Enhanced Catalytic Activity of a de novo Enzyme in a Coacervate Phase DOI Creative Commons

Eugénie Kluczka,

V. Stelitano S. Rinaldo Stelitano S Rinaldo,

Angélique Coutable‐Pennarun

et al.

ChemCatChem, Journal Year: 2024, Volume and Issue: unknown

Published: May 8, 2024

Abstract Biomolecular condensates are membraneless organelles that orchestrate various metabolic pathways in living cells. Understanding how these crowded structures regulate enzyme reactions remains yet challenging due to their dynamic and intricate nature. Coacervate microdroplets formed by associative liquid‐liquid phase separation of oppositely charged polyions have emerged as relevant condensate models study catalysis. Enzyme within droplets show altered kinetics, influenced factors such substrate partitioning, crowding, interactions with coacervate components; it is often disentangle the contributions each. Here, we investigate peroxidase activity a de novo polysaccharide‐based coacervates. By comparing reaction kinetics buffer, suspension coacervates bulk collected after centrifugation droplets, significantly increases catalytic efficiency. We demonstrate main origin this enhanced lies macromolecular crowding coupled changes conformational dynamics environment. Altogether, findings underline crucial role matrix catalysis, beyond simple partitioning effects. The observed boost provides insights for designing biocatalytically active synthetic organelles.

Language: Английский

Modulating biomolecular condensates: a novel approach to drug discovery DOI Creative Commons
Diana M. Mitrea, Matthäus Mittasch, Beatriz Ferreira Gomes

et al.

Nature Reviews Drug Discovery, Journal Year: 2022, Volume and Issue: 21(11), P. 841 - 862

Published: Aug. 16, 2022

In the past decade, membraneless assemblies known as biomolecular condensates have been reported to play key roles in many cellular functions by compartmentalizing specific proteins and nucleic acids subcellular environments with distinct properties. Furthermore, growing evidence supports view that often form phase separation, which a single-phase system demixes into two-phase consisting of condensed dilute particular biomolecules. Emerging understanding condensate function normal aberrant states, mechanisms formation, is providing new insights human disease revealing novel therapeutic opportunities. this Perspective, we propose such could enable previously unexplored drug discovery approach based on identifying condensate-modifying therapeutics (c-mods), discuss strategies, techniques challenges involved.

Language: Английский

Citations

232
Higher-order organization of biomolecular condensates DOI Creative Commons
Charlotte M. Fare, Alexis Villani, Lauren E. Drake

et al.

Open Biology, Journal Year: 2021, Volume and Issue: 11(6)

Published: June 1, 2021

A guiding principle of biology is that biochemical reactions must be organized in space and time. One way this spatio-temporal organization achieved through liquid–liquid phase separation (LLPS), which generates biomolecular condensates. These condensates are dynamic reactive, often contain a complex mixture proteins nucleic acids. In review, we discuss how underlying physical chemical processes generate internal condensate architectures. We then outline the diverse architectures observed biological systems. Finally, specific critical for functions.

Language: Английский

Citations

143
Liquid–Liquid Phase Separation in Chromatin DOI Open Access
Karsten Rippe

Cold Spring Harbor Perspectives in Biology, Journal Year: 2021, Volume and Issue: 14(2), P. a040683 - a040683

Published: June 14, 2021

Karsten Rippe Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany Correspondence: Karsten.Rippe{at}dkfz.de

Language: Английский

Citations

110
Principles and functions of metabolic compartmentalization DOI
Liron Bar‐Peled, Nora Kory

Nature Metabolism, Journal Year: 2022, Volume and Issue: 4(10), P. 1232 - 1244

Published: Oct. 20, 2022

Language: Английский

Citations

78
Disrupting the phase separation of KAT8–IRF1 diminishes PD-L1 expression and promotes antitumor immunity DOI Creative Commons
Yuanzhong Wu, Liwen Zhou,

Yezi Zou

et al.

Nature Cancer, Journal Year: 2023, Volume and Issue: 4(3), P. 382 - 400

Published: March 9, 2023

Abstract Immunotherapies targeting the PD-1/PD-L1 axis have become first-line treatments in multiple cancers. However, only a limited subset of individuals achieves durable benefits because elusive mechanisms regulating PD-1/PD-L1. Here, we report that cells exposed to interferon-γ (IFNγ), KAT8 undergoes phase separation with induced IRF1 and forms biomolecular condensates upregulate PD-L1. Multivalency from both specific promiscuous interactions between is required for condensate formation. KAT8–IRF1 condensation promotes K78 acetylation binding CD247 (PD-L1) promoter further enriches transcription apparatus promote PD-L1 mRNA. Based on mechanism formation, identified 2142–R8 blocking peptide, which disrupts formation consequently inhibits expression enhances antitumor immunity vitro vivo. Our findings reveal key role regulation provide competitive peptide enhance immune responses.

Language: Английский

Citations

63
Molecular Crowding: The History and Development of a Scientific Paradigm DOI Creative Commons
Caterina Alfano, Yann Fichou, Klaus Huber

et al.

Chemical Reviews, Journal Year: 2024, Volume and Issue: 124(6), P. 3186 - 3219

Published: March 11, 2024

It is now generally accepted that macromolecules do not act in isolation but "live" a crowded environment, is, an environment populated by numerous different molecules. The field of molecular crowding has its origins the far 80s became only end 90s. In present issue, we discuss various aspects are influenced and need to consider effects. This Review meant as introduction theme analysis evolution concept through time from colloidal polymer physics more biological perspective. We introduce themes will be thoroughly treated other Reviews issue. our intentions, each may stand itself, complete collection aspiration provide complementary perspectives propose holistic view crowding.

Language: Английский

Citations

37
Substrate-induced condensation activates plant TIR domain proteins DOI Creative Commons
Wen Song,

Li Liu,

Dongli Yu

et al.

Nature, Journal Year: 2024, Volume and Issue: 627(8005), P. 847 - 853

Published: March 13, 2024

Abstract Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain mediate recognition of strain-specific pathogen effectors, typically via their C-terminal ligand-sensing domains 1 . Effector binding enables TIR-encoded enzymatic activities that are required for TIR–NLR (TNL)-mediated immunity 2,3 Many truncated TNL proteins lack effector-sensing but retain similar and 4,5 The mechanism underlying the activation these TIR remain unclear. Here we show substrates NAD + ATP induces phase separation in vitro. A condensation occurs a protein expressed its native promoter response to inoculation planta. formation condensates is mediated by conserved self-association interfaces predicted intrinsically disordered loop region TIRs. Mutations disrupt impair cell death activity proteins. Our data reveal as provide insight into substrate-induced autonomous signalling confer plant immunity.

Language: Английский

Citations

19
Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription DOI Creative Commons
Megan Palacio, Dylan J. Taatjes

Journal of Molecular Biology, Journal Year: 2021, Volume and Issue: 434(1), P. 167216 - 167216

Published: Aug. 30, 2021

The regulation of RNA polymerase II (pol II) transcription requires a complex and context-specific array proteins protein complexes, as well nucleic acids metabolites. Every major physiological process coordinated specific sets genes at the appropriate time, breakdown in this is hallmark human disease. A proliferation recent studies has revealed that many general components, including sequence-specific, DNA-binding factors, Mediator, pol itself, are capable liquid–liquid phase separation, to form condensates partition these factors away from bulk aqueous phase. These findings hold great promise for next-level understanding transcription; however, mechanistic aspects align with more conventional models, whether separation per se regulates activity cells remains controversial. In review, we describe condensate-dependent why their similarities differences important. We also compare contrast models context genome organization (initiation, elongation, termination), highlight central role processes. Finally, discuss mutations disrupt normal partitioning how may contribute

Language: Английский

Citations

85
Biomolecular condensates at sites of DNA damage: More than just a phase DOI Creative Commons

Vincent Spegg,

Matthias Altmeyer

DNA repair, Journal Year: 2021, Volume and Issue: 106, P. 103179 - 103179

Published: July 14, 2021

Protein recruitment to DNA break sites is an integral part of the damage response (DDR). Elucidation hierarchy and temporal order with which sensors as well repair signaling factors assemble around chromosome breaks has painted a complex picture tightly regulated macromolecular interactions that build specialized compartments facilitate maintenance genome integrity. While many underlying interactions, e.g. between damage-induced histone marks, can be explained by lock-and-key or induced fit binding models assuming fixed stoichiometries, structurally less defined such highly dynamic multivalent implicated in phase separation, also participate formation multi-protein assemblies genotoxic stress. Although much remains learned about these types cooperative their functional roles, rapidly growing interest material properties biomolecular condensates concepts from polymer chemistry soft matter physics understand biological processes at different scales holds great promises. Here, we discuss nuclear context integrity maintenance, highlighting potential clustered stoichiometric separation. Rather than viewing them opposing scenarios, combined effects balance structural specificity favorable physicochemical relevant for regulation function multilayered condensates.

Language: Английский

Citations

79
The intertwined physics of active chemical reactions and phase separation DOI
David Zwicker

Current Opinion in Colloid & Interface Science, Journal Year: 2022, Volume and Issue: 61, P. 101606 - 101606

Published: Aug. 2, 2022

Language: Английский

Citations

65