1
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van Haren MHI, Visser BS, Spruijt E. Probing the surface charge of condensates using microelectrophoresis. Nat Commun 2024; 15:3564. [PMID: 38670952 PMCID: PMC11053090 DOI: 10.1038/s41467-024-47885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Biomolecular condensates play an important role in cellular organization. Coacervates are commonly used models that mimic the physicochemical properties of biomolecular condensates. The surface of condensates plays a key role in governing molecular exchange between condensates, accumulation of species at the interface, and the stability of condensates against coalescence. However, most important surface properties, including the surface charge and zeta potential, remain poorly characterized and understood. The zeta potential of coacervates is often measured using laser doppler electrophoresis, which assumes a size-independent electrophoretic mobility. Here, we show that this assumption is incorrect for liquid-like condensates and present an alternative method to study the electrophoretic mobility of coacervates and in vitro condensate models by microelectrophoresis and single-particle tracking. Coacervates have a size-dependent electrophoretic mobility, originating from their fluid nature, from which a well-defined zeta potential is calculated. Interestingly, microelectrophoresis measurements reveal that polylysine chains are enriched at the surface of polylysine/polyaspartic acid complex coacervates, which causes the negatively charged protein ɑ-synuclein to adsorb and accumulate at the interface. Addition of ATP inverts the surface charge, displaces ɑ-synuclein from the surface and may help to suppress its interface-catalyzed aggregation. Together, these findings show how condensate surface charge can be measured and altered, making this microelectrophoresis platform combined with automated single-particle tracking a promising characterization technique for both biomolecular condensates and coacervate protocells.
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Affiliation(s)
- Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6523, AJ, Nijmegen, The Netherlands
| | - Brent S Visser
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6523, AJ, Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6523, AJ, Nijmegen, The Netherlands.
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2
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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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3
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Wang J, Abbas M, Wang J, Spruijt E. Selective amide bond formation in redox-active coacervate protocells. Nat Commun 2023; 14:8492. [PMID: 38129391 PMCID: PMC10739716 DOI: 10.1038/s41467-023-44284-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Coacervate droplets are promising protocell models because they sequester a wide range of guest molecules and may catalyze their conversion. However, it remains unclear how life's building blocks, including peptides, could be synthesized from primitive precursor molecules inside such protocells. Here, we develop a redox-active protocell model formed by phase separation of prebiotically relevant ferricyanide (Fe(CN)63-) molecules and cationic peptides. Their assembly into coacervates can be regulated by redox chemistry and the coacervates act as oxidizing hubs for sequestered metabolites, like NAD(P)H and gluthathione. Interestingly, the oxidizing potential of Fe(CN)63- inside coacervates can be harnessed to drive the formation of new amide bonds between prebiotically relevant amino acids and α-amidothioacids. Aminoacylation is enhanced in Fe(CN)63-/peptide coacervates and selective for amino acids that interact less strongly with the coacervates. We finally use Fe(CN)63--containing coacervates to spatially control assembly of fibrous networks inside and at the surface of coacervate protocells. These results provide an important step towards the prebiotically relevant integration of redox chemistry in primitive cell-like compartments.
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Affiliation(s)
- Jiahua Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Department of Radiology, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Manzar Abbas
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Junyou Wang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
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4
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Lu T, Javed S, Bonfio C, Spruijt E. Interfacing Coacervates with Membranes: From Artificial Organelles and Hybrid Protocells to Intracellular Delivery. Small Methods 2023; 7:e2300294. [PMID: 37354057 DOI: 10.1002/smtd.202300294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Compartmentalization is crucial for the functioning of cells. Membranes enclose and protect the cell, regulate the transport of molecules entering and exiting the cell, and organize cellular machinery in subcompartments. In addition, membraneless condensates, or coacervates, offer dynamic compartments that act as biomolecular storage centers, organizational hubs, or reaction crucibles. Emerging evidence shows that phase-separated membraneless bodies in the cell are involved in a wide range of functional interactions with cellular membranes, leading to transmembrane signaling, membrane remodeling, intracellular transport, and vesicle formation. Such functional and dynamic interplay between phase-separated droplets and membranes also offers many potential benefits to artificial cells, as shown by recent studies involving coacervates and liposomes. Depending on the relative sizes and interaction strength between coacervates and membranes, coacervates can serve as artificial membraneless organelles inside liposomes, as templates for membrane assembly and hybrid artificial cell formation, as membrane remodelers for tubulation and possibly division, and finally, as cargo containers for transport and delivery of biomolecules across membranes by endocytosis or direct membrane crossing. Here, recent experimental examples of each of these functions are reviewed and the underlying physicochemical principles and possible future applications are discussed.
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Affiliation(s)
- Tiemei Lu
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
| | - Sadaf Javed
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
| | - Claudia Bonfio
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, Strasbourg, 67083, France
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
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5
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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6
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Lu T, Hu X, van Haren MHI, Spruijt E, Huck WTS. Structure-Property Relationships Governing Membrane-Penetrating Behaviour of Complex Coacervates. Small 2023; 19:e2303138. [PMID: 37218010 DOI: 10.1002/smll.202303138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Indexed: 05/24/2023]
Abstract
Complex coacervates are phase-separated liquid droplets composed of oppositely charged multivalent molecules. The unique material properties of the complex coacervate interior favours the sequestration of biomolecules and facilitates reactions. Recently, it is shown that coacervates can be used for direct cytosolic delivery of sequestered biomolecules in living cells. Here, it is studied that the physical properties required for complex coacervates composed of oligo-arginine and RNA to cross phospholipid bilayers and enter liposomes penetration depends on two main parameters: the difference in ζ-potential between the complex coacervates and the liposomes, and the partitioning coefficient (Kp ) of lipids into the complex coacervates. Following these guidelines, a range of complex coacervates is found that is able to penetrate the membrane of living cells, thus paving the way for further development of coacervates as delivery vehicles of therapeutic agents.
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Affiliation(s)
- Tiemei Lu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, the Netherlands
| | - Xinyu Hu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, the Netherlands
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, the Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, the Netherlands
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7
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Wang J, Lu T, Li Y, Wang J, Spruijt E. Aqueous coordination polymer complexes: From colloidal assemblies to bulk materials. Adv Colloid Interface Sci 2023; 318:102964. [PMID: 37515864 DOI: 10.1016/j.cis.2023.102964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/19/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
1-dimensional (1D) coordination polymers refer to the macromolecules that have metal ions incorporated in their pendent groups or main chain through metal-binding ligand groups. They have intrinsic advantages over traditional polymers to regulate the polymer structures and functions owing to the nature of the metal-ligand bond. Consequently, they have great potential for the development of smart and functional structures and materials and therapeutic agents. Water-soluble 1D coordination polymers and assemblies are an important subtype of coordination polymers with distinctive interests for demanding applications in aqueous systems, such as biological and medical applications. This review highlights the recent progress and research achievements in the design and use of water-soluble 1D coordination polymers and assemblies. The overview covers the design and structure control of 1D coordination polymers, their colloidal assemblies, including nanoparticles, nanofibers, micelles and vesicles, and fabricated bulk materials such as membraneless liquid condensates, security ink, hydrogel actuators, and smart fabrics. Finally, we discuss the potential applications of several of these coordination polymeric structures and materials and give an outlook on the field of aqueous coordination polymers.
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Affiliation(s)
- Jiahua Wang
- Department of Radiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China; Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Tiemei Lu
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Yuehua Li
- Department of Radiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Junyou Wang
- State Key Laboratory of Chemical Engineering and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
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8
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Schoenmakers LLJ, Yewdall NA, Lu T, André AAM, Nelissen FHT, Spruijt E, Huck WTS. In Vitro Transcription-Translation in an Artificial Biomolecular Condensate. ACS Synth Biol 2023. [PMID: 37343188 PMCID: PMC10393115 DOI: 10.1021/acssynbio.3c00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Biomolecular condensates are a promising platform for synthetic cell formation and constitute a potential missing link between the chemical and cellular stage of the origins of life. However, it has proven challenging to integrate complex reaction networks into biomolecular condensates, such as a cell-free in vitro transcription-translation (IVTT) system. Integrating IVTT into biomolecular condensates successfully is one precondition for condensation-based synthetic cell formation. Moreover, it would provide a proof of concept that biomolecular condensates are in principle compatible with the central dogma, one of the hallmarks of cellular life. Here, we have systemically investigated the compatibility of eight different (bio)molecular condensates with IVTT incorporation. Of these eight candidates, we have found that a green fluorescent protein-labeled, intrinsically disordered cationic protein (GFP-K72) and single-stranded DNA (ssDNA) can form biomolecular condensates that are compatible with up to μM fluorescent protein expression. This shows that biomolecular condensates can indeed integrate complex reaction networks, confirming their use as synthetic cell platforms and hinting at a possible role in the origin of life.
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Affiliation(s)
- Ludo L J Schoenmakers
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Tiemei Lu
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Alain A M André
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
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9
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Joosten J, van Sluijs B, Vree Egberts W, Emmaneel M, W T C Jansen P, Vermeulen M, Boelens W, Bonger KM, Spruijt E. Dynamics and composition of small heat shock protein condensates and aggregates. J Mol Biol 2023; 435:168139. [PMID: 37146746 DOI: 10.1016/j.jmb.2023.168139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
Small heat shock proteins (sHSPs) are essential ATP-independent chaperones that protect the cellular proteome. These proteins assemble into polydisperse oligomeric structures, the composition of which dramatically affects their chaperone activity. The biomolecular consequences of variations in sHSP ratios, especially inside living cells, remain elusive. Here, we study the consequences of altering the relative expression levels of HspB2 and HspB3 in HEK293T cells. These chaperones are partners in a hetero-oligomeric complex, and genetic mutations that abolish their mutual interaction are associated with myopathic disorders. HspB2 displays three distinct phenotypes when co-expressed with HspB3 at varying ratios. Expression of HspB2 alone leads to formation of liquid nuclear condensates, while shifting the stoichiometry towards HspB3 resulted in the formation of large solid-like aggregates. Only cells co-expressing HspB2 with a limited amount of HspB3 formed fully soluble complexes that were distributed homogeneously throughout the nucleus. Strikingly, both condensates and aggregates were reversible, as shifting the HspB2:HspB3 balance in situ resulted in dissolution of these structures. To uncover the molecular composition of HspB2 condensates and aggregates, we used APEX-mediated proximity labelling. Most proteins interact transiently with the condensates and were neither enriched nor depleted in these cells. In contrast, we found that HspB2:HspB3 aggregates sequestered several disordered proteins and autophagy factors, suggesting that the cell is actively attempting to clear these aggregates. This study presents a striking example of how changes in the relative expression levels of interacting proteins affects their phase behavior. Our approach could be applied to study the role of protein stoichiometry and the influence of client binding on phase behavior in other biomolecular condensates and aggregates.
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Affiliation(s)
- Joep Joosten
- Biomolecular Chemistry, Radboud University Institute for Molecular and Materials, Nijmegen, the Netherlands; Physical Organic Chemistry, Radboud University Institute for Molecular and Materials, Nijmegen, the Netherlands; Synthetic Organic Chemistry, Radboud University Institute for Molecular and Materials, the Netherlands.
| | - Bob van Sluijs
- Physical Organic Chemistry, Radboud University Institute for Molecular and Materials, Nijmegen, the Netherlands
| | - Wilma Vree Egberts
- Biomolecular Chemistry, Radboud University Institute for Molecular and Materials, Nijmegen, the Netherlands
| | - Martin Emmaneel
- Biomolecular Chemistry, Radboud University Institute for Molecular and Materials, Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Molecular Biology, Radboud University Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Molecular Biology, Radboud University Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Wilbert Boelens
- Biomolecular Chemistry, Radboud University Institute for Molecular and Materials, Nijmegen, the Netherlands
| | - Kimberly M Bonger
- Synthetic Organic Chemistry, Radboud University Institute for Molecular and Materials, the Netherlands
| | - Evan Spruijt
- Physical Organic Chemistry, Radboud University Institute for Molecular and Materials, Nijmegen, the Netherlands
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10
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André AAM, Yewdall NA, Spruijt E. Crowding-induced phase separation and gelling by co-condensation of PEG in NPM1-rRNA condensates. Biophys J 2023; 122:397-407. [PMID: 36463407 PMCID: PMC9892608 DOI: 10.1016/j.bpj.2022.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The crowdedness of the cell calls for adequate intracellular organization. Biomolecular condensates, formed by liquid-liquid phase separation of intrinsically disordered proteins and nucleic acids, are important organizers of cellular fluids. To underpin the molecular mechanisms of protein condensation, cell-free studies are often used where the role of crowding is not investigated in detail. Here, we investigate the effects of macromolecular crowding on the formation and material properties of a model heterotypic biomolecular condensate, consisting of nucleophosmin (NPM1) and ribosomal RNA (rRNA). We studied the effect of the macromolecular crowding agent poly(ethylene glycol) (PEG), which is often considered an inert crowding agent. We observed that PEG could induce both homotypic and heterotypic phase separation of NPM1 and NPM1-rRNA, respectively. Crowding increases the condensed concentration of NPM1 and decreases its equilibrium dilute phase concentration, although no significant change in the concentration of rRNA in the dilute phase was observed. Interestingly, the crowder itself is concentrated in the condensates, suggesting that co-condensation rather than excluded volume interactions underlie the enhanced phase separation by PEG. Fluorescence recovery after photobleaching measurements indicated that both NPM1 and rRNA become immobile at high PEG concentrations, indicative of a liquid-to-gel transition. Together, these results provide more insight into the role of synthetic crowding agents in phase separation and demonstrate that condensate properties determined in vitro depend strongly on the addition of crowding agents.
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Affiliation(s)
- Alain A M André
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
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11
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Lipiński WP, Visser BS, Robu I, Fakhree MAA, Lindhoud S, Claessens MMAE, Spruijt E. Biomolecular condensates can both accelerate and suppress aggregation of α-synuclein. Sci Adv 2022; 8:eabq6495. [PMID: 36459561 PMCID: PMC10942789 DOI: 10.1126/sciadv.abq6495] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
Biomolecular condensates present in cells can fundamentally affect the aggregation of amyloidogenic proteins and play a role in the regulation of this process. While liquid-liquid phase separation of amyloidogenic proteins by themselves can act as an alternative nucleation pathway, interaction of partly disordered aggregation-prone proteins with preexisting condensates that act as localization centers could be a far more general mechanism of altering their aggregation behavior. Here, we show that so-called host biomolecular condensates can both accelerate and slow down amyloid formation. We study the amyloidogenic protein α-synuclein and two truncated α-synuclein variants in the presence of three types of condensates composed of nonaggregating peptides, RNA, or ATP. Our results demonstrate that condensates can markedly speed up amyloid formation when proteins localize to their interface. However, condensates can also significantly suppress aggregation by sequestering and stabilizing amyloidogenic proteins, thereby providing living cells with a possible protection mechanism against amyloid formation.
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Affiliation(s)
- Wojciech P. Lipiński
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Brent S. Visser
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Irina Robu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Mohammad A. A. Fakhree
- Nanobiophysics, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, Netherlands
| | - Saskia Lindhoud
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
| | - Mireille M. A. E. Claessens
- Nanobiophysics, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
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12
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Yewdall NA, André AAM, van Haren MHI, Nelissen FHT, Jonker A, Spruijt E. ATP:Mg 2+ shapes material properties of protein-RNA condensates and their partitioning of clients. Biophys J 2022; 121:3962-3974. [PMID: 36004782 PMCID: PMC9674983 DOI: 10.1016/j.bpj.2022.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/29/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022] Open
Abstract
Many cellular condensates are heterotypic mixtures of proteins and RNA formed in complex environments. Magnesium ions (Mg2+) and ATP can impact RNA folding, and local intracellular levels of these factors can vary significantly. However, the effect of ATP:Mg2+ on the material properties of protein-RNA condensates is largely unknown. Here, we use an in vitro condensate model of nucleoli, made from nucleophosmin 1 (NPM1) proteins and ribosomal RNA (rRNA), to study the effect of ATP:Mg2+. While NPM1 dynamics remain unchanged at increasing Mg2+ concentrations, the internal RNA dynamics dramatically slowed until a critical point, where gel-like states appeared, suggesting the RNA component alone forms a viscoelastic network that undergoes maturation driven by weak multivalent interactions. ATP reverses this arrest and liquefies the gel-like structures. ATP:Mg2+ also influenced the NPM1-rRNA composition of condensates and enhanced the partitioning of two clients: an arginine-rich peptide and a small nuclear RNA. By contrast, larger ribosome partitioning shows dependence on ATP:Mg2+ and can become reversibly trapped around NPM1-rRNA condensates. Lastly, we show that dissipative enzymatic reactions that deplete ATP can be used to control the shape, composition, and function of condensates. Our results illustrate how intracellular environments may regulate the state and client partitioning of RNA-containing condensates.
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Affiliation(s)
- N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
| | - Alain A M André
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Aafke Jonker
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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13
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Castaño Osorio S, Biesheuvel PM, Spruijt E, Dykstra JE, van der Wal A. Modeling micropollutant removal by nanofiltration and reverse osmosis membranes: considerations and challenges. Water Res 2022; 225:119130. [PMID: 36240724 DOI: 10.1016/j.watres.2022.119130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Organic micropollutants (OMPs) in drinking water constitute a potential risk to human health; therefore, effective removal of these pollutants is required. Nanofiltration (NF) and reverse osmosis (RO) are promising membrane-based technologies to remove OMPs. In NF and RO, the rejection of OMPs depends on the properties and characteristics of the membrane, the solute, and the solution. In this review, we discuss how these properties can be included in models to study and predict the rejection of OMPs. Initially, an OMP classification is proposed to capture the relevant properties of 58 OMPs. Following the methodology described in this study, more and new OMPs can be easily included in this classification. The classification aims to increase the comprehension and mechanistic understanding of OMP removal. Based on the physicochemical principles used to classify the 58 OMPs, it is expected that other OMPs in the same groups will be similarly rejected. From this classification, we present an overview of the rejection mechanisms involved in the removal of specific OMP groups. For instance, we discuss the removal of OMPs classified as perfluoroalkyl substances (e.g., perfluorooctanoic acid, PFOA). These substances are highly relevant due to their human toxicity at extremely low concentration as well as their persistence and omnipresence in the environment. Finally, we discuss how the rejection of OMPs can be predicted by describing both the membrane-solution interface and calculating the transport of solutes inside the membrane. We illustrate the importance and impact of different rejection mechanisms and interfacial phenomena on OMP removal and propose an extended Nernst-Plank equation to calculate the transport of solutes across the membrane due to convection, diffusion, and electromigration. Finally, we show how the theory discussed in this review leads to improved predictions of OMP rejection by the membranes.
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Affiliation(s)
- S Castaño Osorio
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, Leeuwarden 8911 MA, the Netherlands; Environmental Technology, Wageningen University & Research, P.O. Box 17, Wageningen 6700 AA, the Netherlands
| | - P M Biesheuvel
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, Leeuwarden 8911 MA, the Netherlands
| | - E Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - J E Dykstra
- Environmental Technology, Wageningen University & Research, P.O. Box 17, Wageningen 6700 AA, the Netherlands.
| | - A van der Wal
- Environmental Technology, Wageningen University & Research, P.O. Box 17, Wageningen 6700 AA, the Netherlands; Evides Water Company, P.O. Box 4472, Rotterdam 3006 AL, the Netherlands.
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14
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Slootbeek AD, van Haren MHI, Smokers IBA, Spruijt E. Growth, replication and division enable evolution of coacervate protocells. Chem Commun (Camb) 2022; 58:11183-11200. [PMID: 36128910 PMCID: PMC9536485 DOI: 10.1039/d2cc03541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
Living and proliferating cells undergo repeated cycles of growth, replication and division, all orchestrated by complex molecular networks. How a minimal cell cycle emerged and helped primitive cells to evolve remains one of the biggest mysteries in modern science, and is an active area of research in chemistry. Protocells are cell-like compartments that recapitulate features of living cells and may be seen as the chemical ancestors of modern life. While compartmentalization is not strictly required for primitive, open-ended evolution of self-replicating systems, it gives such systems a clear identity by setting the boundaries and it can help them overcome three major obstacles of dilution, parasitism and compatibility. Compartmentalization is therefore widely considered to be a central hallmark of primitive life, and various types of protocells are actively investigated, with the ultimate goal of developing a protocell capable of autonomous proliferation by mimicking the well-known cell cycle of growth, replication and division. We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are. Considerations are given for designing chemical networks in coacervates that can lead to sustained growth, selective replication and controlled division, in a way that they are linked together like in the cell cycle. Ultimately, such a system may undergo evolution by natural selection of certain phenotypes, leading to adaptation and the gain of new functions, and we end with a brief discussion of the opportunities for coacervates to facilitate this.
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Affiliation(s)
- Annemiek D Slootbeek
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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15
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Abbas M, Law JO, Grellscheid SN, Huck WTS, Spruijt E. Peptide-Based Coacervate-Core Vesicles with Semipermeable Membranes. Adv Mater 2022; 34:e2202913. [PMID: 35796384 DOI: 10.1002/adma.202202913] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Coacervates droplets have long been considered as potential protocells to mimic living cells. However, these droplets lack a membrane and are prone to coalescence, limiting their ability to survive, interact, and organize into higher-order assemblies. This work shows that tyrosine-rich peptide conjugates can undergo liquid-liquid phase separation in a well-defined pH window and transform into stable membrane-enclosed protocells by enzymatic oxidation and cross-linking at the liquid-liquid interface. The oxidation of the tyrosine-rich peptides into dityrosine creates a semipermeable, flexible membrane around the coacervates with tunable thickness, which displays strong intrinsic fluorescence, and stabilizes the coacervate protocells against coalescence. The membranes have an effective molecular weight cut-off of 2.5 kDa, as determined from the partitioning of small dyes and labeled peptides, RNA, and polymers into the membrane-enclosed coacervate protocells. Flicker spectroscopy reveals a membrane bending rigidity of only 0.1kB T, which is substantially lower than phospholipid bilayers despite a larger membrane thickness. Finally, it is shown that enzymes can be stably encapsulated inside the protocells and be supplied with substrates from outside, which opens the way for these membrane-bound compartments to be used as molecularly crowded artificial cells capable of communication or as a vehicle for drug delivery.
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Affiliation(s)
- Manzar Abbas
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Jack O Law
- Computational Biology Unit, University of Bergen, Bergen, 5020, Norway
| | - Sushma N Grellscheid
- Computational Biology Unit, University of Bergen, Bergen, 5020, Norway
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
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16
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Abstract
Recent studies have shown that the interactions between condensates and biological membranes are of functional importance. Here, we study how the interaction between complex coacervates and liposomes as model systems can lead to wetting, membrane deformation, and endocytosis. Depending on the interaction strength between coacervates and liposomes, the wetting behavior ranged from nonwetting to engulfment (endocytosis) and complete wetting. Endocytosis of coacervates was found to be a general phenomenon: coacervates made from a wide range of components could be taken up by liposomes. A simple theory taking into account surface energies and coacervate sizes can explain the observed morphologies. Our findings can help to better understand condensate-membrane interactions in cellular systems and provide new avenues for intracellular delivery using coacervates.
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Affiliation(s)
- Tiemei Lu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Susanne Liese
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
| | - Ludo Schoenmakers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Christoph A Weber
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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17
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Smokers IBA, van Haren MHI, Lu T, Spruijt E. Complex Coacervation and Compartmentalized Conversion of Prebiotically Relevant Metabolites. ChemSystemsChem 2022. [DOI: 10.1002/syst.202200017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Iris B. A. Smokers
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Merlijn H. I. van Haren
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Tiemei Lu
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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18
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Smokers IBA, van Haren MHI, Lu T, Spruijt E. Front Cover: Complex Coacervation and Compartmentalized Conversion of Prebiotically Relevant Metabolites (ChemSystemsChem 4/2022). ChemSystemsChem 2022. [DOI: 10.1002/syst.202200018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Iris B. A. Smokers
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6523 AJ Nijmegen The Netherlands
| | - Merlijn H. I. van Haren
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6523 AJ Nijmegen The Netherlands
| | - Tiemei Lu
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6523 AJ Nijmegen The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6523 AJ Nijmegen The Netherlands
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19
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Smokers IBA, van Haren MHI, Lu T, Spruijt E. Complex coacervation and compartmentalized conversion of prebiotically relevant metabolites. ChemSystemsChem 2022. [DOI: 10.1002/syst.202200004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Iris B. A. Smokers
- Radboud University Nijmegen: Radboud Universiteit Institute for Molecules and Materials NETHERLANDS
| | | | - Tiemei Lu
- Radboud University Nijmegen: Radboud Universiteit Institute for Molecules and Materials NETHERLANDS
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20
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Affiliation(s)
- Lili Zhou
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190
- University of Chinese Academy of Sciences, Beijing 100049
| | - Yaxun Fan
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190
| | - Zhang Liu
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190
| | - Lina Chen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen
| | - Yilin Wang
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190
- University of Chinese Academy of Sciences, Beijing 100049
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21
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Abbas M, Lipiński WP, Nakashima KK, Huck WTS, Spruijt E. A short peptide synthon for liquid-liquid phase separation. Nat Chem 2021; 13:1046-1054. [PMID: 34645986 DOI: 10.1038/s41557-021-00788-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Liquid-liquid phase separation of disordered proteins has emerged as a ubiquitous route to membraneless compartments in living cells, and similar coacervates may have played a role when the first cells formed. However, existing coacervates are typically made of multiple macromolecular components, and designing short peptide analogues capable of self-coacervation has proven difficult. Here we present a short peptide synthon for phase separation, made of only two dipeptide stickers linked via a flexible, hydrophilic spacer. These small-molecule compounds self-coacervate into micrometre-sized liquid droplets at sub-millimolar concentrations, which retain up to 75 wt% water. The design is general and we derive guidelines for the required sticker hydrophobicity and spacer polarity. To illustrate their potential as protocells, we create a disulfide-linked derivative that undergoes reversible compartmentalization controlled by redox chemistry. The resulting coacervates sequester and melt nucleic acids, and act as microreactors that catalyse two different anabolic reactions yielding molecules of increasing complexity. This provides a stepping stone for new coacervate-based protocells made of single peptide species.
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Affiliation(s)
- Manzar Abbas
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Wojciech P Lipiński
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Karina K Nakashima
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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22
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Nakashima KK, van Haren MHI, André AAM, Robu I, Spruijt E. Active coacervate droplets are protocells that grow and resist Ostwald ripening. Nat Commun 2021; 12:3819. [PMID: 34155210 PMCID: PMC8217494 DOI: 10.1038/s41467-021-24111-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/03/2021] [Indexed: 11/26/2022] Open
Abstract
Active coacervate droplets are liquid condensates coupled to a chemical reaction that turns over their components, keeping the droplets out of equilibrium. This turnover can be used to drive active processes such as growth, and provide an insight into the chemical requirements underlying (proto)cellular behaviour. Moreover, controlled growth is a key requirement to achieve population fitness and survival. Here we present a minimal, nucleotide-based coacervate model for active droplets, and report three key findings that make these droplets into evolvable protocells. First, we show that coacervate droplets form and grow by the fuel-driven synthesis of new coacervate material. Second, we find that these droplets do not undergo Ostwald ripening, which we attribute to the attractive electrostatic interactions and translational entropy within complex coacervates, active or passive. Finally, we show that the droplet growth rate reflects experimental conditions such as substrate, enzyme and protein concentration, and that a different droplet composition (addition of RNA) leads to altered growth rates and droplet fitness. These findings together make active coacervate droplets a powerful platform to mimic cellular growth at a single-droplet level, and to study fitness at a population level.
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Affiliation(s)
- Karina K Nakashima
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Alain A M André
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Irina Robu
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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23
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24
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Abstract
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Coacervates are a
type of liquid–liquid phase separated
(LLPS) droplets that can serve as models of membraneless organelles
(MLOs) in living cells. Peptide–nucleotide coacervates have
been widely used to mimic properties of ribonucleoprotein (RNP) granules,
but the thermal stability and the role of base stacking is still poorly
understood. Here, we report a systematic investigation of coacervates
formed by five different nucleoside triphosphates (NTPs) with poly-l-lysine and poly-l-arginine as a function of temperature.
All studied combinations exhibit an upper critical solution temperature
(UCST), and a temperature-dependent critical salt concentration, originating
from a significant nonelectrostatic contribution to the mixing free
energy. Both the enthalpic and entropic parts of this nonelectrostatic
interaction decrease in the order G/A/U/C/T, in accordance with nucleobase
stacking free energies. Partitioning of two dyes proves that the local
hydrophobicity inside the peptide–nucleotide coacervates is
different for every nucleoside triphosphate. We derive a simple relation
between the temperature and salt concentration at the critical point
based on a mean-field model of phase separation. Finally, when different
NTPs are mixed with one common oppositely charged peptide, hybrid
coacervates were formed, characterized by a single intermediate UCST
and critical salt concentration. NTPs with lower critical salt concentrations
can remain condensed in mixed coacervates far beyond their original
critical salt concentration. Our results show that NTP-based coacervates
have a strong temperature sensitivity due to base stacking interactions
and that mixing NTPs can significantly influence the stability of
condensates and, by extension, their bioavailability.
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Affiliation(s)
- Tiemei Lu
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Karina K Nakashima
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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25
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Abstract
Coacervates are condensed liquid-like droplets formed by liquid-liquid phase separation of molecules through multiple weak associative interactions. In recent years it has emerged that not only long polymers, but also short peptides are capable of forming simple and complex coacervates. The coacervate droplets they form act as compartments that sequester and concentrate a wide range of solutes, and their spontaneous formation make coacervates attractive protocell models. The main advantage of peptides as building blocks lies in the functional diversity of the amino acid residues, which allows for tailoring of the peptide's phase separation propensity, their selectivity in guest molecule uptake and the physicochemical and catalytic properties of the compartments. The aim of this tutorial review is to illustrate the recent developments in the field of peptide-based coacervates in a systematic way and to deduce the basic requirements for both simple and complex coacervation of peptides. We review a selection of peptide coacervates that illustrates the essentials of phase separation, the limitations, and the properties that make peptide coacervates biomimetic protocells. Finally, we provide some perspectives of this novel research field in the direction of active droplets, moving away from thermodynamic equilibrium.
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Affiliation(s)
- Manzar Abbas
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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26
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Vibhute MA, Schaap MH, Maas RJM, Nelissen FHT, Spruijt E, Heus HA, Hansen MMK, Huck WTS. Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions. ACS Synth Biol 2020; 9:2797-2807. [PMID: 32976714 PMCID: PMC7573978 DOI: 10.1021/acssynbio.0c00330] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
The formation of
cytomimetic protocells that capture the physicochemical
aspects of living cells is an important goal in bottom-up synthetic
biology. Here, we recreated the crowded cytoplasm in liposome-based
protocells and studied the kinetics of cell-free gene expression in
these crowded containers. We found that diffusion of key components
is affected not only by macromolecular crowding but also by enzymatic
activity in the protocell. Surprisingly, size-dependent diffusion
in crowded conditions yielded two distinct maxima for protein synthesis,
reflecting the differential impact of crowding on transcription and
translation. Our experimental data show, for the first time, that
macromolecular crowding induces a switch from reaction to diffusion
control and that this switch depends on the sizes of the macromolecules
involved. These results highlight the need to control the physical
environment in the design of synthetic cells.
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Affiliation(s)
- Mahesh A. Vibhute
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mark H. Schaap
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roel J. M. Maas
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Frank H. T. Nelissen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maike M. K. Hansen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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27
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Abstract
The discovery of membraneless organelles (MLOs) formed by liquid-liquid phase separation raised many questions about the spatial organization of biomolecular processes in cells, but also offered a new tool to mimic cellular media. Since disordered and charged protein domains are often necessary for phase separation, coacervates can be used as models both to understand MLO regulation and to develop dynamic cellular-like compartments. A versatile way to turn passive coacervate droplets into active and dynamic compartments is by introducing enzymatic reactions that affect parameters relevant for complex coacervation, such as the charge and length of the components. However, these reactions strictly take place in a heterogeneous medium, and the complexity thereof is hardly addressed, making it difficult to achieve true control. In this chapter we help close this gap by describing two coacervate systems in which enzymatic reactions endow coacervate droplets with a dynamic character. We further highlight the technical challenges posed by the two-phase systems and strategies to overcome them.
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Affiliation(s)
- Karina K Nakashima
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Alain A M André
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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28
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Abstract
Bidisperse mixtures of charged nanoparticles form separate layers upon centrifugation as a result of minimization of the system's free energy in sedimentation-diffusion equilibrium. Different factors were investigated experimentally for their effects on the layering, and are supported by theoretical calculations of the full sedimentation profiles. Surprisingly, lighter/smaller nanoparticles can even sink below heavier/larger ones when the particle surface charge is carefully tuned. This study provides deeper insights into the control of layering in polydisperse particle mixtures during sedimentation.
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Affiliation(s)
- Xufeng Xu
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5612 AE Eindhoven, The Netherlands.
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29
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Ajao V, Nam K, Chatzopoulos P, Spruijt E, Bruning H, Rijnaarts H, Temmink H. Regeneration and reuse of microbial extracellular polymers immobilised on a bed column for heavy metal recovery. Water Res 2020; 171:115472. [PMID: 31931379 DOI: 10.1016/j.watres.2020.115472] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Microbial extracellular polymeric substances (EPS) have gained increasing attention for various water treatment applications. In this study, EPS produced from nitrogen-limited glycerol/ethanol-rich wastewater were used to recover Cu2+ and Pb2+ from aqueous solutions. Continuous flow-through tests were conducted on a column packed with silica gel coated with polyethyleneimine, to which EPS were irreversibly attached as shown by optical reflectometry. These immobilised EPS excellently adsorbed Cu2+ and Pb2+, with 99.9% of influent metal adsorbed before the breakthrough points. Metal desorption was achieved with 0.1M HCl, with an average recovery of 86% for Cu2+ and 90% recovery for Pb2+. For the first time, we successfully showed the possibility to regenerate and reuse the immobilised EPS for five adsorption-desorption cycles (using Cu2+ as an example) with no reduction in the adsorbed amount at the breakthrough point (qbp). Based on the mass balance of the associated metal ions participating in the adsorption process, ion exchange was identified as the major mechanism responsible for Cu2+ and Pb2+ adsorption by EPS. The results demonstrate the potential of wastewater-produced EPS as an attractive and perhaps, cost-effective biosorbent for heavy metal removal (to trace effluent concentrations) and recovery (86-99%).
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Affiliation(s)
- Victor Ajao
- Wetsus - European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, the Netherlands; Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands.
| | - Kang Nam
- School of Life Sciences and Environmental Technology, Avans University of Applied Science, Breda, the Netherlands
| | - Paraschos Chatzopoulos
- Wetsus - European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Harry Bruning
- Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
| | - Huub Rijnaarts
- Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
| | - Hardy Temmink
- Wetsus - European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, the Netherlands; Sub-department of Environmental Technology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, the Netherlands
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30
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Abstract
Liquid-liquid phase separation plays an important role in cellular organization. Many subcellular condensed bodies are hierarchically organized into multiple coexisting domains or layers. However, our molecular understanding of the assembly and internal organization of these multicomponent droplets is still incomplete, and rules for the coexistence of condensed phases are lacking. Here, we show that the formation of hierarchically organized multiphase droplets with up to three coexisting layers is a generic phenomenon in mixtures of complex coacervates, which serve as models of charge-driven liquid-liquid phase separated systems. We present simple theoretical guidelines to explain both the hierarchical arrangement and the demixing transition in multiphase droplets using the interfacial tensions and critical salt concentration as inputs. Multiple coacervates can coexist if they differ sufficiently in macromolecular density, and we show that the associated differences in critical salt concentration can be used to predict multiphase droplet formation. We also show that the coexisting coacervates present distinct chemical environments that can concentrate guest molecules to different extents. Our findings suggest that condensate immiscibility may be a very general feature in biological systems, which could be exploited to design self-organized synthetic compartments to control biomolecular processes.
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Affiliation(s)
- Tiemei Lu
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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31
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Abstract
Biochemical processes inside the cell take place in a complex environment that is highly crowded, heterogeneous, and replete with interfaces. The recently recognized importance of biomolecular condensates in cellular organization has added new elements of complexity to our understanding of chemistry in the cell. Many of these condensates are formed by liquid-liquid phase separation (LLPS) and behave like liquid droplets. Such droplet organelles can be reproduced and studied in vitro by using coacervates and have some remarkable features, including regulated assembly, differential partitioning of macromolecules, permeability to small molecules, and a uniquely crowded environment. Here, we review the main principles of biochemical organization in model membraneless compartments. We focus on some promising in vitro coacervate model systems that aptly mimic part of the compartmentalized cellular environment. We address the physicochemical characteristics of these liquid phase separated compartments, and their impact on biomolecular chemistry and assembly. These model systems enable a systematic investigation of the role of spatiotemporal organization of biomolecules in controlling biochemical processes in the cell, and they provide crucial insights for the development of functional artificial organelles and cells.
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Affiliation(s)
| | | | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, Netherlands
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32
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Virga E, Spruijt E, de Vos WM, Biesheuvel PM. Wettability of Amphoteric Surfaces: The Effect of pH and Ionic Strength on Surface Ionization and Wetting. Langmuir 2018; 34:15174-15180. [PMID: 30427683 PMCID: PMC6328277 DOI: 10.1021/acs.langmuir.8b02875] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/11/2018] [Indexed: 06/09/2023]
Abstract
We present a novel theory to predict the contact angle of water on amphoteric surfaces, as a function of pH and ionic strength. To validate our theory, experiments were performed on two commonly used amphoteric materials, alumina (Al2O3) and titania (TiO2). We find good agreement at all pH values, and at different salt concentrations. With increasing salt concentration, the theory predicts the contact angle-pH curve to get steeper, while keeping the same contact angle at pH = PZC (point of zero charge), in agreement with data. Our model is based on the amphoteric 1-p K model and includes the electrostatic free energy of an aqueous system as well as the surface energy of a droplet in contact with the surface. In addition, we show how our theory suggests the possibility of a novel responsive membrane design, based on amphoteric groups. At pH ∼ PZC, this membrane resists flow of water but at slightly more acidic or basic conditions the wettability of the membrane pores may change sufficiently to allow passage of water and solutes. Moreover, these membranes could act as active sensors that only allow solutions of high ionic strength to flow through in wastewater treatment.
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Affiliation(s)
- Ettore Virga
- Membrane
Science and Technology, University of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
- Wetsus, European
Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911
MA Leeuwarden, The Netherlands
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wiebe M. de Vos
- Membrane
Science and Technology, University of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
| | - P. M. Biesheuvel
- Wetsus, European
Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911
MA Leeuwarden, The Netherlands
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33
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André AAM, Spruijt E. Rigidity Rules in DNA Droplets: Nucleic Acid Flexibility Affects Model Membraneless Organelles. Biophys J 2018; 115:1837-1839. [PMID: 30322797 PMCID: PMC6303229 DOI: 10.1016/j.bpj.2018.09.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Alain A M André
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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34
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Te Brinke E, Groen J, Herrmann A, Heus HA, Rivas G, Spruijt E, Huck WTS. Dissipative adaptation in driven self-assembly leading to self-dividing fibrils. Nat Nanotechnol 2018; 13:849-855. [PMID: 30013214 DOI: 10.1038/s41565-018-0192-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/11/2018] [Indexed: 05/24/2023]
Abstract
Out-of-equilibrium self-assembly of proteins such as actin and tubulin is a key regulatory process controlling cell shape, motion and division. The design of functional nanosystems based on dissipative self-assembly has proven to be remarkably difficult due to a complete lack of control over the spatial and temporal characteristics of the assembly process. Here, we show the dissipative self-assembly of FtsZ protein (a bacterial homologue of tubulin) within coacervate droplets. More specifically, we show how such barrier-free compartments govern the local availability of the energy-rich building block guanosine triphosphate, yielding highly dynamic fibrils. The increased flux of FtsZ monomers at the tips of the fibrils results in localized FtsZ assembly, elongation of the coacervate compartments, followed by division of the fibrils into two. We rationalize the directional growth and division of the fibrils using dissipative reaction-diffusion kinetics and capillary action of the filaments as main inputs. The principle presented here, in which open compartments are used to modulate the rates of dissipative self-assembly by restricting the absorption of energy from the environment, may provide a general route to dissipatively adapting nanosystems exhibiting life-like behaviour.
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Affiliation(s)
- Esra Te Brinke
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Joost Groen
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Andreas Herrmann
- DWI Leibniz Institute for Interactive Materials, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Germán Rivas
- Systems Biochemistry Lab, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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35
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Spruijt E, Tusk SE, Bayley H. DNA scaffolds support stable and uniform peptide nanopores. Nat Nanotechnol 2018; 13:739-745. [PMID: 29808001 DOI: 10.1038/s41565-018-0139-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/04/2018] [Indexed: 05/18/2023]
Abstract
The assembly of peptides into membrane-spanning nanopores might be promoted by scaffolds to pre-organize the structures. Such scaffolds could enable the construction of uniform pores of various sizes and pores with controlled permutations around a central axis. Here, we show that DNA nanostructures can serve as scaffolds to arrange peptides derived from the octameric polysaccharide transporter Wza to form uniform nanopores in planar lipid bilayers. Our ring-shaped DNA scaffold is assembled from short synthetic oligonucleotides that are connected to Wza peptides through flexible linkers. When scaffolded, the Wza peptides form conducting nanopores of which only octamers are stable and of uniform conductance. Removal of the DNA scaffold by cleavage of the linkers leads to a rapid loss of the nanopores from the lipid bilayer, which shows that the scaffold is essential for their stability. The DNA scaffold also adds functionality to the nanopores by enabling reversible and permanent binding of complementary tagged oligonucleotides near the nanopore entrance.
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Affiliation(s)
- Evan Spruijt
- Chemistry Research Laboratory, University of Oxford, Oxford, UK.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Samuel E Tusk
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, UK.
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36
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Abstract
Cells can control the assembly and disassembly of membraneless organelles by enzymatic processes, but similar control has not been achieved in vitro yet. Here we develop ATP-based coacervate droplets as artificial membraneless organelles that can be fully controlled by two cooperating enzymes. Droplets can be generated within a minute following the addition of phosphoenolpyruvate as a substrate, and they can be dissolved within tens of seconds by adding glucose as the second substrate. We show how the rates of droplet generation and dissolution can be tuned by varying the enzyme and substrate concentrations, and we support our findings with a kinetic model of the underlying enzymatic reaction network. As all steps of the coacervate droplet life cycle, including nucleation, coarsening, and dissolution, occur under the same reaction conditions, the cycle can be repeated multiple times. In addition, by carefully balancing the rates of both enzymatic reactions, our system can be programmed to either form or dissolve droplets at specified times, acting as a chemical timer.
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Affiliation(s)
- Karina K Nakashima
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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37
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Hansen MMK, Meijer LHH, Spruijt E, Maas RJM, Rosquelles MV, Groen J, Heus HA, Huck WTS. Macromolecular crowding creates heterogeneous environments of gene expression in picolitre droplets. Nat Nanotechnol 2016; 11:191-7. [PMID: 26501750 PMCID: PMC4740931 DOI: 10.1038/nnano.2015.243] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 09/15/2015] [Indexed: 05/02/2023]
Abstract
Understanding the dynamics of complex enzymatic reactions in highly crowded small volumes is crucial for the development of synthetic minimal cells. Compartmentalized biochemical reactions in cell-sized containers exhibit a degree of randomness due to the small number of molecules involved. However, it is unknown how the physical environment contributes to the stochastic nature of multistep enzymatic processes. Here, we present a robust method to quantify gene expression noise in vitro using droplet microfluidics. We study the changes in stochasticity in the cell-free gene expression of two genes compartmentalized within droplets as a function of DNA copy number and macromolecular crowding. We find that decreased diffusion caused by a crowded environment leads to the spontaneous formation of heterogeneous microenvironments of mRNA as local production rates exceed the diffusion rates of macromolecules. This heterogeneity leads to a higher probability of the molecular machinery staying in the same microenvironment, directly increasing the system's stochasticity.
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Affiliation(s)
- Maike M K Hansen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Lenny H H Meijer
- Eindhoven University of Technology, Institute for Complex Molecular Systems and Computational Biology Group, Eindhoven 5600 MB, The Netherlands
| | - Evan Spruijt
- ESPCI ParisTech, Laboratoire de Physique et Mécanique des Milieux Hétérogènes, UMR 7636 du CNRS, Paris 75005, France
| | - Roel J M Maas
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Marta Ventosa Rosquelles
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Joost Groen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A Heus
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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38
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Spruijt E, Biesheuvel PM, de Vos WM. Adsorption of charged and neutral polymer chains on silica surfaces: the role of electrostatics, volume exclusion, and hydrogen bonding. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:012601. [PMID: 25679636 DOI: 10.1103/physreve.91.012601] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Indexed: 06/04/2023]
Abstract
We develop an off-lattice (continuum) model to describe the adsorption of neutral polymer chains and polyelectrolytes to surfaces. Our continuum description allows taking excluded volume interactions between polymer chains and ions directly into account. To implement those interactions, we use a modified hard-sphere equation of state, adapted for mixtures of connected beads. Our model is applicable to neutral, charged, and ionizable surfaces and polymer chains alike and accounts for polarizability effects of the adsorbed layer and chemical interactions between polymer chains and the surface. We compare our model predictions to data of a classical system for polymer adsorption: neutral poly(N-vinylpyrrolidone) (PVP) on silica surfaces. The model shows that PVP adsorption on silica is driven by surface hydrogen bonding with an effective maximum binding energy of about 1.3k(B)T per PVP segment at low pH. As the pH increases, the Si-OH groups become increasingly dissociated, leading to a lower capacity for H bonding and simultaneous counterion accumulation and volume exclusion close to the surface. Together these effects result in a characteristic adsorption isotherm, with the adsorbed amount dropping sharply at a critical pH. Using this model for adsorption data on silica surfaces cleaned by either a piranha solution or an O(2) plasma, we find that the former have a significantly higher density of silanol groups.
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Affiliation(s)
- Evan Spruijt
- ESPCI ParisTech, Physique et Mécanique des Milieux Hétérogènes, UMR 7636 du CNRS, 10 rue Vauquelin, 75005 Paris, France and Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - P M Biesheuvel
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands and Wageningen University, Laboratory of Physical Chemistry and Colloid Science, Dreijenplein 6, 6703 HB The Netherlands
| | - Wiebe M de Vos
- University of Twente, Membrane Science and Technology, MESA+ Institute of Nanotechnology, P.O. Box 217, 7500 AE Enschede, The Netherlands
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39
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Affiliation(s)
- Evan Spruijt
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Ekaterina Sokolova
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Wilhelm T S Huck
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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40
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Abstract
In this paper we give a general theoretical framework that describes the sedimentation of multicomponent mixtures of particles with sizes ranging from molecules to macroscopic bodies. Both equilibrium sedimentation profiles and the dynamic process of settling, or its converse, creaming, are modeled. Equilibrium profiles are found to be in perfect agreement with experiments. Our model reconciles two apparently contradicting points of view about buoyancy, thereby resolving a long-lived paradox about the correct choice of the buoyant density. On the one hand, the buoyancy force follows necessarily from the suspension density, as it relates to the hydrostatic pressure gradient. On the other hand, sedimentation profiles of colloidal suspensions can be calculated directly using the fluid density as apparent buoyant density in colloidal systems in sedimentation-diffusion equilibrium (SDE) as a result of balancing gravitational and thermodynamic forces. Surprisingly, this balance also holds in multicomponent mixtures. This analysis resolves the ongoing debate of the correct choice of buoyant density (fluid or suspension): both approaches can be used in their own domain. We present calculations of equilibrium sedimentation profiles and dynamic sedimentation that show the consequences of these insights. In bidisperse mixtures of colloids, particles with a lower mass density than the homogeneous suspension will first cream and then settle, whereas particles with a suspension-matched mass density form transient, bimodal particle distributions during sedimentation, which disappear when equilibrium is reached. In all these cases, the centers of the distributions of the particles with the lowest mass density of the two, regardless of their actual mass, will be located in equilibrium above the so-called isopycnic point, a natural consequence of their hard-sphere interactions. We include these interactions using the Boublik-Mansoori-Carnahan-Starling-Leland (BMCSL) equation of state. Finally, we demonstrate that our model is not limited to hard spheres, by extending it to charged spherical particles, and to dumbbells, trimers and short chains of connected beads.
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Affiliation(s)
- E Spruijt
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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41
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Spruijt E, Leermakers FAM, Fokkink R, Schweins R, van Well AA, Cohen Stuart MA, van der Gucht J. Structure and Dynamics of Polyelectrolyte Complex Coacervates Studied by Scattering of Neutrons, X-rays, and Light. Macromolecules 2013. [DOI: 10.1021/ma400132s] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evan Spruijt
- Laboratory of Physical Chemistry
and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB
Wageningen, The Netherlands
| | - Frans A. M. Leermakers
- Laboratory of Physical Chemistry
and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB
Wageningen, The Netherlands
| | - Remco Fokkink
- Laboratory of Physical Chemistry
and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB
Wageningen, The Netherlands
| | - Ralf Schweins
- DS/LSS Group, Institute Laue-Langevin, 6 Rue Jules Horowitz, F-38042 Grenoble
Cedex 9, France, and
| | - Ad A. van Well
- Department
of Radiation Science
and Technology, Delft University of Technology, Mekelweg 15, 2629
JB Delft, The Netherlands
| | - Martien A. Cohen Stuart
- Laboratory of Physical Chemistry
and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB
Wageningen, The Netherlands
| | - Jasper van der Gucht
- Laboratory of Physical Chemistry
and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB
Wageningen, The Netherlands
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42
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Affiliation(s)
- Evan Spruijt
- Laboratory of Physical
Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen,
The Netherlands
| | - Martien A. Cohen Stuart
- Laboratory of Physical
Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen,
The Netherlands
| | - Jasper van der Gucht
- Laboratory of Physical
Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen,
The Netherlands
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43
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Pujari SP, Spruijt E, Cohen Stuart MA, van Rijn CJM, Paulusse JMJ, Zuilhof H. Ultralow adhesion and friction of fluoro-hydro alkyne-derived self-assembled monolayers on H-terminated Si(111). Langmuir 2012; 28:17690-17700. [PMID: 23234602 DOI: 10.1021/la303893u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
New fluorine-containing terminal alkynes were synthesized and self-assembled onto Si(111) substrates to obtain fluorine-containing organic monolayers. The monolayers were analyzed in detail by ellipsometry, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS), static water contact angle measurements (CA), and atomic force microscopy (AFM). The SAMs exhibit excellent hydrophobicity, with static water contact angles of up to 119° and low critical surface tensions of 5-20 mN/m depending on the number of F atoms per molecule. IRRAS confirmed the formation of highly ordered monolayers, as indicated by the antisymmetric and symmetric stretching vibrations of the CH(2) moieties at 2918-2920 and 2850-2851 cm(-1), respectively. Upon increasing the number of fluorine atoms in the alkyne chains from 0 to 17, the adhesion of bare silica probes to the SAMs in air decreases from 11.6 ± 0.20 mJ/m(2) for fluorine-free (F0) alkyne monolayers to as low as 3.2 ± 0.03 mJ/m(2) for a heptadecafluoro-hexadecyne (F17)-based monolayer. Likewise, the friction coefficient decreases from 5.7 × 10(-2) to 1.2 × 10(-2). The combination of high ordering, excellent hydrophobicity, low adhesion, and low friction makes these fluoro-hydro alkyne-derived monolayers highly promising candidates for use in high-performance microelectronic devices.
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Affiliation(s)
- Sidharam P Pujari
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, The Netherlands
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44
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van der Kooij HM, Spruijt E, Voets IK, Fokkink R, Cohen Stuart MA, van der Gucht J. On the stability and morphology of complex coacervate core micelles: from spherical to wormlike micelles. Langmuir 2012; 28:14180-14191. [PMID: 22978707 DOI: 10.1021/la303211b] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present a systematic study of the stability and morphology of complex coacervate core micelles (C3Ms) formed from poly(acrylic acid) (PAA) and poly(N-methyl-2-vinylpyridinium)-b-poly(ethylene oxide) (PM2VP-b-PEO). We use polarized and depolarized dynamic and static light scattering, combined with small-angle X-ray scattering, to investigate how the polymer chain length and salt concentration affect the stability, size, and shape of these micelles. We show that C3Ms are formed in aqueous solution below a critical salt concentration, which increases considerably with increasing PAA and PM2VP length and levels off for long chains. This trend is in good agreement with a mean-field model of polyelectrolyte complexation based on the Voorn-Overbeek theory. In addition, we find that salt induces morphological changes in C3Ms when the PAA homopolymer is sufficiently short: from spherical micelles with a diameter of several tens of nanometers at low salt concentration to wormlike micelles with a contour length of several hundreds of nanometers just before the critical salt concentration. By contrast, C3Ms of long PAA homopolymers remain spherical upon addition of salt and shrink slightly. A critical review of existing literature on other C3Ms reveals that the transition from spherical to wormlike micelles is probably a general phenomenon, which can be rationalized in terms of a classical packing parameter for amphiphiles.
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Affiliation(s)
- Hanne M van der Kooij
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands.
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45
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Lemmers M, Spruijt E, Akerboom S, Voets IK, van Aelst AC, Stuart MAC, van der Gucht J. Physical gels based on charge-driven bridging of nanoparticles by triblock copolymers. Langmuir 2012; 28:12311-12318. [PMID: 22834713 DOI: 10.1021/la301917e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We have prepared an aqueous physical gel consisting of negatively charged silica nanoparticles bridged by ABA triblock copolymers, in which the A blocks are positively charged and the B block is neutral and water-soluble. Irreversible aggregation of the silica nanoparticles was prevented by precoating them with a neutral hydrophilic polymer. Both the elastic plateau modulus and the relaxation time increase slowly as the gel ages, indicating an increase both in the number of active bridges and in the strength with which the end blocks are adsorbed. The rate of this aging process can be increased significantly by applying a small shear stress to the sample. Our results indicate that charge-driven bridging of nanoparticles by triblock copolymers is a promising strategy for thickening of aqueous particle containing materials, such as water-based coatings.
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Affiliation(s)
- Marc Lemmers
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Wageningen, The Netherlands
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Spruijt E, van den Berg SA, Cohen Stuart MA, van der Gucht J. Direct measurement of the strength of single ionic bonds between hydrated charges. ACS Nano 2012; 6:5297-5303. [PMID: 22559075 DOI: 10.1021/nn301097y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The strength of ionic bonds is essentially unknown, despite their widespread occurrence in natural and man-made assemblies. Here, we use single-molecule force spectroscopy to measure their strength directly. We disrupt a complex between two oppositely charged polyelectrolyte chains and find two modes of rupture: one ionic bond at a time, or cooperative rupture of many bonds at once. For both modes, disruption of the ionic bonds can be described quantitatively as an activated process. The height of the energy barrier is not only lowered by added salt, but also by the applied force. We extract unperturbed ionic bond lifetimes that range from milliseconds for single ionic bonds at high salt concentration to tens of years for small complexes of five ionic bonds at low salt concentration.
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Affiliation(s)
- Evan Spruijt
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands.
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Gucht JVD, Spruijt E, Lemmers M, Cohen Stuart MA. Polyelectrolyte complexes: Bulk phases and colloidal systems. J Colloid Interface Sci 2011; 361:407-22. [DOI: 10.1016/j.jcis.2011.05.080] [Citation(s) in RCA: 408] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/27/2011] [Accepted: 05/28/2011] [Indexed: 11/17/2022]
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Spruijt E, Sprakel J, Lemmers M, Stuart MAC, van der Gucht J. Relaxation dynamics at different time scales in electrostatic complexes: time-salt superposition. Phys Rev Lett 2010; 105:208301. [PMID: 21231268 DOI: 10.1103/physrevlett.105.208301] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Indexed: 05/03/2023]
Abstract
In this Letter we show that in the rheology of electrostatically assembled soft materials, salt concentration plays a similar role as temperature for polymer melts, and as strain rate for soft solids. We rescale linear and nonlinear rheological data of a set of model electrostatic complexes at different salt concentrations to access a range of time scales that is otherwise inaccessible. This provides new insights into the relaxation mechanisms of electrostatic complexes, which we rationalize in terms of a microscopic mechanism underlying salt-enhanced activated processes.
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Affiliation(s)
- Evan Spruijt
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands.
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Affiliation(s)
- Evan Spruijt
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
- MicroSpectroscopy Centre, P.O. Box 8128, 6700 ET Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
- MicroSpectroscopy Centre, P.O. Box 8128, 6700 ET Wageningen, The Netherlands
| | - Martien A. Cohen Stuart
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Jasper van der Gucht
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
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Affiliation(s)
- Evan Spruijt
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Martien A. Cohen Stuart
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Jasper van der Gucht
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
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