1
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De Luca G, Sancataldo G, Militello B, Vetri V. Surface-catalyzed liquid-liquid phase separation and amyloid-like assembly in microscale compartments. J Colloid Interface Sci 2024; 676:569-581. [PMID: 39053405 DOI: 10.1016/j.jcis.2024.07.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Liquid-liquid phase separation is a key phenomenon in the formation of membrane-less structures within the cell, appearing as liquid biomolecular condensates. Protein condensates are the most studied for their biological relevance, and their tendency to evolve, resulting in the formation of aggregates with a high level of order called amyloid. In this study, it is demonstrated that Human Insulin forms micrometric, round amyloid-like structures at room temperature within sub-microliter scale aqueous compartments. These distinctive particles feature a solid core enveloped by a fluid-like corona and form at the interface between the aqueous compartment and the glass coverslip upon which they are cast. Quantitative fluorescence microscopy is used to study in real-time the formation of amyloid-like superstructures. Their formation results driven by liquid-liquid phase separation process that arises from spatially heterogeneous distribution of nuclei at the glass-water interface. The proposed experimental setup allows modifying the surface-to-volume ratio of the aqueous compartments, which affects the aggregation rate and particle size, while also inducing fine alterations in the molecular structures of the final assemblies. These findings enhance the understanding of the factors governing amyloid structure formation, shedding light on the catalytic role of surfaces in this process.
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Affiliation(s)
- Giuseppe De Luca
- Department Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, 16, 90128, Palermo, Italy; Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Giuseppe Sancataldo
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Benedetto Militello
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy; INFN Sezione di Catania, Via Santa Sofia 64, 95123 Catania, Italy.
| | - Valeria Vetri
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
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2
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Khodarahmi S, Eslami F, Zargarzadeh L. Oiling-Out: Insights from Gibbsian Surface Thermodynamics by Stability Analysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:4669-4683. [PMID: 38373199 DOI: 10.1021/acs.langmuir.3c03329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The crystallization process is a significant stage in the pharmaceutical industry. During the process of crystallization with cooling, it is possible for a secondary liquid phase to appear before the formation of crystals. This phenomenon is called "oiling out" or liquid-liquid phase separation (LLPS). In this article, we explore the oiling-out phenomenon in a binary system of water and vanillin using stability analysis based on Gibbsian surface thermodynamics. To obtain the full picture of oiling out, we investigated three cases: droplet-solute-lean liquid equilibrium (DLE), crystal-solute-rich liquid equilibrium (CL'E), and crystal-solute-lean liquid equilibrium (CLE). The phase diagram of the system is plotted using the NRTL model for activity coefficients, along with considering the effect of the interfacial curvature on the phase diagram. From the phase boundaries and free-energy diagram of each case, we showed that the occurrence of the oiling-out phenomenon is justified based on the lower energy barrier of the droplet formation compared to that of the crystal formation. However, the energy level of a stable crystal is significantly lower and hence more stable than that of a stable droplet. Finally, we have determined different regions for droplet and crystal formation in the metastable phase diagram based on their supersaturation and provide insight for the oiling-out phenomenon.
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Affiliation(s)
- Shima Khodarahmi
- Department of Chemical Engineering, Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box 14115-111, Tehran, Iran
| | - Fatemeh Eslami
- Department of Chemical Engineering, Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box 14115-111, Tehran, Iran
| | - Leila Zargarzadeh
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), No. 424, Hafez Avenue, P.O. Box 15875-4413 Tehran, Iran
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3
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Hansen J, Moll CJ, López Flores L, Castañeda-Priego R, Medina-Noyola M, Egelhaaf SU, Platten F. Phase separation and dynamical arrest of protein solutions dominated by short-range attractions. J Chem Phys 2023; 158:024904. [PMID: 36641409 DOI: 10.1063/5.0128643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The interplay of liquid-liquid phase separation (LLPS) and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as condensed matter physics, materials science, food engineering, and the pharmaceutical industry. In this context, protein solutions exhibit remarkable equilibrium and non-equilibrium behaviors. In the regime where attractive and repulsive forces compete, it has been demonstrated, for example, that the location of the dynamical arrest line seems to be independent of ionic strength, so that the arrest lines at different ionic screening lengths overlap, in contrast to the LLPS coexistence curves, which strongly depend on the salt concentration. In this work, we show that the same phenomenology can also be observed when the electrostatic repulsions are largely screened, and the range and strength of the attractions are varied. In particular, using lysozyme in brine as a model system, the metastable gas-liquid binodal and the dynamical arrest line as well as the second virial coefficient have been determined for various solution conditions by cloud-point measurements, optical microscopy, centrifugation experiments, and light scattering. With the aim of understanding this new experimental phenomenology, we apply the non-equilibrium self-consistent generalized Langevin equation theory to a simple model system with only excluded volume plus short-range attractions, to study the dependence of the predicted arrest lines on the range of the attractive interaction. The theoretical predictions find a good qualitative agreement with experiments when the range of the attraction is not too small compared with the size of the protein.
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Affiliation(s)
- Jan Hansen
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
| | - Carolyn J Moll
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
| | - Leticia López Flores
- Instituto de Física "Manuel Sandoval Vallarta," Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, Mexico
| | | | - Magdaleno Medina-Noyola
- Instituto de Física "Manuel Sandoval Vallarta," Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, Mexico
| | - Stefan U Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, Düsseldorf, Germany
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4
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Félix SS, Laurents DV, Oroz J, Cabrita EJ. Fused in sarcoma undergoes cold denaturation: Implications for phase separation. Protein Sci 2023; 32:e4521. [PMID: 36453011 PMCID: PMC9793971 DOI: 10.1002/pro.4521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The mediation of liquid-liquid phase separation (LLPS) for fused in sarcoma (FUS) protein is generally attributed to the low-complexity, disordered domains and is enhanced at low temperature. The role of FUS folded domains on the LLPS process remains relatively unknown since most studies are mainly based on fragmented FUS domains. Here, we investigate the effect of metabolites on full-length (FL) FUS LLPS using turbidity assays and differential interference contrast (DIC) microscopy, and explore the behavior of the folded domains by nuclear magnetic resonance (NMR) spectroscopy. FL FUS LLPS is maximal at low concentrations of glucose and glutamate, moderate concentrations of NaCl, Zn2+ , and Ca2+ and at the isoelectric pH. The FUS RNA recognition motif (RRM) and zinc-finger (ZnF) domains are found to undergo cold denaturation above 0°C at a temperature that is determined by the conformational stability of the ZnF domain. Cold unfolding exposes buried nonpolar residues that can participate in LLPS-promoting hydrophobic interactions. Therefore, these findings constitute the first evidence that FUS globular domains may have an active role in LLPS under cold stress conditions and in the assembly of stress granules, providing further insight into the environmental regulation of LLPS.
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Affiliation(s)
- Sara S. Félix
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | | | - Javier Oroz
- Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | - Eurico J. Cabrita
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal
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5
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Molecular and environmental determinants of biomolecular condensate formation. Nat Chem Biol 2022; 18:1319-1329. [DOI: 10.1038/s41589-022-01175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022]
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6
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Sun Y, Li X, Chen R, Liu F, Wei S. Recent advances in structural characterization of biomacromolecules in foods via small-angle X-ray scattering. Front Nutr 2022; 9:1039762. [PMID: 36466419 PMCID: PMC9714470 DOI: 10.3389/fnut.2022.1039762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/03/2022] [Indexed: 08/04/2023] Open
Abstract
Small-angle X-ray scattering (SAXS) is a method for examining the solution structure, oligomeric state, conformational changes, and flexibility of biomacromolecules at a scale ranging from a few Angstroms to hundreds of nanometers. Wide time scales ranging from real time (milliseconds) to minutes can be also covered by SAXS. With many advantages, SAXS has been extensively used, it is widely used in the structural characterization of biomacromolecules in food science and technology. However, the application of SAXS in charactering the structure of food biomacromolecules has not been reviewed so far. In the current review, the principle, theoretical calculations and modeling programs are summarized, technical advances in the experimental setups and corresponding applications of in situ capabilities: combination of chromatography, time-resolved, temperature, pressure, flow-through are elaborated. Recent applications of SAXS for monitoring structural properties of biomacromolecules in food including protein, carbohydrate and lipid are also highlighted, and limitations and prospects for developing SAXS based on facility upgraded and artificial intelligence to study the structural properties of biomacromolecules are finally discussed. Future research should focus on extending machine time, simplifying SAXS data treatment, optimizing modeling methods in order to achieve an integrated structural biology based on SAXS as a practical tool for investigating the structure-function relationship of biomacromolecules in food industry.
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Affiliation(s)
- Yang Sun
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Xiujuan Li
- Pharmaceutical Department, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Ruixin Chen
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Fei Liu
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Song Wei
- Tumor Precise Intervention and Translational Medicine Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
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7
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Villois A, Capasso Palmiero U, Mathur P, Perone G, Schneider T, Li L, Salvalaglio M, deMello A, Stavrakis S, Arosio P. Droplet Microfluidics for the Label-Free Extraction of Complete Phase Diagrams and Kinetics of Liquid-Liquid Phase Separation in Finite Volumes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202606. [PMID: 36180409 DOI: 10.1002/smll.202202606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Liquid-liquid phase separation of polymer and protein solutions is central in many areas of biology and material sciences. Here, an experimental and theoretical framework is provided to investigate the thermodynamics and kinetics of liquid-liquid phase separation in volumes comparable to cells. The strategy leverages droplet microfluidics to accurately measure the volume of the dense phase generated by liquid-liquid phase separation of solutions confined in micro-sized compartments. It is shown that the measurement of the volume fraction of the dense phase at different temperatures allows the evaluation of the binodal lines that determine the coexistence region of the two phases in the temperature-concentration phase diagram. By applying a thermodynamic model of phase separation in finite volumes, it is further shown that the platform can predict and validate kinetic barriers associated with the formation of a dense droplet in a parent dilute phase, therefore connecting thermodynamics and kinetics of liquid-liquid phase separation.
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Affiliation(s)
- Alessia Villois
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Prerit Mathur
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Gaia Perone
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Timo Schneider
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Lunna Li
- Thomas Young Centre and Department of Chemical Engineering, University College London, London, WC1E 7JE, UK
| | - Matteo Salvalaglio
- Thomas Young Centre and Department of Chemical Engineering, University College London, London, WC1E 7JE, UK
| | - Andrew deMello
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Stavros Stavrakis
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
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8
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Timmermann S, Starostin V, Girelli A, Ragulskaya A, Rahmann H, Reiser M, Begam N, Randolph L, Sprung M, Westermeier F, Zhang F, Schreiber F, Gutt C. Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn-Hilliard-type simulations using auto-encoder networks. J Appl Crystallogr 2022; 55:751-757. [PMID: 35974741 PMCID: PMC9348880 DOI: 10.1107/s1600576722004435] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/26/2022] [Indexed: 11/10/2022] Open
Abstract
Machine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid-liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn-Hilliard-type simulations of liquid-liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm. The method presented here is a first step towards handling large amounts of dynamic data measured at high-brilliance synchrotron and X-ray free-electron laser sources, facilitating fast comparison with phase field models of phase separation.
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Affiliation(s)
- Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Vladimir Starostin
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Hendrik Rahmann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Lisa Randolph
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
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9
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Ragulskaya A, Starostin V, Begam N, Girelli A, Rahmann H, Reiser M, Westermeier F, Sprung M, Zhang F, Gutt C, Schreiber F. Reverse-engineering method for XPCS studies of non-equilibrium dynamics. IUCRJ 2022; 9:439-448. [PMID: 35844477 PMCID: PMC9252156 DOI: 10.1107/s2052252522004560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
X-ray photon correlation spectroscopy (XPCS) is a powerful tool in the investigation of dynamics covering a broad time and length scale. It has been widely used to probe dynamics for systems in both equilibrium and non-equilibrium states; in particular, for systems undergoing a phase transition where the structural growth kinetics and the microscopic dynamics are strongly intertwined. The resulting time-dependent dynamic behavior can be described using the two-time correlation function (TTC), which, however, often contains more interesting features than the component along the diagonal, and cannot be easily interpreted via the classical simulation methods. Here, a reverse engineering (RE) approach is proposed based on particle-based heuristic simulations. This approach is applied to an XPCS measurement on a protein solution undergoing a liquid-liquid phase separation. It is demonstrated that the rich features of experimental TTCs can be well connected with the key control parameters including size distribution, concentration, viscosity and mobility of domains. The dynamic information obtained from this RE analysis goes beyond the existing theory. The RE approach established in this work is applicable for other processes such as film growth, coarsening or evolving systems.
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Affiliation(s)
- Anastasia Ragulskaya
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Vladimir Starostin
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Nafisa Begam
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anita Girelli
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Hendrik Rahmann
- Department of Physics, University of Siegen, Emmy-Noether-Campus, Walter-Flex-Straße 3, 57076 Siegen, Germany
| | - Mario Reiser
- Department of Physics, University of Siegen, Emmy-Noether-Campus, Walter-Flex-Straße 3, 57076 Siegen, Germany
- European X-ray free-electron laser GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Fajun Zhang
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Gutt
- Department of Physics, University of Siegen, Emmy-Noether-Campus, Walter-Flex-Straße 3, 57076 Siegen, Germany
| | - Frank Schreiber
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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10
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Moron M, Al-Masoodi A, Lovato C, Reiser M, Randolph L, Surmeier G, Bolle J, Westermeier F, Sprung M, Winter R, Paulus M, Gutt C. Gelation Dynamics upon Pressure-Induced Liquid-Liquid Phase Separation in a Water-Lysozyme Solution. J Phys Chem B 2022; 126:4160-4167. [PMID: 35594491 DOI: 10.1021/acs.jpcb.2c01947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Employing X-ray photon correlation spectroscopy, we measure the kinetics and dynamics of a pressure-induced liquid-liquid phase separation (LLPS) in a water-lysozyme solution. Scattering invariants and kinetic information provide evidence that the system reaches the phase boundary upon pressure-induced LLPS with no sign of arrest. The coarsening slows down with increasing quench depths. The g2 functions display a two-step decay with a gradually increasing nonergodicity parameter typical for gelation. We observe fast superdiffusive (γ ≥ 3/2) and slow subdiffusive (γ < 0.6) motion associated with fast viscoelastic fluctuations of the network and a slow viscous coarsening process, respectively. The dynamics age linearly with time τ ∝ tw, and we observe the onset of viscoelastic relaxation for deeper quenches. Our results suggest that the protein solution gels upon reaching the phase boundary.
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Affiliation(s)
- M Moron
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - A Al-Masoodi
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
| | - C Lovato
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
| | - M Reiser
- Department of Physics, Stockholm University, 10691 Stockholm, Sweden
| | - L Randolph
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
| | - G Surmeier
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - J Bolle
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - F Westermeier
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - M Sprung
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - R Winter
- Fakultät Chemie und Chemische Biologie, Physikalische Chemie, TU Dortmund, 44227 Dortmund, Germany
| | - M Paulus
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - C Gutt
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
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11
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Chen D, Kuzmenko I, Ilavsky J, Pinho L, Campanella O. Structural evolution during gelation of pea and whey proteins envisaged by time-resolved ultra-small-angle x-ray scattering (USAXS). Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Temporal and spatial characterisation of protein liquid-liquid phase separation using NMR spectroscopy. Nat Commun 2022; 13:1767. [PMID: 35365630 PMCID: PMC8976059 DOI: 10.1038/s41467-022-29408-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of protein solutions is increasingly recognised as an important phenomenon in cell biology and biotechnology. However, opalescence and concentration fluctuations render LLPS difficult to study, particularly when characterising the kinetics of the phase transition and layer separation. Here, we demonstrate the use of a probe molecule trifluoroethanol (TFE) to characterise the kinetics of protein LLPS by NMR spectroscopy. The chemical shift and linewidth of the probe molecule are sensitive to local protein concentration, with this sensitivity resulting in different characteristic signals arising from the dense and lean phases. Monitoring of these probe signals by conventional bulk-detection 19F NMR reports on the formation and evolution of both phases throughout the sample, including their concentrations and volumes. Meanwhile, spatially-selective 19F NMR, in which spectra are recorded from smaller slices of the sample, was used to track the distribution of the different phases during layer separation. This experimental strategy enables comprehensive characterisation of the process and kinetics of LLPS, and may be useful to study phase separation in protein systems as a function of their environment.
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13
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Effect of Temperature on Re-entrant Condensation of Globular Protein in Presence of Tri-valent Ions. J Fluoresc 2022; 32:791-797. [DOI: 10.1007/s10895-021-02874-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022]
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14
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Martel A, Gabel F. Time-resolved small-angle neutron scattering (TR-SANS) for structural biology of dynamic systems: Principles, recent developments, and practical guidelines. Methods Enzymol 2022; 677:263-290. [DOI: 10.1016/bs.mie.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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15
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Chowdhury S, Reynard-Feytis Q, Roizard C, Frath D, Chevallier F, Bucher C, Gibaud T. Light-Controlled Aggregation and Gelation of Viologen-Based Coordination Polymers. J Phys Chem B 2021; 125:12063-12071. [PMID: 34677961 DOI: 10.1021/acs.jpcb.1c06090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ditopic bis-(triazole/pyridine)viologens are bidentate ligands that self-assemble into coordination polymers. In such photo-responsive materials, light irradiation initiates photo-induced electron transfer to generate π-radicals that can self-associate to form π-dimers. This leads to a cascade of events: processes at the supramolecular scale associated with mechanical and structural transition at the macroscopic scale. By tuning the irradiation power and duration, we evidence the formation of aggregates and gels. Using microscopy, we show that the aggregates are dense, polydisperse, micron-sized, spindle-shaped particles which grow in time. Using microscopy and time-resolved micro-rheology, we follow the gelation kinetics which leads to a gel characterized by a correlation length of a few microns and a weak elastic modulus. The analysis of the aggregates and the gel states vouch for an arrested phase separation process, a new scenario to supramolecular systems.
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Affiliation(s)
- Shagor Chowdhury
- Laboratoire de Chimie, Université de Lyon, Ens de Lyon, CNRS UMR 5182, F69342 Lyon, France
| | - Quentin Reynard-Feytis
- Laboratoire de Chimie, Université de Lyon, Ens de Lyon, CNRS UMR 5182, F69342 Lyon, France
| | - Clément Roizard
- Laboratoire de Chimie, Université de Lyon, Ens de Lyon, CNRS UMR 5182, F69342 Lyon, France
| | - Denis Frath
- Laboratoire de Chimie, Université de Lyon, Ens de Lyon, CNRS UMR 5182, F69342 Lyon, France
| | - Floris Chevallier
- Laboratoire de Chimie, Université de Lyon, Ens de Lyon, CNRS UMR 5182, F69342 Lyon, France
| | - Christophe Bucher
- Laboratoire de Chimie, Université de Lyon, Ens de Lyon, CNRS UMR 5182, F69342 Lyon, France
| | - Thomas Gibaud
- Laboratoire de Physique, Université de Lyon, Ens de Lyon, University Claude Bernard, CNRS, F69342 Lyon, France
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16
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Constantinou AP, Tall A, Li Q, Georgiou TK. Liquid–liquid phase separation in aqueous solutions of poly(ethylene glycol) methacrylate homopolymers. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anna P. Constantinou
- Department of Materials Imperial College London, South Kensington Campus, Royal School of Mines London UK
| | - Amy Tall
- Department of Materials Imperial College London, South Kensington Campus, Royal School of Mines London UK
| | - Qian Li
- Department of Materials Imperial College London, South Kensington Campus, Royal School of Mines London UK
| | - Theoni K. Georgiou
- Department of Materials Imperial College London, South Kensington Campus, Royal School of Mines London UK
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17
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Ragulskaya A, Begam N, Girelli A, Rahmann H, Reiser M, Westermeier F, Sprung M, Zhang F, Gutt C, Schreiber F. Interplay between Kinetics and Dynamics of Liquid-Liquid Phase Separation in a Protein Solution Revealed by Coherent X-ray Spectroscopy. J Phys Chem Lett 2021; 12:7085-7090. [PMID: 34292744 DOI: 10.1021/acs.jpclett.1c01940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microscopic dynamics of complex fluids in the early stage of spinodal decomposition (SD) is strongly intertwined with the kinetics of structural evolution, which makes a quantitative characterization challenging. In this work, we use X-ray photon correlation spectroscopy to study the dynamics and kinetics of a protein solution undergoing liquid-liquid phase separation (LLPS). We demonstrate that in the early stage of SD, the kinetics relaxation is up to 40 times slower than the dynamics and thus can be decoupled. The microscopic dynamics can be well described by hyper-diffusive ballistic motions with a relaxation time exponentially growing with time in the early stage followed by a power-law increase with fluctuations. These experimental results are further supported by simulations based on the Cahn-Hilliard equation. The established framework is applicable to other condensed matter and biological systems undergoing phase transitions and may also inspire further theoretical work.
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Affiliation(s)
- Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Hendrik Rahmann
- Department Physik, Universität Siegen, Emmy-Noether-Campus, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Mario Reiser
- Department Physik, Universität Siegen, Emmy-Noether-Campus, Walter-Flex-Strasse 3, 57072 Siegen, Germany
- European X-ray Free-Electron Laser GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Emmy-Noether-Campus, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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18
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Girelli A, Rahmann H, Begam N, Ragulskaya A, Reiser M, Chandran S, Westermeier F, Sprung M, Zhang F, Gutt C, Schreiber F. Microscopic Dynamics of Liquid-Liquid Phase Separation and Domain Coarsening in a Protein Solution Revealed by X-Ray Photon Correlation Spectroscopy. PHYSICAL REVIEW LETTERS 2021; 126:138004. [PMID: 33861109 DOI: 10.1103/physrevlett.126.138004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
While the interplay between liquid-liquid phase separation (LLPS) and glass formation in biological systems is highly relevant for their structure formation and thus function, the exact underlying mechanisms are not well known. The kinetic arrest originates from the slowdown at the molecular level, but how this propagates to the dynamics of microscopic phase domains is not clear. Since with diffusion, viscoelasticity, and hydrodynamics, distinctly different mechanisms are at play, the dynamics needs to be monitored on the relevant time and length scales and compared to theories of phase separation. Using x-ray photon correlation spectroscopy, we determine the LLPS dynamics of a model protein solution upon low temperature quenches and find distinctly different dynamical regimes. We observe that the early stage LLPS is driven by the curvature of the free energy and speeds up upon increasing quench depth. In contrast, the late stage dynamics slows down with increasing quench depth, fingerprinting a nearby glass transition. The dynamics observed shows a ballistic type of motion, implying that viscoelasticity plays an important role during LLPS. We explore possible explanations based on the Cahn-Hilliard theory with nontrivial mobility parameters and find that these can only partially explain our findings.
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Affiliation(s)
- Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Hendrik Rahmann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Mario Reiser
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
- European X-Ray Free-Electron Laser XFEL, Holzkoppel 4,22869 Schenefeld, Germany
| | - Sivasurender Chandran
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Department of Physics, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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19
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Perakis F, Gutt C. Towards molecular movies with X-ray photon correlation spectroscopy. Phys Chem Chem Phys 2021; 22:19443-19453. [PMID: 32870200 DOI: 10.1039/d0cp03551c] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective article we highlight research opportunities and challenges in probing structural dynamics of molecular systems using X-ray Photon Correlation Spectroscopy (XPCS). The development of new X-ray sources, such as 4th generation storage rings and X-ray free-electron lasers (XFELs), provides promising new insights into molecular motion. Employing XPCS at these sources allows to capture a very broad range of timescales and lengthscales, spanning from femtoseconds to minutes and atomic scales to the mesoscale. Here, we discuss the scientific questions that can be addressed with these novel tools for two prominent examples: the dynamics of proteins in biomolecular condensates and the dynamics of supercooled water. Finally, we provide practical tips for designing and estimating feasibility of XPCS experiments as well as on detecting and mitigating radiation damage.
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Affiliation(s)
- Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Christian Gutt
- Department Physik, Universität Siegen, D-57072 Siegen, Germany.
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20
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Hentschel L, Hansen J, Egelhaaf SU, Platten F. The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson–Boltzmann model of tetragonal lysozyme crystals. Phys Chem Chem Phys 2021; 23:2686-2696. [DOI: 10.1039/d0cp06113a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microcalorimetric and van't Hoff determinations as well as a theoretical description provide a consistent picture of the crystallization enthalpy and entropy of protein solutions and their dependence on physicochemical solution parameters.
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Affiliation(s)
- Lorena Hentschel
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Jan Hansen
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
- Institute of Biological Information Processing (IBI-4: Biomacromolecular Systems and Processes)
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21
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Brocca S, Grandori R, Longhi S, Uversky V. Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions. Int J Mol Sci 2020; 21:E9045. [PMID: 33260713 PMCID: PMC7730420 DOI: 10.3390/ijms21239045] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are unable to adopt a unique 3D structure under physiological conditions and thus exist as highly dynamic conformational ensembles. IDPs are ubiquitous and widely spread in the protein realm. In the last decade, compelling experimental evidence has been gathered, pointing to the ability of IDPs and intrinsically disordered regions (IDRs) to undergo liquid-liquid phase separation (LLPS), a phenomenon driving the formation of membrane-less organelles (MLOs). These biological condensates play a critical role in the spatio-temporal organization of the cell, where they exert a multitude of key biological functions, ranging from transcriptional regulation and silencing to control of signal transduction networks. After introducing IDPs and LLPS, we herein survey available data on LLPS by IDPs/IDRs of viral origin and discuss their functional implications. We distinguish LLPS associated with viral replication and trafficking of viral components, from the LLPS-mediated interference of viruses with host cell functions. We discuss emerging evidence on the ability of plant virus proteins to interfere with the regulation of MLOs of the host and propose that bacteriophages can interfere with bacterial LLPS, as well. We conclude by discussing how LLPS could be targeted to treat phase separation-associated diseases, including viral infections.
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Affiliation(s)
- Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milano, Italy
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille University and CNRS, 13288 Marseille, France
| | - Vladimir Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33601, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia
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22
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Cochereau R, Renard D, Noûs C, Boire A. Semi-permeable vesicles produced by microfluidics to tune the phase behaviour of encapsulated macromolecules. J Colloid Interface Sci 2020; 580:709-719. [PMID: 32712477 DOI: 10.1016/j.jcis.2020.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/28/2020] [Accepted: 07/05/2020] [Indexed: 12/11/2022]
Abstract
Understanding the dynamics of macromolecular assemblies in solution, such as Liquid-Liquid Phase Separation (LLPS), represents technologic and fundamental challenges in many fields. In cell biology, such dynamics are of great interest, because of their involvement in subcellular processes. In our study, we aimed to control the assembly of macromolecules in aqueous semi-permeable vesicles, that we named osmosomes, using microfluidics. We developed a microfluidic chip that allows for producting and trapping Giant Unilamellar Vesicles (GUVs) encapsulating macromolecules. This device also allows for modification of the composition of the inner phase and of the membranes of the trapped GUVs. The vesicles are produced from water-in-oil-in-water (w/o/w) double emulsions in less than 20 min after discarding the oil phase. They are highly monodisperse and their diameter can be modulated between 20 and 110 µm by tuning the flow rates of fluid phases. Their unilamellarity is proofed by two techniques: (1) fluorescence quenching experiments and (2) the insertion of the α-hemolysin membrane protein pore. We demonstrate that the internal pH of osmosomes can be tuned in less than 1 min by controlling solvent exchanges through the α-hemolysin pores. The detailed analysis of the exchange kinetics suggests that the microfluidic chip provides an efficient pore formation due to the physical trapping of vesicles and the constant flow rate. Finally, we show a proof of concept for macromolecular assembly within osmosomes by pH-triggered LLPS of wheat proteins within a few minutes.
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23
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Da Vela S, Begam N, Dyachok D, Schäufele RS, Matsarskaia O, Braun MK, Girelli A, Ragulskaya A, Mariani A, Zhang F, Schreiber F. Interplay between Glass Formation and Liquid-Liquid Phase Separation Revealed by the Scattering Invariant. J Phys Chem Lett 2020; 11:7273-7278. [PMID: 32787309 DOI: 10.1021/acs.jpclett.0c02110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The interplay of the glass transition with liquid-liquid phase separation (LLPS) is a subject of intense debate. We use the scattering invariant Q to probe how approaching the glass transition affects the shape of LLPS boundaries in the temperature/volume fraction plane. Two protein systems featuring kinetic arrest with a lower and an upper critical solution temperature phase behavior, respectively, are studied varying the quench depth. Using Q we noninvasively identify system-dependent differences for the effect of glass formation on the LLPS boundary. The glassy dense phase appears to enter the coexistence region for the albumin-YCl3 system, whereas it follows the equilibrium binodal for the γ-globulin-PEG system.
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Affiliation(s)
- Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Danylo Dyachok
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | | | - Olga Matsarskaia
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Michal K Braun
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | | | - Alessandro Mariani
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, F-38043 Grenoble Cedex 9, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
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24
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Begam N, Da Vela S, Matsarskaia O, Braun MK, Mariani A, Zhang F, Schreiber F. Packing and dynamics of a protein solution approaching the jammed state. SOFT MATTER 2020; 16:7751-7759. [PMID: 32744265 DOI: 10.1039/d0sm00962h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The packing of proteins and their collective behavior in crowded media is crucial for the understanding of biological processes. Here we study the structural and dynamical evolution of solutions of the globular protein bovine serum albumin with increasing concentration via drying using small angle X-ray scattering and dynamic light scattering. We probe an evolving correlation peak on the scattering profile, corresponding to the inter-protein distance, ξ, which decreases following a power law of the protein volume fraction, φ. The rate of decrease in ξ becomes faster above a protein concentration of ∼200 mg ml-1 (φ = 0.15). The power law exponent changes from 0.33, which is typical of colloidal or protein solutions, to 0.41. During the entire drying process, we observe the development and the growth of two-step relaxation dynamics with increasing φ as revealed by dynamic light scattering. We find three different regimes of the dependence of ξ as a function of φ. In the dilute regime (φ < 0.22), protein molecules are far apart from each other compared to their size. In this case, the dynamics mainly corresponds to Brownian motion. At an intermediate concentration (0.22 < φ < 0.47), inter-protein distances become comparable to the size of protein molecules, leading to a preferential orientation of the ellipsoidal protein molecules along with a possible deformation. In this regime, the dynamics shows two distinct relaxation times. At a very high concentration (φ > 0.47), the system reaches a jammed state. Subsequently, the secondary relaxation time in this state becomes extremely slow. In this state, the protein molecules have approximately one hydration layer. This study contributes to the understanding of protein molecular packing in crowded environments and the phenomenon of density-driven jamming for soft matter systems.
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Affiliation(s)
- Nafisa Begam
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Stefano Da Vela
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Olga Matsarskaia
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Michal K Braun
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Alessandro Mariani
- ESRF-The European Synchrotron, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
| | - Frank Schreiber
- Institut für Angewandte Physik, Universtitat Tübingen, 70276, Tübingen, Germany.
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25
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Matsarskaia O, Roosen‐Runge F, Schreiber F. Multivalent ions and biomolecules: Attempting a comprehensive perspective. Chemphyschem 2020; 21:1742-1767. [PMID: 32406605 PMCID: PMC7496725 DOI: 10.1002/cphc.202000162] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.
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Affiliation(s)
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Faculty of Health and SocietyMalmö UniversitySweden
- Division of Physical ChemistryLund UniversitySweden
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26
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Harada M, Yamamoto S, Yatsuhashi T, Sakota K. Cooperative dissociation of J-aggregates into monomers in the 2-isobutoxyethanol/water binary solvent with the lower critical solution temperature. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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27
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Isobe N, Shimizu S. Salt-induced LCST-type thermal gelation of methylcellulose: quantifying non-specific interactions via fluctuation theory. Phys Chem Chem Phys 2020; 22:15999-16006. [PMID: 32632420 DOI: 10.1039/d0cp01687j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
What drives the phase separation of water-soluble polymers in the presence of electrolytes was quantified on a molecular scale via statistical thermodynamic fluctuation theory. Quantifying polymer-water and polymer-salt interactions enabled us to identify the dominant interaction for phase separation. As a model system, the lower critical solution temperature (LCST) type thermal gelation of methylcellulose (MC) in aqueous salt solutions was chosen. The Kirkwood-Buff integrals for intermolecular interactions, calculated from the published calorimetric and volumetric data, showed that (1) the accumulation of salts around MC molecules (favourable interaction between salts and MC) inhibits thermal gelation and the depletion of salts from MC (unfavourable interaction between salts and MC) promotes the gelation, and (2) this salt-MC interaction is the dominant factor (50-100 times stronger than the water-MC interaction). This insight from the fluctuation theory is at odds with the age-old consensus regarding the driving force of thermal gelation: water structure change in the presence of salts induces the promotion or inhibition of thermal gelation. However, our conclusion is founded upon the ability of the fluctuation theory to quantify water-MC and salt-MC interaction independently via the Kirkwood-Buff integrals. Flory-Huggins (FH) theory, on the contrary, could not separate these two interactions owing to the lack of a thermodynamic degree of freedom because the lattice solution is assumed to be fully packed. In addition, the dominant contribution from salt depletion poses difficulty for the χ parameter, which is essentially the difference of contact energies. Our approach, requiring calorimetric and volumetric data alone as input, provides a simple and versatile method towards elucidating the effect of cosolvents on biopolymer phase separation of physiological importance.
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Affiliation(s)
- Noriyuki Isobe
- Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
| | - Seishi Shimizu
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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28
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Meng Z, Huang Y, Cheng S, Wang J. Investigation of Oiling‐Out Phenomenon of Small Organic Molecules in Crystallization Processes: A Review. ChemistrySelect 2020. [DOI: 10.1002/slct.202001255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Zichao Meng
- School of Chemical Engineering and TechnologyTianjin University No. 92 Weijin Road Tianjin 300072 P.R. China
| | - Yan Huang
- School of Chemical Engineering and TechnologyTianjin University No. 92 Weijin Road Tianjin 300072 P.R. China
| | - Shuo Cheng
- School of Chemical Engineering and TechnologyTianjin University No. 92 Weijin Road Tianjin 300072 P.R. China
| | - Jingtao Wang
- School of Chemical Engineering and TechnologyTianjin University No. 92 Weijin Road Tianjin 300072 P.R. China
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29
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Begam N, Matsarskaia O, Sztucki M, Zhang F, Schreiber F. Unification of lower and upper critical solution temperature phase behavior of globular protein solutions in the presence of multivalent cations. SOFT MATTER 2020; 16:2128-2134. [PMID: 32016274 DOI: 10.1039/c9sm02329a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In globular protein systems, upper critical solution temperature (UCST) behavior is common, but lower critical solution temperature (LCST) phase transitions are rare. In addition, the temperature sensitivity of such systems is usually difficult to tune. Here we demonstrate that the charge state of globular proteins in aqueous solutions can alter their temperature-dependent phase behavior. We show a universal way to tune the effective protein interactions and induce both UCST and LCST-type transitions in the system using trivalent salts. We provide a phase diagram identifying LCST and UCST regimes as a function of protein and salt concentrations. We further propose a model based on an entropy-driven cation binding mechanism to explain the experimental observations.
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Affiliation(s)
- Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany.
| | - Olga Matsarskaia
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany.
| | - Michael Sztucki
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany.
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany.
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Narayanan T, Konovalov O. Synchrotron Scattering Methods for Nanomaterials and Soft Matter Research. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E752. [PMID: 32041363 PMCID: PMC7040635 DOI: 10.3390/ma13030752] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/17/2022]
Abstract
This article aims to provide an overview of broad range of applications of synchrotron scattering methods in the investigation of nanoscale materials. These scattering techniques allow the elucidation of the structure and dynamics of nanomaterials from sub-nm to micron size scales and down to sub-millisecond time ranges both in bulk and at interfaces. A major advantage of scattering methods is that they provide the ensemble averaged information under in situ and operando conditions. As a result, they are complementary to various imaging techniques which reveal more local information. Scattering methods are particularly suitable for probing buried structures that are difficult to image. Although, many qualitative features can be directly extracted from scattering data, derivation of detailed structural and dynamical information requires quantitative modeling. The fourth-generation synchrotron sources open new possibilities for investigating these complex systems by exploiting the enhanced brightness and coherence properties of X-rays.
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Falke S, Brognaro H, Martirosyan A, Dierks K, Betzel C. A multi-channel in situ light scattering instrument utilized for monitoring protein aggregation and liquid dense cluster formation. Heliyon 2019; 5:e03016. [PMID: 31886430 PMCID: PMC6921120 DOI: 10.1016/j.heliyon.2019.e03016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/29/2019] [Accepted: 12/06/2019] [Indexed: 12/18/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) phenomena have been observed in vitro as well as in vivo and came in focus of interdisciplinary research activities particularly aiming at understanding the physico-chemical pathways of LLPS and its functionality in recent years. Dynamic light scattering (DLS) has been proven to be a most efficient method to analyze macromolecular clustering in solutions and suspensions with diverse applications in life sciences, material science and biotechnology. For spatially and time-resolved investigations of LLPS, i.e. formation of liquid dense protein clusters (LDCs) and aggregation, a novel eight-channel in situ DLS instrument was designed, constructed and applied. The real time formation of LDCs of glucose isomerase (GI) and bovine pancreatic trypsin inhibitor (BPTI) under different physico-chemical conditions was investigated in situ. Complex shifts in the particle size distributions indicated growth of LDCs up to the μm size regime. Additionally, near-UV circular dichroism spectroscopy was performed to monitor the folding state of the proteins in the process of LDC formation.
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Affiliation(s)
- Sven Falke
- University Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, c/o DESY, Luruper Chaussee 149, Hamburg, 22607, Germany
| | - Hévila Brognaro
- University Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany
- Centre for Free-Electron-Laser Science, c/o DESY, Luruper Chaussee 149, Hamburg, 22607, Germany
| | - Arayik Martirosyan
- University Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany
| | - Karsten Dierks
- Xtal Concepts GmbH, Schnackenburgallee 13, 22525, Hamburg, Germany
| | - Christian Betzel
- University Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, c/o DESY, Luruper Chaussee 149, Hamburg, 22607, Germany
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Multi-Step Concanavalin A Phase Separation and Early-Stage Nucleation Monitored Via Dynamic and Depolarized Light Scattering. CRYSTALS 2019. [DOI: 10.3390/cryst9120620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein phase separation and protein liquid cluster formation have been observed and analysed in protein crystallization experiments and, in recent years, have been reported more frequently, especially in studies related to membraneless organelles and protein cluster formation in cells. A detailed understanding about the phase separation process preceding liquid dense cluster formation will elucidate what has, so far, been poorly understood—despite intracellular crowding and phase separation being very common processes—and will also provide more insights into the early events of in vitro protein crystallization. In this context, the phase separation and crystallization kinetics of concanavalin A were analysed in detail, which applies simultaneous dynamic light scattering and depolarized dynamic light scattering to obtain insights into metastable intermediate states between the soluble phase and the crystalline form. A multi-step mechanism was identified for ConA phase separation, according to the resultant ACF decay, acquired after an increase in the concentration of the crowding agent until a metastable ConA gel intermediate between the soluble and final crystalline phases was observed. The obtained results also revealed that ConA is trapped in a macromolecular network due to short-range intermolecular protein interactions and is unable to transform back into a non-ergodic solution.
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Banc A, Pincemaille J, Costanzo S, Chauveau E, Appavou MS, Morel MH, Menut P, Ramos L. Phase separation dynamics of gluten protein mixtures. SOFT MATTER 2019; 15:6160-6170. [PMID: 31317157 DOI: 10.1039/c9sm00966c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We investigate by time-resolved synchrotron ultra-small X-ray scattering the dynamics of liquid-liquid phase-separation (LLPS) of gluten protein suspensions following a temperature quench. Samples at a fixed concentration (237 mg ml-1) but with different protein compositions are investigated. In our experimental conditions, we show that fluid viscoelastic samples depleted in polymeric glutenin phase-separate following a spinodal decomposition process. We quantitatively probe the late stage coarsening that results from a competition between thermodynamics that speeds up the coarsening rate as the quench depth increases and transport that slows down the rate. For even deeper quenches, the even higher viscoelasticity of the continuous phase leads to a "quasi" arrested phase separation. Anomalous phase-separation dynamics is by contrast measured for a gel sample rich in glutenin, due to elastic constraints. This work illustrates the role of viscoelasticity in the dynamics of LLPS in protein dispersions.
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Affiliation(s)
- Amélie Banc
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France.
| | - Justine Pincemaille
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France. and Ingénierie des Agro-polymères et Technologies Emergentes (IATE), Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Salvatore Costanzo
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France.
| | - Edouard Chauveau
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France.
| | - Marie-Sousai Appavou
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) Lichtenbergstr. 1, 85748 Garching, Germany
| | - Marie-Hélène Morel
- Ingénierie des Agro-polymères et Technologies Emergentes (IATE), Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Paul Menut
- Ingénierie des Agro-polymères et Technologies Emergentes (IATE), Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France and Ingénierie Procédés Aliments, AgroParisTech, INRA, Université Paris-Saclay, Massy, France
| | - Laurence Ramos
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France.
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Le Ferrand H, Duchamp M, Gabryelczyk B, Cai H, Miserez A. Time-Resolved Observations of Liquid–Liquid Phase Separation at the Nanoscale Using in Situ Liquid Transmission Electron Microscopy. J Am Chem Soc 2019; 141:7202-7210. [DOI: 10.1021/jacs.9b03083] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hortense Le Ferrand
- Biological and Biomimetic Material Laboratory and Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553
| | - Martial Duchamp
- Laboratory for in Situ & Operando Electron Nanoscopy, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637371
| | - Bartosz Gabryelczyk
- Biological and Biomimetic Material Laboratory and Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553
| | - Hao Cai
- Biological and Biomimetic Material Laboratory and Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory and Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
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Matsarskaia O, Da Vela S, Mariani A, Fu Z, Zhang F, Schreiber F. Phase-Separation Kinetics in Protein-Salt Mixtures with Compositionally Tuned Interactions. J Phys Chem B 2019; 123:1913-1919. [PMID: 30702291 DOI: 10.1021/acs.jpcb.8b10725] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Liquid-liquid phase separation (LLPS) in protein systems is relevant for many phenomena, from protein condensation diseases to subcellular organization to possible pathways toward protein crystallization. Understanding and controlling LLPS in proteins is therefore highly relevant for various areas of (biological) soft matter research. Solutions of the protein bovine serum albumin (BSA) have been shown to have a lower critical solution temperature-LLPS (LCST-LLPS) induceable by multivalent salts. Importantly, the nature of the multivalent cation used influences the LCST-LLPS in such systems. Here, we present a systematic ultrasmall-angle X-ray scattering investigation of the kinetics of LCST-LLPS of BSA in the presence of different mixtures of HoCl3 and LaCl3, resulting in different effective interprotein attraction strengths. We monitor the characteristic length scales ξ( t, Tfin) after inducing LLPS by subjecting the respective systems to temperature jumps in their liquid-liquid coexistence regions. With increasing interprotein attraction and increasing Tfin, we observe an increasing deviation from the growth law of ξ ∼ t1/3 and an increased trend toward arrest. We thus establish a multidimensional method to tune phase transitions in our systems. Our findings help shed light on general questions regarding LLPS and the tunability of its kinetics in both proteins and colloidal systems.
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Affiliation(s)
- Olga Matsarskaia
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Stefano Da Vela
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Alessandro Mariani
- European Synchrotron Radiation Facility , 71 Avenue des Martyrs , 38043 Grenoble Cedex 9 , France
| | - Zhendong Fu
- Forschungszentrum Jülich GmbH, JCNS@MLZ , Lichtenbergstrasse 1 , 85747 Garching , Germany
| | - Fajun Zhang
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Frank Schreiber
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
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36
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Pandit S, Kundu S. Optical responses of BSA protein under re-entrant condensation in presence of trivalent ions. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Boire A, Renard D, Bouchoux A, Pezennec S, Croguennec T, Lechevalier V, Le Floch-Fouéré C, Bouhallab S, Menut P. Soft-Matter Approaches for Controlling Food Protein Interactions and Assembly. Annu Rev Food Sci Technol 2019; 10:521-539. [PMID: 30633568 DOI: 10.1146/annurev-food-032818-121907] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animal- and plant-based proteins are present in a wide variety of raw and processed foods. They play an important role in determining the final structure of food matrices. Food proteins are diverse in terms of their biological origin, molecular structure, and supramolecular assembly. This diversity has led to segmented experimental studies that typically focus on one or two proteins but hinder a more general understanding of food protein structuring as a whole. In this review, we propose a unified view of how soft-matter physics can be used to control food protein assembly. We discuss physical models from polymer and colloidal science that best describe and predict the phase behavior of proteins. We explore the occurrence of phase transitions along two axes: increasing protein concentration and increasing molecular attraction. This review provides new perspectives on the link between the interactions, phase transitions, and assembly of proteins that can help in designing new food products and innovative food processing operations.
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Affiliation(s)
- Adeline Boire
- Biopolymères Interactions Assemblages, INRA UR1268, F-44300 Nantes, France;
| | - Denis Renard
- Biopolymères Interactions Assemblages, INRA UR1268, F-44300 Nantes, France;
| | - Antoine Bouchoux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, F-31077 Toulouse, France
| | | | | | | | | | - Saïd Bouhallab
- STLO, INRA UMR1253, Agrocampus Ouest, F-35042 Rennes, France
| | - Paul Menut
- Montpellier SupAgro, 34060 Montpellier, France; .,Ingénierie Procédés Aliments, AgroParisTech, INRA, Université Paris-Saclay, 91300 Massy, France
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Narayanan T, Sztucki M, Van Vaerenbergh P, Léonardon J, Gorini J, Claustre L, Sever F, Morse J, Boesecke P. A multipurpose instrument for time-resolved ultra-small-angle and coherent X-ray scattering. J Appl Crystallogr 2018; 51:1511-1524. [PMID: 30546286 PMCID: PMC6276275 DOI: 10.1107/s1600576718012748] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/08/2018] [Indexed: 11/17/2022] Open
Abstract
This article presents the main technical features and performance of the upgraded beamline ID02 at the ESRF. The beamline combines different small-angle X-ray scattering techniques in one unique instrument, enabling static and kinetic investigations from ångström to micrometre size scales and time resolution down to the sub-millisecond range. The main component of the instrument is an evacuated detector tube of length 34 m and diameter 2 m. Several different detectors are housed inside a motorized wagon that travels along a rail system, allowing an automated change of the sample-detector distance from about 1 to 31 m as well as selection of the desired detector. For optional combined wide-angle scattering measurements, a wide-angle detector is installed at the entrance cone of the tube. A scattering vector (of magnitude q) range of 0.002 ≤ q ≤ 50 nm-1 is covered with two sample-detector distances and a single-beam setting for an X-ray wavelength of 1 Å. In the high-resolution mode, two-dimensional ultra-small-angle X-ray scattering patterns down to q < 0.001 nm-1 can be recorded, and the resulting one-dimensional profiles have superior quality as compared to those measured with an optimized Bonse-Hart instrument. In the highest-resolution mode, the beam is nearly coherent, thereby permitting multispeckle ultra-small-angle X-ray photon correlation spectroscopy measurements. The main applications of the instrument include the elucidation of static and transient hierarchical structures, and nonequilibrium dynamics in soft matter and biophysical systems.
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Affiliation(s)
| | | | | | | | | | | | - Franc Sever
- ESRF – The European Synchrotron, 38043 Grenoble, France
| | - John Morse
- ESRF – The European Synchrotron, 38043 Grenoble, France
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Braun MK, Sauter A, Matsarskaia O, Wolf M, Roosen-Runge F, Sztucki M, Roth R, Zhang F, Schreiber F. Reentrant Phase Behavior in Protein Solutions Induced by Multivalent Salts: Strong Effect of Anions Cl - Versus NO 3.. J Phys Chem B 2018; 122:11978-11985. [PMID: 30461282 DOI: 10.1021/acs.jpcb.8b10268] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this work, the effects of the two anions Cl- and NO3- on the phase behavior of bovine serum albumin (BSA) in solution with trivalent salts are compared systematically. In the presence of trivalent metal salts, negatively charged proteins such as BSA in solution undergo a reentrant condensation (RC) phase behavior, which has been established for several proteins with chlorides of trivalent salts. Here, we show that replacing Cl- by NO3- leads to a marked change in the phase behavior. The effect is investigated for the two different cations Y3+ and La3+. The salts are thus YCl3, Y(NO3)3, LaCl3, and La(NO3)3. The experimental phase behavior shows that while the chloride salts induce both liquid-liquid phase separation (LLPS) and RC, the nitrate salts also induce LLPS, but RC becomes partial with La(NO3)3 and disappears with Y(NO3)3. The observed phase behavior is rationalized by effective protein-protein interactions which are characterized using small-angle X-ray scattering. The results based on the reduced second virial coefficients B2/ B2HS and 1/ I( q → 0) demonstrate that the NO3- salts induce a stronger attraction than the Cl- salts. Overall, the effective attraction, the width of the condensed regime in the RC phase diagram, and the nature of LLPS follow the order LaCl3 < YCl3 < La(NO3)3 < Y(NO3)3. Despite the decisive role of cations in RC phase behavior, isothermal titration calorimetry measurements indicate that replacing anions does not significantly influence the cation binding to proteins. The experimental results observed are discussed based on an "enhanced Hofmeister effect" including electrostatic and hydrophobic interactions between protein-cation complexes.
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Affiliation(s)
- Michal K Braun
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Andrea Sauter
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Olga Matsarskaia
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Marcell Wolf
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Felix Roosen-Runge
- Division of Physical Chemistry, Department of Chemistry , Lund University , Naturvetarvägen 14 , 22100 Lund , Sweden
| | - Michael Sztucki
- ESRF-The European Synchrotron Radiation Facility , 71 avenue des Martyrs , 38000 Grenoble , France
| | - Roland Roth
- Institut für Theoretische Physik , Universität Tübingen , Auf der Morgenstelle 14 , 72076 Tübingen , Germany
| | - Fajun Zhang
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Frank Schreiber
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
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40
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Matsarskaia O, Roosen-Runge F, Lotze G, Möller J, Mariani A, Zhang F, Schreiber F. Tuning phase transitions of aqueous protein solutions by multivalent cations. Phys Chem Chem Phys 2018; 20:27214-27225. [PMID: 30351336 DOI: 10.1039/c8cp05884a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the presence of trivalent cations, negatively charged globular proteins show a rich phase behaviour including reentrant condensation, crystallisation, clustering and lower critical solution temperature metastable liquid-liquid phase separation (LCST-LLPS). Here, we present a systematic study on how different multivalent cations can be employed to tune the interactions and the associated phase behaviour of proteins. We focus our investigations on the protein bovine serum albumin (BSA) in the presence of HoCl3, LaCl3 and YCl3. Using UV-Vis spectroscopy and small-angle X-ray scattering (SAXS), we find that the interprotein attraction induced by Ho3+ is very strong, while the one induced by La3+ is comparatively weak when comparing the data to BSA-Y3+ systems based on our previous work. Using zeta potential and isothermal titration calorimetry (ITC) measurements, we establish different binding affinities of cations to BSA with Ho3+ having the highest one. We propose that a combination of different cation features such as radius, polarisability and in particular hydration effects determine the protein-protein interaction induced by these cations. Our findings imply that subtle differences in cation properties can be a sensitive tool to fine-tune protein-protein interactions and phase behaviour in solution.
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Affiliation(s)
- Olga Matsarskaia
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.
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Erdel F, Rippe K. Formation of Chromatin Subcompartments by Phase Separation. Biophys J 2018; 114:2262-2270. [PMID: 29628210 DOI: 10.1016/j.bpj.2018.03.011] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/19/2018] [Accepted: 03/06/2018] [Indexed: 10/17/2022] Open
Abstract
Chromatin is partitioned on multiple length scales into subcompartments that differ from each other with respect to their molecular composition and biological function. It is a key question how these compartments can form even though diffusion constantly mixes the nuclear interior and rapidly balances concentration gradients of soluble nuclear components. Different biophysical concepts are currently used to explain the formation of "chromatin bodies" in a self-organizing manner and without consuming energy. They rationalize how soluble protein factors that are dissolved in the liquid nuclear phase, the nucleoplasm, bind and organize transcriptionally active or silenced chromatin domains. In addition to cooperative binding of proteins to a preformed chromatin structure, two different mechanisms for the formation of phase-separated chromatin subcompartments have been proposed. One is based on bridging proteins that cross-link polymer segments with particular properties. Bridging can induce a collapse of the nucleosome chain and associated factors into an ordered globular phase. The other mechanism is based on multivalent interactions among soluble molecules that bind to chromatin. These interactions can induce liquid-liquid phase separation, which drives the assembly of liquid-like nuclear bodies around the respective binding sites on chromatin. Both phase separation mechanisms can explain that chromatin bodies are dynamic spherical structures, which can coalesce and are in constant and rapid exchange with the surrounding nucleoplasm. However, they make distinct predictions about how the size, density, and stability of chromatin bodies depends on the concentration and interaction behavior of the molecules involved. Here, we compare the different biophysical mechanisms for the assembly of chromatin bodies and discuss experimental strategies to distinguish them from each other. Furthermore, we outline the implications for the establishment and memory of functional chromatin state patterns.
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Affiliation(s)
- Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
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Da Vela S, Exner C, Schäufele RS, Möller J, Fu Z, Zhang F, Schreiber F. Arrested and temporarily arrested states in a protein-polymer mixture studied by USAXS and VSANS. SOFT MATTER 2017; 13:8756-8765. [PMID: 29130090 DOI: 10.1039/c7sm01434a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigate the transition of the phase separation kinetics from a complete to an arrested liquid-liquid phase separation (LLPS) in mixtures of bovine γ-globulin with polyethylene glycol (PEG). The solutions feature LLPS with upper critical solution temperature phase behavior. At higher PEG concentrations or low temperatures, non-equilibrium, gel-like states are found. The kinetics is followed during off-critical quenches by ultra-small angle X-ray scattering (USAXS) and very-small angle neutron scattering (VSANS). For shallow quenches a kinetics consistent with classical spinodal decomposition is found, with the characteristic length (ξ) growing with time as ξ ∼ t1/3. For deep quenches, ξ grows only very slowly with a growth exponent smaller than 0.05 during the observation time, indicating an arrested phase separation. For intermediate quench depths, a novel growth kinetics featuring a three-stage coarsening is observed, with an initial classical coarsening, a subsequent slowdown of the growth, and a later resumption of coarsening approaching again ξ ∼ t1/3. Samples featuring the three-stage coarsening undergo a temporarily arrested state. We hypothesize that, while intermittent coarsening and collapse might contribute to the temporary nature of the arrested state, migration-coalescence of the minority liquid phase through the majority glassy phase may be the main mechanism underlying this kinetics, which is also consistent with earlier simulation results.
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Affiliation(s)
- Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.
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Zhang F. Nonclassical nucleation pathways in protein crystallization. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:443002. [PMID: 28984274 DOI: 10.1088/1361-648x/aa8253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.
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Affiliation(s)
- Fajun Zhang
- Universität Tübingen, Institut für Angewandte Physik, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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