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Cubuk J, Soranno A. Macromolecular crowding and intrinsically disordered proteins: a polymer physics perspective. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202100051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Cubuk
- Washington University in St Louis Biochemistry and Molecular Biophysics UNITED STATES
| | - Andrea Soranno
- Washington University in St Louis Biochemistry and Molecular Biophysics 660 St Euclid Ave 63110 St Louis UNITED STATES
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2
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Müller M, Abetz V. Nonequilibrium Processes in Polymer Membrane Formation: Theory and Experiment. Chem Rev 2021; 121:14189-14231. [PMID: 34032399 DOI: 10.1021/acs.chemrev.1c00029] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Porous polymer and copolymer membranes are useful for ultrafiltration of functional macromolecules, colloids, and water purification. In particular, block copolymer membranes offer a bottom-up approach to form isoporous membranes. To optimize permeability, selectivity, longevity, and cost, and to rationally design fabrication processes, direct insights into the spatiotemporal structure evolution are necessary. Because of a multitude of nonequilibrium processes in polymer membrane formation, theoretical predictions via continuum models and particle simulations remain a challenge. We compiled experimental observations and theoretical approaches for homo- and block copolymer membranes prepared by nonsolvent-induced phase separation and highlight the interplay of multiple nonequilibrium processes─evaporation, solvent-nonsolvent exchange, diffusion, hydrodynamic flow, viscoelasticity, macro- and microphase separation, and dynamic arrest─that dictates the complex structure of the membrane on different scales.
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Affiliation(s)
- Marcus Müller
- Georg-August Universität, Institut für Theoretische Physik, 37073 Göttingen, Germany
| | - Volker Abetz
- Helmholtz-Zentrum Hereon, Institut für Membranforschung, 21502 Geesthacht, Germany.,Universität Hamburg, Institut für Physikalische Chemie, 20146 Hamburg, Germany
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3
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Classical Critical Behaviors and Ginzburg Criteria for Polymer Mixtures. Macromol Res 2021. [DOI: 10.1007/s13233-021-2083-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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König I, Soranno A, Nettels D, Schuler B. Impact of In‐Cell and In‐Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Iwo König
- Department of Biochemistry and Department of Physics University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics Center for Science and Engineering of Living Systems (CSELS) Washington University in St. Louis St. Louis USA
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland
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König I, Soranno A, Nettels D, Schuler B. Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2021; 60:10724-10729. [PMID: 33587794 DOI: 10.1002/anie.202016804] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/08/2021] [Indexed: 01/23/2023]
Abstract
The conformations and dynamics of proteins can be influenced by crowding from the large concentrations of macromolecules within cells. Intrinsically disordered proteins (IDPs) exhibit chain compaction in crowded solutions in vitro, but no such effects were observed in cultured mammalian cells. Here, to increase intracellular crowding, we reduced the cell volume by hyperosmotic stress and used an IDP as a crowding sensor for in-cell single-molecule spectroscopy. In these more crowded cells, the IDP exhibits compaction, slower chain dynamics, and much slower translational diffusion, indicating a pronounced concentration and length-scale dependence of crowding. In vitro, these effects cannot be reproduced with small but only with large polymeric crowders. The observations can be explained with polymer theory and depletion interactions and indicate that IDPs can diffuse much more efficiently through a crowded cytosol than a globular protein of similar dimensions.
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Affiliation(s)
- Iwo König
- Department of Biochemistry and Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, USA
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
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Bian Y, Yan R, Li P, Zhao N. Unusual crowding-induced chain looping kinetics in hard-sphere fluids: a contrastive study with polymer solutions. SOFT MATTER 2019; 15:4976-4988. [PMID: 31173026 DOI: 10.1039/c9sm00400a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A theoretical framework is developed to investigate the looping kinetics of a chain in hard-sphere (HS) fluids, based on a generalized Smoluchowski diffusion-reaction equation. A contrastive study with polymer solutions is performed. The crowding-associated effective viscosity and collapse effects are properly taken into account, which obey different scaling relations in HS and polymer fluids. We examine the dependence of the looping time on both concentration and size of crowders, demonstrating unusual and distinct discrepancies in the two crowded media. Firstly, in the solution of large polymers, the looping rate grows monotonically with polymer concentration. On the other hand, in the solution of large HSs, a caging regime can be observed, where the looping time tends to the value in the absence of crowders. Secondly, polymers in moderate size generally impede chain looping due to the enhanced viscosity. However, in HS fluids, the looping time exhibits a rather complicated variation with increasing HS size. We show a possible mechanism where in the case of small crowders with a relatively strong compaction in the probed chain, the looping kinetics can be facilitated. As the crowder size increases, the collapse effect is reduced and looping is dominated by viscosity-induced inhibition. Simultaneously, our theory rationalizes another possibility of the mechanism observed by recent simulation work. We conclude that the looping kinetics in specific systems actually should be governed by the critical competition between the two crowding factors. By giving reasonable measurements of effective viscosity and collapse, our theoretical framework can provide a unified strategy to analyze crowding effects on the looping rate in a systematic manner.
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Affiliation(s)
- Yukun Bian
- College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
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Bian Y, Cao X, Li P, Zhao N. Understanding chain looping kinetics in polymer solutions: crowding effects of microviscosity and collapse. SOFT MATTER 2018; 14:8060-8072. [PMID: 30255917 DOI: 10.1039/c8sm01499j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A theoretical framework based on a generalized Langevin equation with fractional Gaussian noise is presented to describe the looping kinetics of chains in polymer solutions. Particular attention is paid to quantitatively revealing crowding effects on the loop formation rate in terms of microviscosity and collapse. By the aid of empirical relations for these two crowding associated physical quantities, we explicitly investigate the relationship between the looping rate and polymer concentration, the degree of polymerization, and system parameters. According to our analysis, the dependence of the looping rate on the crowder volume fraction exhibits three typical regimes: monotonic decreasing, a non-monotonic trend and monotonic increasing. We reveal that these non-trivial behaviors can be attributed to the competition between the two opposing factors of viscosity-associated inhibition and collapse-induced facilitation of loop formation. We apply our theory to analyze the kinetics of single-stranded DNA hairpin base pairing in polyethylene glycol solutions. The theoretical results can reproduce the experimental data on the closing rate of hairpins quantitatively to a certain degree with reasonable fitting parameters. The unexpected increase of the closing rate upon the addition of increasing amounts of polymer is well rationalised. Such good agreements clearly demonstrate the validity of our theory, appropriately addressing the very role of crowding effects in the relevant kinetics.
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Affiliation(s)
- Yukun Bian
- College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
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Schuler B, Soranno A, Hofmann H, Nettels D. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Annu Rev Biophys 2016; 45:207-31. [PMID: 27145874 DOI: 10.1146/annurev-biophys-062215-010915] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
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Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. Proc Natl Acad Sci U S A 2014; 111:4874-9. [PMID: 24639500 DOI: 10.1073/pnas.1322611111] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect of crowding as mimicked by commonly used biocompatible polymers. We observe a compaction of IDPs not only with increasing concentration, but also with increasing size of the crowding agents, at variance with the predictions from scaled-particle theory, the prevalent paradigm in the field. However, the observed behavior can be explained quantitatively if the polymeric nature of both the IDPs and the crowding molecules is taken into account explicitly. Our results suggest that excluded volume interactions between overlapping biopolymers and the resulting criticality of the system can be essential contributions to the physics governing the crowded cellular milieu.
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Kayillo S, Shalliker RA, Dennis GR. Thermodynamic Differences Between Deuterated and Protonated Polystyrenes Evaluated Using Reversed Phase Liquid Chromatography. MACROMOL CHEM PHYS 2005. [DOI: 10.1002/macp.200500207] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Irurzun I, Figini R, Marx-Figini M, Grigera J. Dynamics properties of polymer solutions (I). Dilute–semidilute transition. POLYMER 2000. [DOI: 10.1016/s0032-3861(99)00197-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Müller M. Single-Chain Conformations in Symmetric Binary Polymer Blends: Quantitative Comparison between Self-Consistent Field Calculations and Monte Carlo Simulations. Macromolecules 1998. [DOI: 10.1021/ma9807973] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Müller
- Institut für Physik, WA 331, Johannes Gutenberg Universität, D-55099 Mainz, Germany
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13
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Garas GE, Kosmas MK. The effect of chain correlations on the size of polymer coils in binary polymer blends. J Chem Phys 1996. [DOI: 10.1063/1.472317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ebert U, Baumgärtner A, Schäfer L. Universal short-time motion of a polymer in a random environment: Analytical calculations, a blob picture, and Monte Carlo results. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1996; 53:950-965. [PMID: 9964330 DOI: 10.1103/physreve.53.950] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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15
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On the thermodynamic treatment of poly(vinylidene fluoride)/polystyrene blend under liquid—liquid phase separation conditions. POLYMER 1995. [DOI: 10.1016/0032-3861(95)95928-t] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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