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Rajput S, Panigrahy S, Nayar D. In Silico View of Crowding: Biomolecular Processes to Nanomaterial Design. ACS OMEGA 2024; 9:29953-29965. [PMID: 39035939 PMCID: PMC11256109 DOI: 10.1021/acsomega.4c03344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024]
Abstract
It is widely accepted that deciphering biomolecular structure and function requires going beyond the single-molecule or single-complex paradigm. The densely packed macromolecules, cosolutes, and metabolites in the living cell impose crowding effects on the biomolecular structure and dynamics that need to be accounted for. Molecular simulations have proven to be a powerful tool to advance the current molecular-level understanding of such a highly concentrated, complex milieu. This Mini-Review focuses on summarizing the understanding achieved so far for the effects of crowding on biomolecular processes using computational methods, along with highlighting a new direction in employing crowding as a tool for tunable nanomaterial design. The two schools of thought that form the pillars of the current understanding of crowding effects are discussed. The investigation of crowded solutions using physics-based models that encompass different time and length scales to mimic the intracellular environment are described. The limitations and challenges faced by the current models and simulation methods are addressed, highlighting the gaps to be filled for better agreement with experiments. Crowding can also act as an effective tool to modulate the structure-property-function relationships of nanomaterials, leading to the development of novel functional materials. A few recent studies, mostly experimental, have been summarized in this direction. The Mini-Review concludes with an outlook for future developments in this field in order to enable accurate mimicking of the intracellular environment using simulations and to bridge the gap between biological processes and nanomaterial design.
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Affiliation(s)
- Satyendra Rajput
- Department of Materials Science
and Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
| | - Sibasankar Panigrahy
- Department of Materials Science
and Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
| | - Divya Nayar
- Department of Materials Science
and Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
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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] [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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Fu H, Huang J, van der Tol JJB, Su L, Wang Y, Dey S, Zijlstra P, Fytas G, Vantomme G, Dankers PYW, Meijer EW. Supramolecular polymers form tactoids through liquid-liquid phase separation. Nature 2024; 626:1011-1018. [PMID: 38418913 PMCID: PMC10901743 DOI: 10.1038/s41586-024-07034-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/05/2024] [Indexed: 03/02/2024]
Abstract
Liquid-liquid phase separation (LLPS) of biopolymers has recently been shown to play a central role in the formation of membraneless organelles with a multitude of biological functions1-3. The interplay between LLPS and macromolecular condensation is part of continuing studies4,5. Synthetic supramolecular polymers are the non-covalent equivalent of macromolecules but they are not reported to undergo LLPS yet. Here we show that continuously growing fibrils, obtained from supramolecular polymerizations of synthetic components, are responsible for phase separation into highly anisotropic aqueous liquid droplets (tactoids) by means of an entropy-driven pathway. The crowding environment, regulated by dextran concentration, affects not only the kinetics of supramolecular polymerizations but also the properties of LLPS, including phase-separation kinetics, morphology, internal order, fluidity and mechanical properties of the final tactoids. In addition, substrate-liquid and liquid-liquid interfaces proved capable of accelerating LLPS of supramolecular polymers, allowing the generation of a myriad of three-dimensional-ordered structures, including highly ordered arrays of micrometre-long tactoids at surfaces. The generality and many possibilities of supramolecular polymerizations to control emerging morphologies are demonstrated with several supramolecular polymers, opening up a new field of matter ranging from highly structured aqueous solutions by means of stabilized LLPS to nanoscopic soft matter.
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Affiliation(s)
- Hailin Fu
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Jingyi Huang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Biomedical Engineering and Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Joost J B van der Tol
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Lu Su
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Swayandipta Dey
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Peter Zijlstra
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, The Netherlands
- Eindhoven Hendrik Casimir Institute, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - George Fytas
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Max Planck Institute for Polymer Research, Mainz, Germany
- Institute of Electronic Structure and Laser, FO.R.T.H, Heraklion, Greece
| | - Ghislaine Vantomme
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Patricia Y W Dankers
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Biomedical Engineering and Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Department of Chemistry and Chemical Engineering and Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
- School of Chemistry and RNA Institute, University of New South Wales, Sydney, New South Wales, Australia.
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Koch L, Pollak R, Ebbinghaus S, Huber K. A Comparative Study on Cyanine Dyestuffs as Sensor Candidates for Macromolecular Crowding In Vitro and In Vivo. BIOSENSORS 2023; 13:720. [PMID: 37504118 PMCID: PMC10377163 DOI: 10.3390/bios13070720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Pseudo isocyanine chloride (PIC) has been identified in a preceding work as a sensor suited to probe macromolecular crowding both in test tubes with solutions of synthetic crowding agents and in HeLa cells as a representative of living systems. The sensing is based on a delicate response of the self-assembly pattern of PIC towards a variation in macromolecular crowding. Based on a suitable selection of criteria established in the present study, four additional cyanine dyestuffs (TDBC, S071, S2275, and PCYN) were scrutinized for their ability to act as such a sensor, and the results were compared with the corresponding performance of PIC. UV-VIS and fluorescence spectroscopy were applied to investigate the photo-physical properties of the four candidates and, if possible, light scattering was used to characterize the self-assembly of the dyestuffs in solution. Finally, HeLa cells were exposed to solutions of the most promising candidates in order to analyze their ability to infiltrate the cells and to self-assemble therein. None of the dyestuff candidates turned out to be as similarly promising in probing crowding effects in cells as PIC turned out to be. S0271 and S2275 are at least stable enough and meet the photophysical requirements necessary to act as sensors responding to changes in macromolecular crowding.
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Affiliation(s)
- Leon Koch
- Physical Chemistry, Department of Chemistry, Paderborn University, 33098 Paderborn, Germany
| | - Roland Pollak
- Physical and Theoretical Chemistry, Faculty of Live Science, TU Braunschweig, 38106 Braunschweig, Germany
| | - Simon Ebbinghaus
- Physical and Theoretical Chemistry, Faculty of Live Science, TU Braunschweig, 38106 Braunschweig, Germany
| | - Klaus Huber
- Physical Chemistry, Department of Chemistry, Paderborn University, 33098 Paderborn, Germany
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Bäumer N, Castellanos E, Soberats B, Fernández G. Bioinspired crowding directs supramolecular polymerisation. Nat Commun 2023; 14:1084. [PMID: 36841784 PMCID: PMC9968348 DOI: 10.1038/s41467-023-36540-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/06/2023] [Indexed: 02/27/2023] Open
Abstract
Crowding effects are crucial to maintaining functionality in biological systems, but little is known about their role in analogous artificial counterparts. Within the growing field of supramolecular polymer science, crowding effects have hitherto remained underappreciated. Herein, we show that crowding effects exhibit strong and distinct control over the kinetics, accessible pathways and final outcomes of supramolecular polymerisation processes. In the presence of a pre-formed supramolecular polymer as crowding agent, a model supramolecular polymer dramatically changes its self-assembly behaviour and undergoes a morphological transformation from bundled fibres into flower-like hierarchical assemblies, despite no co-assembly taking place. Notably, this new pathway can only be accessed in crowded environments and when the crowding agent exhibits a one-dimensional morphology. These results allow accessing diverse morphologies and properties in supramolecular polymers and pave the way towards a better understanding of high-precision self-assembly in nature.
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Affiliation(s)
- Nils Bäumer
- grid.5949.10000 0001 2172 9288Westfälische-Wilhelms Universität Münster, Organisch Chemisches Institut, Corrensstraße 36, 48149 Münster, Germany
| | - Eduardo Castellanos
- grid.9563.90000 0001 1940 4767Department of Chemistry, University of the Balearic Islands, Cra. Valldemossa, Km. 7.5, Palma de Mallorca, 07122 Spain
| | - Bartolome Soberats
- grid.9563.90000 0001 1940 4767Department of Chemistry, University of the Balearic Islands, Cra. Valldemossa, Km. 7.5, Palma de Mallorca, 07122 Spain
| | - Gustavo Fernández
- Westfälische-Wilhelms Universität Münster, Organisch Chemisches Institut, Corrensstraße 36, 48149, Münster, Germany.
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6
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Gräfenstein A, Rumancev C, Pollak R, Hämisch B, Galbierz V, Schroeder WH, Garrevoet J, Falkenberg G, Vöpel T, Huber K, Ebbinghaus S, Rosenhahn A. Spatial Distribution of Intracellular Ion Concentrations in Aggregate-Forming HeLa Cells Analyzed by μ-XRF Imaging. Chemistry 2022; 11:e202200024. [PMID: 35363437 PMCID: PMC8973254 DOI: 10.1002/open.202200024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/25/2022] [Indexed: 12/21/2022]
Abstract
Protein aggregation is a hallmark of several severe neurodegenerative disorders such as Huntington's, Parkinson's, or Alzheimer's disease. Metal ions play a profound role in protein aggregation and altered metal‐ion homeostasis is associated with disease progression. Here we utilize μ‐X‐ray fluorescence imaging in combination with rapid freezing to resolve the elemental distribution of phosphorus, sulfur, potassium, and zinc in huntingtin exon‐1‐mYFP expressing HeLa cells. Using quantitative XRF analysis, we find a threefold increase in zinc and a 10‐fold enrichment of potassium that can be attributed to cellular stress response. While the averaged intracellular ion areal masses are significantly different in aggregate‐containing cells, a local intracellular analysis shows no different ion content at the location of intracellular inclusion bodies. The results are compared to corresponding experiments on HeLa cells forming pseudoisocyanine chloride aggregates. As those show similar results, changes in ion concentrations are not exclusively linked to huntingtin exon‐1 amyloid formation.
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Affiliation(s)
- Andreas Gräfenstein
- Analytical Chemistry - Biointerfaces, Ruhr University Bochum, 44801, Bochum, Germany
| | - Christoph Rumancev
- Analytical Chemistry - Biointerfaces, Ruhr University Bochum, 44801, Bochum, Germany
| | - Roland Pollak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Benjamin Hämisch
- Physical Chemistry, University of Paderborn, 33098, Paderborn, Germany
| | - Vanessa Galbierz
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, Germany
| | - Walter H Schroeder
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, Germany.,Nanotech Consulting, Liblarer Strasse 8, 50321, Brühl, Germany
| | - Jan Garrevoet
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, Germany
| | - Gerald Falkenberg
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, Germany
| | - Tobias Vöpel
- Physical Chemistry II, Ruhr University Bochum, 44801, Bochum, Germany
| | - Klaus Huber
- Physical Chemistry, University of Paderborn, 33098, Paderborn, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Axel Rosenhahn
- Analytical Chemistry - Biointerfaces, Ruhr University Bochum, 44801, Bochum, Germany
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7
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Hämisch B, Huber K. Mechanism and equilibrium thermodynamics of H- and J-aggregate formation from pseudo isocyanine chloride in water. SOFT MATTER 2021; 17:8140-8152. [PMID: 34525155 DOI: 10.1039/d1sm00979f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pseudo isocyanine chloride (PIC) has a strong tendency to self-assemble with a concentration dependent temperature threshold separating a regime with small H-oligomers in equilibrium with monomeric PIC from a regime where large J-aggregates form. In complementing the known set of absorption spectra by the spectrum of a trimer, which represents all H-aggregates with N ≥ 3, a full description of the sample composition of PIC in the regime of oligomers became possible by means of UV-vis spectroscopy and gave access to the equilibrium thermodynamics of oligomerisation. Successful interpretation of the concentration dependent temperature threshold as a ceiling temperature of J-aggregation made also accessible equilibrium thermodynamics of the formation of J-aggregates together with a full analysis of composition also in the regime of J-aggregates. Evolution of an invariant spectrum for the J-aggregates demonstrates full consistency of the composition analysis. Complementary light scattering experiments led to a comprehensive characterisation of all aggregate species above and below the aggregation threshold. Once initiated, J-aggregates always grow to a final length of 650 nm. Time-resolved light scattering confirmed that the self-assembly of J-aggregates follows a monomer addition process in analogy to a chain growth in polymer chemistry. Initiation and growth of individual aggregates turned out to be always much faster than the progress of aggregation.
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Affiliation(s)
- Benjamin Hämisch
- Physical Chemistry, Paderborn University, 33098 Paderborn, Germany.
| | - Klaus Huber
- Physical Chemistry, Paderborn University, 33098 Paderborn, Germany.
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Hämisch B, Pollak R, Ebbinghaus S, Huber K. Thermodynamic Analysis of the Self‐Assembly of Pseudo Isocyanine Chloride in the Presence of Crowding Agents. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Roland Pollak
- Physical and Theoretical Chemistry TU Braunschweig 38106 Braunschweig Germany
| | - Simon Ebbinghaus
- Physical and Theoretical Chemistry TU Braunschweig 38106 Braunschweig Germany
| | - Klaus Huber
- Physical Chemistry Paderborn University 33098 Paderborn Germany
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9
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Hämisch B, Pollak R, Ebbinghaus S, Huber K. Self-Assembly of Pseudo-Isocyanine Chloride as a Sensor for Macromolecular Crowding In Vitro and In Vivo. Chemistry 2020; 26:7041-7050. [PMID: 32154954 PMCID: PMC7317963 DOI: 10.1002/chem.202000113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/20/2020] [Indexed: 11/21/2022]
Abstract
Pseudo‐isocyanine chloride (PIC) is a cationic dyestuff that exhibits self‐assembly in aqueous solution, promoted either by increasing the PIC concentration or by decreasing the temperature. PIC‐aggregates exhibit a characteristic and sharp absorption band as well as a fluorescence band at a wavelength of 573 nm making PIC an interesting candidate to analyze the self‐assembly process in various environments. The present work developed PIC‐based, synthetic model systems, suitable to investigate how macromolecular crowding influences self‐assembly processes. Four synthetic additives were used as potential crowders: Triethylene glycol (TEG), polyethylene glycol (PEG), Ficoll 400 as a highly branched polysaccharide, and sucrose corresponding to the monomeric unit of Ficoll. Combined UV/Vis spectroscopy and time‐resolved light scattering revealed a strong impact of crowding based on excluded volume effects only for Ficoll 400. Sucrose had hardly any influence on the self‐assembly of PIC and PEG and TEG impeded the PIC self‐assembly. Development of such a PIC based model system led over to in‐cell experiments. HeLa cells were infiltrated with PIC solutions well below the aggregation threshold in the infiltrating solution. In the cellular environment, PIC was exposed to a significant crowding and immediately started to aggregate. As was demonstrated by fluorescence imaging, the extent of aggregation can be modulated by exposing the cells to salt‐induced osmotic stress. The results suggest future use of such a system as a sensor for the analysis of in vitro and in vivo crowding effects on self‐assembly processes.
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Affiliation(s)
- Benjamin Hämisch
- Physical Chemistry, Paderborn University, 33098, Paderborn, Germany
| | - Roland Pollak
- Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Simon Ebbinghaus
- Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Klaus Huber
- Physical Chemistry, Paderborn University, 33098, Paderborn, Germany
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