cellular environments, where biomolecules can undergo liquid-liquid phase separation (LLPS) and form condensates, leading to important functional outcomes, including the modulation of catalytic action. Similar processes may also play a role in protocellular systems, like primitive coacervates, or in membrane-assisted prebiotic pathways. Here we explore whether the demixing of catalysts could lead to the formation of microenvironments that influence the kinetics of a linear (multistep) reaction pathway, as compared to a WM system. We implemented a general lattice model to simulate LLPS of a collection of different catalysts and extended it to include diffusion and a sequence of reactions of small substrates. We carried out a quantitative analysis of how the phase separation of the catalysts affects reaction times depending on the affinity between substrates and catalysts, the length of the reaction pathway, the system size, and the degree of homogeneity of the condensate. A key aspect underlying the differences reported between the two scenarios is that the scale invariance observed in the WM system is broken by condensation processes. The main theoretical implications of our results for mean-field chemistry are drawn, extending the mass action kinetics scheme to include substrate initial “hitting times“ to reach the catalysts condensate. We finally test this approach by considering open nonlinear conditions, where we successfully predict, through microscopic simulations, that phase separation inhibits chemical oscillatory behavior, providing a possible explanation for the marginal role that this complex dynamic behavior plays in real metabolisms.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Physical Review E

ISSN

2470-0045

e-ISSN

2470-0053

Volume of the periodical

108

Issue of the periodical within the volume

4

Country of publishing house

US - UNITED STATES

Number of pages

15

Pages from-to

044410

UT code for WoS article

001095303400003

EID of the result in the Scopus database

2-s2.0-85175437885