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Shea JE, Best RB, Mittal J. Physics-based computational and theoretical approaches to intrinsically disordered proteins. Curr Opin Struct Biol 2021; 67:219-225. [PMID: 33545530 PMCID: PMC8150118 DOI: 10.1016/j.sbi.2020.12.012] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an important class of proteins that do not fold to a well-defined three-dimensional shape but rather adopt an ensemble of inter-converting conformations. This feature makes their experimental characterization challenging and invites a theoretical and computational approach to complement experimental studies. In this review, we highlight the recent progress in developing new computational and theoretical approaches to study the structure and dynamics of monomeric and order higher assemblies of IDPs, with a particular emphasis on their phase separation into protein-rich condensates.
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Affiliation(s)
- Joan-Emma Shea
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106, United States; Department of Physics, University of California, Santa Barbara, CA 93106, United States.
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, United States.
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Mu D, Li JQ, Feng SY. Self-assembled morphologies of an amphiphilic Y-shaped weak polyelectrolyte in a thin film. Phys Chem Chem Phys 2017; 19:31011-31023. [PMID: 28967926 DOI: 10.1039/c7cp05497a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different from the self-assembly of neutral polymers, polyelectrolytes self-assemble into smaller aggregates with a more loosely assembled structure, which results from the repulsive forces acting between similar electrical compositions with the introduction of ions. The Y-shaped weak polyelectrolytes self-assemble into a core-shell type cylindrical structure with a hexagonal arrangement in a thin film, whose thickness is smaller than the gyration radius of the polymer chain. The corresponding formation mechanism consists of enrichment of the same components, adjustment of the shape of the aggregate, and the subsequent separation into individual aggregates. With the increase in the thickness of the thin film until it exceeds the gyration radius of the polymer chain, combined with the greater freedom of movement along the direction of thin film thickness, the self-assembled structure changes into a micellar structure. Under confinement, the repulsive force to the polymeric components is weakened by the repulsive forces among polyelectrolyte components with like charges, and this helps in generating aggregates with more uniform size and density distribution. In particular, when the repulsive force between the walls and the core forming components is greater than that between the walls and the shell forming components, such asymmetric confinement produces a crossed-cylindrical structure with nearly perpendicular arrangement of two cylinder arrays. Similarly, a novel three-crossed cylinder morphology is self-assembled upon removal of confinement.
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Affiliation(s)
- Dan Mu
- Institute of Research on the Structure and Property of Matter, Zaozhuang University, Shandong 277160, China.
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Lee MT, Vishnyakov A, Neimark AV. Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane. J Chem Phys 2016; 144:014902. [DOI: 10.1063/1.4938271] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ming-Tsung Lee
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854-8058, USA
| | - Aleksey Vishnyakov
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854-8058, USA
| | - Alexander V. Neimark
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854-8058, USA
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Mu D, Li JQ, Feng SY. Morphology of lipid-like structured weak polyelectrolyte poly(ethylene oxide)-block-poly(methyl methacrylate) diblock copolymers induced by confinements. SOFT MATTER 2015; 11:4356-4365. [PMID: 25875915 DOI: 10.1039/c5sm00438a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Combined with quantum calculations and mesoscale simulations, the self-assembly of twelve lipid-structured PEO-b-PMMA copolymers (BCPs) with six types of molecular topologies was investigated. The BCPs with MMA species as the connecting center of the other arms present ample mesoscale structures, such as micelles and lamellae or curved lamellar phases, and even macrophase separation occurs for the long-chained BCPs. The excluded volume effect of confinements helps form vesicle-like structures, which proved to be a possible method of confinement to regulate phase morphologies or segment distributions and, ultimately, the properties of materials. An analysis of the phase formation process of short-chained BCP with two hydrophilic EO segments and one hydrophobic MMA segment indicated that four stages were found in both neutral and non-neutral wall confinement, all of which present a hexagonal columnar phase. Surprisingly, when the repulsion effect of the wall to the EO segment is greater than that of the MMA segment, such BCP self assembles into a crossed columnar phase, and the intersection angle of the orientation of these two sets of cylinder arrays is 75 degrees, which can be used to produce heterogeneous nanotube arrays. For the short-chained BCP with four arms joined at MMA species and EO segments in the outer region, we found a novel method of exchanging the repulsive preference of the wall to the EO or MMA species that can control the adsorption or desorption of the lamellar phase with the interval of EO or MMA segments.
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Affiliation(s)
- Dan Mu
- Institute of Research on the Structure and Property of Matter, Zaozhuang University, Zaozhuang, 277160, China.
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Mu D, Li JQ, Feng SY. Mesoscopic simulation of the self-assembly of the weak polyelectrolyte poly(ethylene oxide)-block-poly(methyl methacrylate) diblock copolymers. SOFT MATTER 2015; 11:4366-4374. [PMID: 25871011 DOI: 10.1039/c5sm00346f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We designed twelve types of weak polyelectrolytes (i.e., PEO-b-PMMA copolymers (BCP) in multi-arm structures, where six include EO blocks as joint points and the other six have MMA blocks as joint points). All of the BCPs with EO as the joint points form disordered phases with the exception of long-chained and four-armed BCP. The main mesophases of all of the BCPs with MMA as joint points are micelle-like and bicontinuous phases. In particular, the short-chained BCP with four-arms and EO segments outside form a new phase type (i.e., crossed lamellar phase). Using MesoDyn, we provide a comprehensive representation of the micelle and crossed lamellar phase formation mechanisms based on both thermodynamic and dynamic analyses. A shear force on a micelle-like phase could promote a hexagonal columnar phase, which is a good technique for generating an ordered arrangement of nanotube arrays. Blending homopolymers with the same constituents could promote uniformity of the micelle size and decrease the polydispersity, especially for blends with a high BCP concentration, which may provide a new approach for regulating the properties of materials.
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Affiliation(s)
- Dan Mu
- Institute of Research on the Structure and Property of Matter, Zaozhuang University, Zaozhuang, 277160, China.
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Vishnyakov A, Neimark AV. Self-assembly in Nafion membranes upon hydration: water mobility and adsorption isotherms. J Phys Chem B 2014; 118:11353-64. [PMID: 25157931 DOI: 10.1021/jp504975u] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
By means of dissipative particle dynamics (DPD) and Monte Carlo (MC) simulations, we explored geometrical, transport, and sorption properties of hydrated Nafion-type polyelectrolyte membranes. Composed of a perfluorinated backbone with sulfonate side chains, Nafion self-assembles upon hydration and segregates into interpenetrating hydrophilic and hydrophobic subphases. This segregated morphology determines the transport properties of Nafion membranes that are widely used as compartment separators in fuel cells and other electrochemical devices, as well as permselective diffusion barriers in protective fabrics. We introduced a coarse-grained model of Nafion, which accounts explicitly for polymer rigidity and electrostatic interactions between anionic side chains and hydrated metal cations. In a series of DPD simulations with increasing content of water, a classical percolation transition from a system of isolated water clusters to a 3D network of hydrophilic channels was observed. The hydrophilic subphase connectivity and water diffusion were studied by constructing digitized replicas of self-assembled morphologies and performing random walk simulations. A non-monotonic dependence of the tracer diffusivity on the water content was found. This unexpected behavior was explained by the formation of large and mostly isolated water domains detected at high water content and high equivalent polymer weight. Using MC simulations, we calculated the chemical potential of water in the hydrated polymer and constructed the water sorption isotherms, which extended to the oversaturated conditions. We determined that the maximum diffusivity and the onset of formation of large water domains corresponded to the saturation conditions at 100% humidity. The oversaturated membrane morphologies generated in the canonical ensemble DPD simulations correspond to the metastable and unstable states of Nafion membrane that are not realized in the experiments.
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Affiliation(s)
- Aleksey Vishnyakov
- Department of Chemical Engineering, Rutgers, the State University of New Jersey , 98 Brett Road, Piscataway, New Jersey 08854, United States
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LI Z, JIA X, ZHANG J, SUN Z, LU Z. DESIGNING NANO-STRUCTURES OF BLOCK COPOLYMERS <I>VIA</I> COMPUTER SIMULATION. ACTA POLYM SIN 2011. [DOI: 10.3724/sp.j.1105.2011.11102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zhang R, Shi T, An L, Sun Z, Tong Z. Conformational Study on Sol−Gel Transition in Telechelic Polyelectrolytes Solutions. J Phys Chem B 2010; 114:3449-56. [DOI: 10.1021/jp9092404] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ran Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China, Graduate University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China, and Research Institute of Materials Science, South China University of Technology, Guangzhou, 510641, China
| | - Tongfei Shi
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China, Graduate University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China, and Research Institute of Materials Science, South China University of Technology, Guangzhou, 510641, China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China, Graduate University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China, and Research Institute of Materials Science, South China University of Technology, Guangzhou, 510641, China
| | - Zhaoyan Sun
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China, Graduate University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China, and Research Institute of Materials Science, South China University of Technology, Guangzhou, 510641, China
| | - Zhen Tong
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China, Graduate University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China, and Research Institute of Materials Science, South China University of Technology, Guangzhou, 510641, China
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Kumar R, Muthukumar M. Microphase separation in polyelectrolytic diblock copolymer melt: Weak segregation limit. J Chem Phys 2007; 126:214902. [PMID: 17567217 DOI: 10.1063/1.2737049] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The authors present a generalized theory of microphase separation for charged-neutral diblock copolymer melt. The stability limit of the disordered phase for salt-free melt has been calculated using random phase approximation (RPA) and self-consistent-field theory (SCFT). Explicit analytical free energy expressions for different classical ordered microstructures (lamellar, cylinder, and sphere) are presented. The authors demonstrate that the chemical mismatch required for the onset of microphase separation (chi*N) in charged-neutral diblock melt is higher and the period of ordered microstructures is lower than those for the corresponding neutral-neutral diblock system. Theoretical predictions on the period of ordered structures in terms of Coulomb electrostatic interaction strength, chain length, block length, and chemical mismatch between blocks are presented. SCFT has been used to go beyond the stability limit, where electrostatic potential and charge distribution are calculated self-consistently. Stability limits calculated using RPA are in perfect agreement with the corresponding SCFT calculations. Limiting laws for the stability limit and the period of ordered structures are presented and comparisons are made with an earlier theory. Also, transition boundaries between different morphologies have been investigated.
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Affiliation(s)
- Rajeev Kumar
- Department of Polymer Science and Engineering, Materials Research Science and Engineering Center, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Kyrylyuk AV, Lohmeijer BGG, Schubert US. Predicting the Morphology of Metallo-Supramolecular Block Copolymers with Bulky Counter Ions. Macromol Rapid Commun 2005. [DOI: 10.1002/marc.200500598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kyrylyuk AV, Fraaije JGEM(H. Three-Dimensional Structure and Motion of Twist Grain Boundaries in Block Copolymer Melts. Macromolecules 2005. [DOI: 10.1021/ma0509356] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andriy V. Kyrylyuk
- Laboratory of Macromolecular Chemistry and Nanoscience, Eindhoven University of Technology and Dutch Polymer Institute (DPI), P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Soft Matter Chemistry Group, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes G. E. M. (Hans) Fraaije
- Laboratory of Macromolecular Chemistry and Nanoscience, Eindhoven University of Technology and Dutch Polymer Institute (DPI), P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Soft Matter Chemistry Group, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Kyrylyuk A, Case F, Fraaije J. Property Prediction and Hybrid Modeling for Combinatorial Materials. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/qsar.200420067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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