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Article: Design rules for reciprocal coupling in chemically fueled assembly.

Chen, Xiaoyao / Kriebisch, Brigitte A K / Bergmann, Alexander M / Boekhoven, Job

2023 Volume 14, Issue 37, Page(s) 10176–10183

Abstract: Biology regulates the function and assembly of proteins through non-equilibrium reaction cycles. Reciprocally, the assembly of proteins can influence the reaction rates of these cycles. Such reciprocal coupling between assembly and reaction cycle is a ... ...

Abstract	Biology regulates the function and assembly of proteins through non-equilibrium reaction cycles. Reciprocally, the assembly of proteins can influence the reaction rates of these cycles. Such reciprocal coupling between assembly and reaction cycle is a prerequisite for behavior like dynamic instabilities, treadmilling, pattern formation, and oscillations between morphologies. While assemblies regulated by chemical reaction cycles gained traction, the concept of reciprocal coupling is under-explored. In this work, we provide two molecular design strategies to tweak the degree of reciprocal coupling between the assembly and reaction cycle. The strategies involve spacing the chemically active site away from the assembly or burying it into the assembly. We envision that design strategies facilitate the creation of reciprocally coupled and, by extension, dynamic supramolecular materials in the future.
Language	English
Publishing date	2023-08-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d3sc02062b
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Fuel-Driven Dynamic Combinatorial Libraries.

Kriebisch, Christine M E / Bergmann, Alexander M / Boekhoven, Job

Journal of the American Chemical Society

2021 Volume 143, Issue 20, Page(s) 7719–7725

Abstract: In dynamic combinatorial libraries, molecules react with each other reversibly to form intricate networks under thermodynamic control. In biological systems, chemical reaction networks operate under kinetic control by the transduction of chemical energy. ...

Abstract	In dynamic combinatorial libraries, molecules react with each other reversibly to form intricate networks under thermodynamic control. In biological systems, chemical reaction networks operate under kinetic control by the transduction of chemical energy. We thus introduced the notion of energy transduction, via chemical reaction cycles, to a dynamic combinatorial library. In the library, monomers can be oligomerized, oligomers can be deoligomerized, and oligomers can recombine. Interestingly, we found that the dynamics of the library's components were dominated by transacylation, which is an equilibrium reaction. In contrast, the library's dynamics were dictated by fuel-driven activation, which is a nonequilibrium reaction. Finally, we found that self-assembly can play a large role in affecting the reaction's kinetics via feedback mechanisms. The interplay of the simultaneously operating reactions and feedback mechanisms can result in hysteresis effects in which the outcome of the competition for fuel depends on events that occurred in the past. In future work, we envision diversifying the library by modifying building blocks with catalytically active motifs and information-containing monomers.
Language	English
Publishing date	2021-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.1c01616
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Article ; Online: Phase Transitions in Chemically Fueled, Multiphase Complex Coacervate Droplets.

Donau, Carsten / Späth, Fabian / Stasi, Michele / Bergmann, Alexander M / Boekhoven, Job

Angewandte Chemie (International ed. in English)

2022 Volume 61, Issue 46, Page(s) e202211905

Abstract: Membraneless organelles are droplets in the cytosol that are regulated by chemical reactions. Increasing studies suggest that they are internally organized. However, how these subcompartments are regulated remains elusive. Herein, we describe a complex ... ...

Abstract	Membraneless organelles are droplets in the cytosol that are regulated by chemical reactions. Increasing studies suggest that they are internally organized. However, how these subcompartments are regulated remains elusive. Herein, we describe a complex coacervate-based model composed of two polyanions and a short peptide. With a chemical reaction cycle, we control the affinity of the peptide for the polyelectrolytes leading to distinct regimes inside the phase diagram. We study the transitions from one regime to another and identify new transitions that can only occur under kinetic control. Finally, we show that the chemical reaction cycle controls the liquidity of the droplets offering insights into how active processes inside cells play an important role in tuning the liquid state of membraneless organelles. Our work demonstrates that not only thermodynamic properties but also kinetics should be considered in the organization of multiple phases in droplets.
MeSH term(s)	Kinetics ; Peptides
Chemical Substances	Peptides
Language	English
Publishing date	2022-10-18
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202211905
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Article ; Online: Evolution and Single-Droplet Analysis of Fuel-Driven Compartments by Droplet-Based Microfluidics.

Bergmann, Alexander M / Donau, Carsten / Späth, Fabian / Jahnke, Kevin / Göpfrich, Kerstin / Boekhoven, Job

Angewandte Chemie (International ed. in English)

2022 Volume 61, Issue 32, Page(s) e202203928

Abstract: Active droplets are a great model for membraneless organelles. However, the analysis of these systems remains challenging and is often limited due to the short timescales of their kinetics. We used droplet-based microfluidics to encapsulate a fuel-driven ...

Abstract	Active droplets are a great model for membraneless organelles. However, the analysis of these systems remains challenging and is often limited due to the short timescales of their kinetics. We used droplet-based microfluidics to encapsulate a fuel-driven cycle that drives phase separation into coacervate-based droplets to overcome this challenge. This approach enables the analysis of every coacervate-based droplet in the reaction container throughout its lifetime. We discovered that the fuel concentration dictates the formation of the coacervate-based droplets and their properties. We observed that coacervate-based droplets grow through fusion, decay simultaneously independent of their volume, and shrinkage rate scales with their initial volume. This method helps to further understand the regulation of membraneless organelles, and we believe the analysis of individual coacervate-based droplets enables future selection- or evolution-based studies.
MeSH term(s)	Kinetics ; Microfluidics/methods
Language	English
Publishing date	2022-06-24
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202203928
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Article ; Online: Liquid spherical shells are a non-equilibrium steady state of active droplets.

Bergmann, Alexander M / Bauermann, Jonathan / Bartolucci, Giacomo / Donau, Carsten / Stasi, Michele / Holtmannspötter, Anna-Lena / Jülicher, Frank / Weber, Christoph A / Boekhoven, Job

Nature communications

2023 Volume 14, Issue 1, Page(s) 6552

Abstract: Liquid-liquid phase separation yields spherical droplets that eventually coarsen to one large, stable droplet governed by the principle of minimal free energy. In chemically fueled phase separation, the formation of phase-separating molecules is coupled ... ...

Abstract	Liquid-liquid phase separation yields spherical droplets that eventually coarsen to one large, stable droplet governed by the principle of minimal free energy. In chemically fueled phase separation, the formation of phase-separating molecules is coupled to a fuel-driven, non-equilibrium reaction cycle. It thus yields dissipative structures sustained by a continuous fuel conversion. Such dissipative structures are ubiquitous in biology but are poorly understood as they are governed by non-equilibrium thermodynamics. Here, we bridge the gap between passive, close-to-equilibrium, and active, dissipative structures with chemically fueled phase separation. We observe that spherical, active droplets can undergo a morphological transition into a liquid, spherical shell. We demonstrate that the mechanism is related to gradients of short-lived droplet material. We characterize how far out of equilibrium the spherical shell state is and the chemical power necessary to sustain it. Our work suggests alternative avenues for assembling complex stable morphologies, which might already be exploited to form membraneless organelles by cells.
Language	English
Publishing date	2023-10-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42344-w
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Article ; Online: The Role of Chemically Innocent Polyanions in Active, Chemically Fueled Complex Coacervate Droplets.

Späth, Fabian / Maier, Anton S / Stasi, Michele / Bergmann, Alexander M / Halama, Kerstin / Wenisch, Monika / Rieger, Bernhard / Boekhoven, Job

Angewandte Chemie (International ed. in English)

2023 Volume 62, Issue 41, Page(s) e202309318

Abstract: Complex coacervation describes the liquid-liquid phase separation of oppositely charged polymers. Active coacervates are droplets in which one of the electrolyte's affinity is regulated by chemical reactions. These droplets are particularly interesting ... ...

Abstract	Complex coacervation describes the liquid-liquid phase separation of oppositely charged polymers. Active coacervates are droplets in which one of the electrolyte's affinity is regulated by chemical reactions. These droplets are particularly interesting because they are tightly regulated by reaction kinetics. For example, they serve as a model for membraneless organelles that are also often regulated by biochemical transformations such as post-translational modifications. They are also a great protocell model or could be used to synthesize life-they spontaneously emerge in response to reagents, compete, and decay when all nutrients have been consumed. However, the role of the unreactive building blocks, e.g., the polymeric compounds, is poorly understood. Here, we show the important role of the chemically innocent, unreactive polyanion of our chemically fueled coacervation droplets. We show that the polyanion drastically influences the resulting droplets' life cycle without influencing the chemical reaction cycle-either they are very dynamic or have a delayed dissolution. Additionally, we derive a mechanistic understanding of our observations and show how additives and rational polymer design help to create the desired coacervate emulsion life cycles.
Language	English
Publishing date	2023-09-06
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202309318
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Article: Fuel-Driven Dynamic Combinatorial Libraries

Kriebisch, Christine M. E / Bergmann, Alexander M / Boekhoven, Job

Journal of the American Chemical Society. 2021 May 12, v. 143, no. 20

2021

Abstract	In dynamic combinatorial libraries, molecules react with each other reversibly to form intricate networks under thermodynamic control. In biological systems, chemical reaction networks operate under kinetic control by the transduction of chemical energy. We thus introduced the notion of energy transduction, via chemical reaction cycles, to a dynamic combinatorial library. In the library, monomers can be oligomerized, oligomers can be deoligomerized, and oligomers can recombine. Interestingly, we found that the dynamics of the library’s components were dominated by transacylation, which is an equilibrium reaction. In contrast, the library’s dynamics were dictated by fuel-driven activation, which is a nonequilibrium reaction. Finally, we found that self-assembly can play a large role in affecting the reaction’s kinetics via feedback mechanisms. The interplay of the simultaneously operating reactions and feedback mechanisms can result in hysteresis effects in which the outcome of the competition for fuel depends on events that occurred in the past. In future work, we envision diversifying the library by modifying building blocks with catalytically active motifs and information-containing monomers.
Keywords	chemical reactions ; energy ; hysteresis ; thermodynamics
Language	English
Dates of publication	2021-0512
Size	p. 7719-7725.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.1c01616
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Morphological transitions in chemically fueled self-assembly.

Dai, Kun / Tena-Solsona, Marta / Rodon Fores, Jennifer / Bergmann, Alexander M / Boekhoven, Job

Nanoscale

2021 Volume 13, Issue 47, Page(s) 19864–19869

Abstract: In chemically fueled self-assembly, a reaction cycle activates and deactivates molecules for self-assembly. The resulting assembly is dynamic and should be endowed with unique behavior in this kinetically controlled regime. Recent works have mainly ... ...

Abstract	In chemically fueled self-assembly, a reaction cycle activates and deactivates molecules for self-assembly. The resulting assembly is dynamic and should be endowed with unique behavior in this kinetically controlled regime. Recent works have mainly focused on design rules for the activation of molecules for self-assembly, thereby assuming that disassembly upon deactivation inherently follows. However, that is not always the case. This work shows a family of peptides that assemble into colloids regulated through a chemical reaction cycle. Despite their similarity in assembly, we find that they follow a different disassembly pathway upon deactivation. The colloids from several peptides completely disassemble as fuel depletes while others transition into fibers. Our findings demonstrate that assembly and disassembly should be taken into account in chemically fueled self-assembly.
Language	English
Publishing date	2021-12-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d1nr04954b
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Article ; Online: Synthesis and characterization of chemically fueled supramolecular materials driven by carbodiimide-based fuels.

Schnitter, Fabian / Bergmann, Alexander M / Winkeljann, Benjamin / Rodon Fores, Jennifer / Lieleg, Oliver / Boekhoven, Job

Nature protocols

2021 Volume 16, Issue 8, Page(s) 3901–3932

Abstract: Many supramolecular materials in biological systems are driven to a nonequilibrium state by the irreversible consumption of high-energy molecules such as ATP or GTP. As a result, they exhibit unique dynamic properties such as a tunable lifetime, ... ...

Abstract	Many supramolecular materials in biological systems are driven to a nonequilibrium state by the irreversible consumption of high-energy molecules such as ATP or GTP. As a result, they exhibit unique dynamic properties such as a tunable lifetime, adaptivity or the ability to self-heal. In contrast, synthetic counterparts that exist in or close to equilibrium are controlled by thermodynamic parameters and therefore lack these dynamic properties. To mimic biological materials more closely, synthetic self-assembling systems have been developed that are driven out of equilibrium by chemical reactions. This protocol describes the synthesis and characterization of such an assembly, which is driven by carbodiimide fuels. Depending on the amount of chemical fuel added to the material, its lifetime can be tuned. In the first step, the protocol details the synthesis and purification of the peptide-based precursors for the fuel-driven assemblies by solid-phase peptide synthesis. Then, we explain how to analyze the kinetic response of the precursors to a carbodiimide-based chemical fuel by HPLC and kinetic models. Finally, we detail how to study the emerging assembly's macro- and microscopic properties by time-lapse photography, UV-visible spectroscopy, shear rheology, confocal laser scanning microscopy and electron microscopy. The procedure is described using the example of a colloid-forming precursor Fmoc-E-OH and a fiber-forming precursor Fmoc-AAD-OH to emphasize the differences in characterization depending on the type of assembly. The characterization of a precursor's transient assembly can be done within 5 d. The synthesis and purification of a peptide precursor requires 2 d of work.
MeSH term(s)	Carbodiimides/chemistry ; Cryoelectron Microscopy ; Humans ; Macromolecular Substances/chemistry ; Microscopy, Confocal ; Microscopy, Electron, Transmission ; Models, Molecular ; Molecular Structure
Chemical Substances	Carbodiimides ; Macromolecular Substances
Language	English
Publishing date	2021-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-021-00563-9
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Article: A chemically fueled supramolecular glue for self-healing gels.

Rodon-Fores, Jennifer / Würbser, Michaela A / Kretschmer, Martin / Rieß, Benedikt / Bergmann, Alexander M / Lieleg, Oliver / Boekhoven, Job

Chemical science

2022 Volume 13, Issue 38, Page(s) 11411–11421

Abstract: Chemically fueled supramolecular materials offer unique properties that include spatial and temporal control and even the ability to self-heal. Indeed, a few studies have demonstrated the ability to self-heal, however, the underlying mechanisms remain ... ...

Abstract	Chemically fueled supramolecular materials offer unique properties that include spatial and temporal control and even the ability to self-heal. Indeed, a few studies have demonstrated the ability to self-heal, however, the underlying mechanisms remain unclear. Here, we designed a peptide that forms a fibrillar network upon chemical fueling. We were surprised that the hydrogel could self-heal despite the lack of dynamics in the fiber assembly and disassembly. We explain this behavior by a mechanism that involves the chemically fueled peptide molecules that cannot self-assemble due to the lack of nucleation sites. When the fibers are perturbed, new nucleation sites form that help the assembly resulting in the healing of the damaged network. Furthermore, we generalized the behavior for other peptides. We refer to this non-assembling, chemically-fueled peptide as a molecular glue. In future work, we aim to explore whether this self-healing mechanism applies to more complex structures, narrowing the gap between biological and synthetic self-assemblies.
Language	English
Publishing date	2022-09-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d2sc03691f
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