1
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Netzer A, Baruch Leshem A, Veretnik S, Edelstein I, Lampel A. Regulation of Peptide Liquid-Liquid Phase Separation by Aromatic Amino Acid Composition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401665. [PMID: 38804888 DOI: 10.1002/smll.202401665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/25/2024] [Indexed: 05/29/2024]
Abstract
Membraneless organelles are cellular biomolecular condensates that are formed by liquid-liquid phase separation (LLPS) of proteins and nucleic acids. LLPS is driven by multiple weak attractive forces, including intermolecular interactions mediated by aromatic amino acids. Considering the contribution of π-electron bearing side chains to protein-RNA LLPS, systematically study sought to how the composition of aromatic amino acids affects the formation of heterotypic condensates and their physical properties. For this, a library of minimalistic peptide building blocks is designed containing varying number and compositions of aromatic amino acids. It is shown that the number of aromatics in the peptide sequence affect LLPS propensity, material properties and (bio)chemical stability of peptide/RNA heterotypic condensates. The findings shed light on the contribution of aromatics' composition to the formation of heterotypic condensates. These insights can be applied for regulation of condensate material properties and improvement of their (bio)chemical stability, for various biomedical and biotechnological applications.
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Affiliation(s)
- Amit Netzer
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Avigail Baruch Leshem
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shirel Veretnik
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ilan Edelstein
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ayala Lampel
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
- Sagol Center for Regenerative Biotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
- Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, 69978, Israel
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2
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Wang A, Yue K, Yan X, Zhong W, Zhang G, Wang L, Zhang H, Zhang X. Inhibition of platelet adhesion to exposed subendothelial collagen by steric hindrance with blocking peptide nanoparticles. Colloids Surf B Biointerfaces 2024; 237:113866. [PMID: 38520952 DOI: 10.1016/j.colsurfb.2024.113866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
The inhibition of platelet adhesion to collagen in exposed vessels represents an innovative approach to the treatment of atherosclerosis and thrombosis. This study aimed to engineer peptide-based nanoparticles that prevent platelet binding to subendothelial collagen by engaging with collagen with high affinity. We examined the interactions between integrin α2/ glycoprotein VI/ von Willebrand factor A3 domain and collagen, as well as between the synthesized peptide nanoparticles and collagen, utilizing molecular dynamics simulations and empirical assays. Our findings indicated that the bond between von Willebrand factor and collagen was more robust. Specifically, the sequences SITTIDV, VDVMQRE, and YLTSEMH in von Willebrand factor were identified as essential for its attachment to collagen. Based on these sequences, three peptide nanoparticles were synthesized (BPa: Capric-GNNQQNYK-SITTIDV, BPb: Capric-GNNQQNYK-VDVMQRE, BPc: Capric-GNNQQNYK-YLTSEMH), each displaying significant affinity towards collagen. Of these, the BPa nanoparticles exhibited the most potent interaction with collagen, leading to a 75% reduction in platelet adhesion.
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Affiliation(s)
- Anqi Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Kai Yue
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Shunde Graduate School of University of Science and Technology Beijing, Shunde, Guangdong Province 528399, China.
| | - Xiaotong Yan
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Weishen Zhong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Genpei Zhang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Lei Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Hua Zhang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xinxin Zhang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Shunde Graduate School of University of Science and Technology Beijing, Shunde, Guangdong Province 528399, China
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3
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Zhang Y, Li S, Gong X, Chen J. Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation. J Am Chem Soc 2024; 146:342-357. [PMID: 38112495 PMCID: PMC10842759 DOI: 10.1021/jacs.3c09195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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4
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Wu X, Sun Y, Yu J, Miserez A. Tuning the viscoelastic properties of peptide coacervates by single amino acid mutations and salt kosmotropicity. Commun Chem 2024; 7:5. [PMID: 38177438 PMCID: PMC10766971 DOI: 10.1038/s42004-023-01094-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Coacervation, or liquid-liquid phase separation (LLPS) of biomacromolecules, is increasingly recognized to play an important role both intracellularly and in the extracellular space. Central questions that remain to be addressed are the links between the material properties of coacervates (condensates) and both the primary and the secondary structures of their constitutive building blocks. Short LLPS-prone peptides, such as GY23 variants explored in this study, are ideal model systems to investigate these links because simple sequence modifications and the chemical environment strongly affect the viscoelastic properties of coacervates. Herein, a systematic investigation of the structure/property relationships of peptide coacervates was conducted using GY23 variants, combining biophysical characterization (plate rheology and surface force apparatus, SFA) with secondary structure investigations by infrared (IR) and circular dichroism (CD) spectroscopy. Mutating specific residues into either more hydrophobic or more hydrophilic residues strongly regulates the viscoelastic properties of GY23 coacervates. Furthermore, the ionic strength and kosmotropic characteristics (Hofmeister series) of the buffer in which LLPS is induced also significantly impact the properties of formed coacervates. Structural investigations by CD and IR indicate a direct correlation between variations in properties induced by endogenous (peptide sequence) or exogenous (ionic strength, kosmotropic characteristics, aging) factors and the β-sheet content within coacervates. These findings provide valuable insights to rationally design short peptide coacervates with programmable materials properties that are increasingly used in biomedical applications.
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Affiliation(s)
- Xi Wu
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Yue Sun
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Jing Yu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, 637553, Singapore.
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- School of Biological Sciences, 60 Nanyang Drive, NTU, Singapore, 636921, Singapore.
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Sun Y, Hiew SH, Miserez A. Bioinspired Squid Peptides─A Tale of Curiosity-Driven Research Leading to Unforeseen Biomedical Applications. Acc Chem Res 2024; 57:164-174. [PMID: 38117659 DOI: 10.1021/acs.accounts.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The molecular design of many peptide-based materials originates from structural proteins identified in living organisms. Prominent examples that have garnered broad interdisciplinary research interest (chemistry, materials science, bioengineering, etc.) include elastin, silk, or mussel adhesive proteins. The critical first steps in this type of research are to identify a convenient model system of interest followed by sequencing the prevailing proteins from which these biological structures are assembled. In our laboratory, the main model systems for many years have been the hard biotools of cephalopods, particularly their parrot-like tough beak and their sucker ring teeth (SRT) embedded within the sucker cuptions that line the interior surfaces of their arms and tentacles. Unlike the majority of biological hard tissues, these structures are devoid of biominerals and consist of protein/polysaccharide biomolecular composites (the beak) or, in the case of SRT, are entirely made of proteins that are assembled by supramolecular interactions.In this Account, we chronicle our journey into the discovery of these intriguing biological materials. We initially focus on their excellent mechanical robustness followed by the identification and sequencing of the structural proteins from which they are built, using the latest "omics" techniques including next-generation sequencing and high-throughput proteomics. A common feature of these proteins is their modular architecture at the molecular level consisting of short peptide repeats. We describe the molecular design of these peptide building blocks, highlighting the consensus motifs identified to play a key role in biofabrication and in regulating the mechanical properties of the macroscopic biological material. Structure/property relationships unveiled through advanced spectroscopic and scattering techniques, including Raman, infrared, circular dichroism, and NMR spectroscopies as well as wide-angle and small-angle X-ray scattering, are also discussed.We then present recent developments in exploiting the discovered molecular designs to engineer peptides and their conjugates for promising biomedical applications. One example includes short peptide hydrogels that self-assemble entirely under aqueous conditions and simultaneously encapsulate large macromolecules during the gelation process. A second example involves peptide coacervate microdroplets produced by liquid-liquid phase separation. These microdroplets are capable of recruiting and delivering large macromolecular therapeutics (genes, mRNA, proteins, peptides, CRISPR/Cas 9 modalities, etc.) into mammalian cells, which introduces exciting prospects in cancer, gene, and immune therapies.This Account also serves as a testament to how curiosity-driven explorations, which may lack an obvious practical goal initially, can lead to discoveries with unexpected and promising translational potential.
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Affiliation(s)
- Yue Sun
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 637553, Singapore
| | - Shu Hui Hiew
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 637553, Singapore
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 637553, Singapore
- School of Biological Sciences, NTU, 637551, Singapore
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6
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Sementa D, Dave D, Fisher RS, Wang T, Elbaum-Garfinkle S, Ulijn RV. Sequence-Tunable Phase Behavior and Intrinsic Fluorescence in Dynamically Interacting Peptides. Angew Chem Int Ed Engl 2023; 62:e202311479. [PMID: 37934145 DOI: 10.1002/anie.202311479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/08/2023]
Abstract
A conceptual framework towards understanding biological condensed phases is emerging, derived from biological, biomimetic, and synthetic sequences. However, de novo peptide condensate design remains a challenge due to an incomplete understanding of the structural and interactive complexity. We designed peptide modules based on a simple repeat motif composed of tripeptide spacers (GSG, SGS, GLG) interspersed with adhesive amino acids (R/H and Y). We show, using sequence editing and a combination of computation and experiment, that n→π* interactions in GLG backbones are a dominant factor in providing sufficient backbone structure, which in turn regulates the water interface, collectively promoting liquid droplet formation. Moreover, these R(GLG)Y and H(GLG)Y condensates unexpectedly display sequence-dependent emission that is a consequence of their non-covalent network interactions, and readily observable by confocal microscopy.
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Affiliation(s)
- Deborah Sementa
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Dhwanit Dave
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York (CUNY), 695 Park Avenue, New York, NY 10065, USA
| | - Rachel S Fisher
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Tong Wang
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Shana Elbaum-Garfinkle
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, NY 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York (CUNY), 695 Park Avenue, New York, NY 10065, USA
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7
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Zhang Y, Li S, Gong X, Chen J. Accurate Simulation of Coupling between Protein Secondary Structure and Liquid-Liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554378. [PMID: 37662293 PMCID: PMC10473686 DOI: 10.1101/2023.08.22.554378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Intrinsically disordered proteins (IDPs) frequently mediate liquid-liquid phase separation (LLPS) that underlies the formation of membraneless organelles. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding sequence-specific phase separation of IDPs. However, the widely-used Cα-only models are severely limited in capturing the peptide nature of IDPs, including backbone-mediated interactions and effects of secondary structures, in LLPS. Here, we describe a hybrid resolution (HyRes) protein model for accurate description of the backbone and transient secondary structures in LLPS. With an atomistic backbone and coarse-grained side chains, HyRes accurately predicts the residue helical propensity and chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for direct simulation of spontaneous phase separation, and at the same time accurate enough to resolve the effects of single mutations. HyRes simulations also successfully predict increased beta-sheet formation in the condensate, consistent with available experimental data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate LLPS propensity. The simulations successfully recapitulate the effect of these mutants on the helicity and LLPS propensity of TDP-43 CR. Analyses reveal that the balance between backbone and sidechain-mediated interactions, but not helicity itself, actually determines LLPS propensity. We believe that the HyRes model represents an important advance in the molecular simulation of LLPS and will help elucidate the coupling between IDP transient secondary structures and phase separation.
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Affiliation(s)
| | | | - Xiping Gong
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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8
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Valdes-Garcia G, Gamage K, Smith C, Martirosova K, Feig M, Lapidus LJ. The effect of polymer length in liquid-liquid phase separation. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101415. [PMID: 37325682 PMCID: PMC10270681 DOI: 10.1016/j.xcrp.2023.101415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Understanding the thermodynamics that drive liquid-liquid phase separation (LLPS) is quite important given the number of diverse biomolecular systems undergoing this phenomenon. Many studies have focused on condensates of long polymers, but very few systems of short-polymer condensates have been observed and studied. Here, we study a short-polymer system of various lengths of poly-adenine RNA and peptides formed by the RGRGG sequence repeats to understand the underlying thermodynamics of LLPS. Using the recently developed COCOMO coarse-grained (CG) model, we predicted condensates for lengths as short as 5-10 residues, which was then confirmed by experiment, making this one of the smallest LLPS systems yet observed. A free-energy model reveals that the length dependence of condensation is driven primarily by entropy of confinement. The simplicity of this system will provide the basis for understanding more biologically realistic systems.
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Affiliation(s)
- Gilberto Valdes-Garcia
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- These authors contributed equally
| | - Kasun Gamage
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
- These authors contributed equally
| | - Casey Smith
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Karina Martirosova
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Lisa J. Lapidus
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
- Lead contact
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9
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Stengel D, Saric M, Johnson HR, Schiller T, Diehl J, Chalek K, Onofrei D, Scheibel T, Holland GP. Tyrosine's Unique Role in the Hierarchical Assembly of Recombinant Spider Silk Proteins: From Spinning Dope to Fibers. Biomacromolecules 2023; 24:1463-1474. [PMID: 36791420 DOI: 10.1021/acs.biomac.2c01467] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Producing recombinant spider silk fibers that exhibit mechanical properties approaching native spider silk is highly dependent on the constitution of the spinning dope. Previously published work has shown that recombinant spider silk fibers spun from dopes with phosphate-induced pre-assembly (biomimetic dopes) display a toughness approaching native spider silks far exceeding the mechanical properties of fibers spun from dopes without pre-assembly (classical dopes). Dynamic light scattering experiments comparing the two dopes reveal that biomimetic dope displays a systematic increase in assembly size over time, while light microscopy indicates liquid-liquid-phase separation (LLPS) as evidenced by the formation of micron-scale liquid droplets. Solution nuclear magnetic resonance (NMR) shows that the structural state in classical and biomimetic dopes displays a general random coil conformation in both cases; however, some subtle but distinct differences are observed, including a more ordered state for the biomimetic dope and small chemical shift perturbations indicating differences in hydrogen bonding of the protein in the different dopes with notable changes occurring for Tyr residues. Solid-state NMR demonstrates that the final wet-spun fibers from the two dopes display no structural differences of the poly(Ala) stretches, but biomimetic fibers display a significant difference in Tyr ring packing in non-β-sheet, disordered helical domains that can be traced back to differences in dope preparations. It is concluded that phosphate pre-orders the recombinant silk protein in biomimetic dopes resulting in LLPS and fibers that exhibit vastly improved toughness that could be due to aromatic ring packing differences in non-β-sheet domains that contain Tyr.
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Affiliation(s)
- Dillan Stengel
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - Merisa Saric
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Hannah R Johnson
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - Tim Schiller
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Johannes Diehl
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Kevin Chalek
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - David Onofrei
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
| | - Thomas Scheibel
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth, Prof.-Rüdiger-Bormann-Street 1, Bayreuth 95447, Germany
| | - Gregory P Holland
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Dr, San Diego, California 92182-1030, United States
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10
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,School of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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11
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Baruch Leshem A, Sloan-Dennison S, Massarano T, Ben-David S, Graham D, Faulds K, Gottlieb HE, Chill JH, Lampel A. Biomolecular condensates formed by designer minimalistic peptides. Nat Commun 2023; 14:421. [PMID: 36702825 PMCID: PMC9879991 DOI: 10.1038/s41467-023-36060-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
Inspired by the role of intracellular liquid-liquid phase separation (LLPS) in formation of membraneless organelles, there is great interest in developing dynamic compartments formed by LLPS of intrinsically disordered proteins (IDPs) or short peptides. However, the molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated, rendering on-demand design of synthetic condensates with tailored physico-chemical functionalities a significant challenge. To address this need, here we design a library of LLPS-promoting peptide building blocks composed of various assembly domains. We show that the LLPS propensity, dynamics, and encapsulation efficiency of compartments can be tuned by changes to the peptide composition. Specifically, with the aid of Raman and NMR spectroscopy, we show that interactions between arginine and aromatic amino acids underlie droplet formation, and that both intra- and intermolecular interactions dictate droplet dynamics. The resulting sequence-structure-function correlation could support the future development of compartments for a variety of applications.
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Affiliation(s)
- Avigail Baruch Leshem
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sian Sloan-Dennison
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Tlalit Massarano
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Shavit Ben-David
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Duncan Graham
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Karen Faulds
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, UK
| | - Hugo E Gottlieb
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Jordan H Chill
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat Gan, 52900, Israel.
| | - Ayala Lampel
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel. .,Center for Nanoscience and Nanotechnology Tel Aviv University, Tel Aviv, 69978, Israel. .,Sagol Center for Regenerative Biotechnology Tel Aviv University, Tel Aviv, 69978, Israel. .,Center for the Physics and Chemistry of Living Systems Tel Aviv University, Tel Aviv 69978, Israel, Tel Aviv, 69978, Israel.
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12
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Ma L, Fang X, Wang C. Peptide-based coacervates in therapeutic applications. Front Bioeng Biotechnol 2023; 10:1100365. [PMID: 36686257 PMCID: PMC9845597 DOI: 10.3389/fbioe.2022.1100365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.
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Affiliation(s)
- Lilusi Ma
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaocui Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
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13
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Renner-Rao M, Jehle F, Priemel T, Duthoo E, Fratzl P, Bertinetti L, Harrington MJ. Mussels Fabricate Porous Glues via Multiphase Liquid-Liquid Phase Separation of Multiprotein Condensates. ACS NANO 2022; 16:20877-20890. [PMID: 36413745 DOI: 10.1021/acsnano.2c08410] [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] [Indexed: 06/16/2023]
Abstract
Mussels (Mytilus edulis) adhere to hard surfaces in intertidal marine habitats with a porous underwater glue called the byssus plaque. The plaque is an established role model for bioinspired underwater glues and comprises at least six proteins, most of which are highly cationic and enriched in the post-translationally modified amino acid 3,4-dihydroxyphenylalanine (DOPA). While much is known about the chemistry of plaque adhesion, less is understood about the natural plaque formation process. Here, we investigated plaque structure and formation using 3D electron microscopic imaging, revealing that micro- and nanopores form spontaneously during secretion of protein-filled secretory vesicles. To better understand this process, we developed a method to purify intact secretory vesicles for in vitro assembly studies. We discovered that each vesicle contains a sulfate-associated fluid condensate consisting of ∼9 histidine- and/or DOPA-rich proteins, which are presumably the required ingredients for building a plaque. Rupturing vesicles under specific buffering conditions relevant for natural assembly led to controlled multiphase liquid-liquid phase separation (LLPS) of different proteins, resulting in formation of a continuous phase with coexisting droplets. Rapid coarsening of the droplet phase was arrested through pH-dependent cross-linking of the continuous phase, producing native-like solid porous "microplaques" with droplet proteins remaining as fluid condensates within the pores. Results indicate that histidine deprotonation and sulfates figure prominently in condensate cross-linking. Distilled concepts suggest that combining phase separation with tunable cross-linking kinetics could be effective for microfabricating hierarchically porous materials via self-assembly.
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Affiliation(s)
- Max Renner-Rao
- Dept. of Chemistry, McGill University, Montreal, Quebec H4A 0B8, Canada
| | - Franziska Jehle
- Dept. of Chemistry, McGill University, Montreal, Quebec H4A 0B8, Canada
- Dept. of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Tobias Priemel
- Dept. of Chemistry, McGill University, Montreal, Quebec H4A 0B8, Canada
| | - Emilie Duthoo
- Dept. of Chemistry, McGill University, Montreal, Quebec H4A 0B8, Canada
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, Mons 7000, Belgium
| | - Peter Fratzl
- Dept. of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
| | - Luca Bertinetti
- Dept. of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
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14
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Katzir I, Haimov E, Lampel A. Tuning the Dynamics of Viral-Factories-Inspired Compartments Formed by Peptide-RNA Liquid-Liquid Phase Separation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2206371. [PMID: 36134527 DOI: 10.1002/adma.202206371] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Viral factories are intracellular microcompartments formed by mammalian viruses in their host cells, and contain necessary machinery for viral genome replication, capsid assembly, and maturation, thus serving as "factories" for formation of new viral particles. Recent evidence suggests that these compartments are formed by liquid-liquid phase separation (LLPS) of viral proteins and nucleic acids and present dynamic properties. In this work, inspired by the remarkable functionalities of viral factories, dynamic compartments that are formed by complexation between a minimalistic, disordered peptide and RNA are designed. By systematic studies using sequence variants it is shown that the material properties of the compartments can be modulated by changes to the peptide sequence, at the single amino acid level. Moreover, by taking this approach to the next step, liquid compartments with light-induced tunable dynamics are developed. The results demonstrate that the material properties of liquid droplets can be temporally regulated by increasing peptide polarity and charge, and that these changes can be further utilized for controlled partitioning and release of payloads from the compartments.
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Affiliation(s)
- Itai Katzir
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Elvira Haimov
- Blavatnik Center for Drug Discovery, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ayala Lampel
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
- Sagol Center for Regenerative Biotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
- Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, 69978, Israel
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15
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Diallo MA, Pirotte S, Hu Y, Morvan L, Rakus K, Suárez NM, PoTsang L, Saneyoshi H, Xu Y, Davison A, Tompa P, Sussman J, Vanderplasschen A. A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion. Nucleic Acids Res 2022; 51:806-830. [PMID: 36130731 PMCID: PMC9881149 DOI: 10.1093/nar/gkac761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 02/06/2023] Open
Abstract
Zalpha (Zα) domains bind to left-handed Z-DNA and Z-RNA. The Zα domain protein family includes cellular (ADAR1, ZBP1 and PKZ) and viral (vaccinia virus E3 and cyprinid herpesvirus 3 (CyHV-3) ORF112) proteins. We studied CyHV-3 ORF112, which contains an intrinsically disordered region and a Zα domain. Genome editing of CyHV-3 indicated that the expression of only the Zα domain of ORF112 was sufficient for normal viral replication in cell culture and virulence in carp. In contrast, its deletion was lethal for the virus. These observations revealed the potential of the CyHV-3 model as a unique platform to compare the exchangeability of Zα domains expressed alone in living cells. Attempts to rescue the ORF112 deletion by a broad spectrum of cellular, viral, and artificial Zα domains showed that only those expressing Z-binding activity, the capacity to induce liquid-liquid phase separation (LLPS), and A-to-Z conversion, could rescue viral replication. For the first time, this study reports the ability of some Zα domains to induce LLPS and supports the biological relevance of dsRNA A-to-Z conversion mediated by Zα domains. This study expands the functional diversity of Zα domains and stimulates new hypotheses concerning the mechanisms of action of proteins containing Zα domains.
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Affiliation(s)
| | | | - Yunlong Hu
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Léa Morvan
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium
| | - Krzysztof Rakus
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow 30387, Poland
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lee PoTsang
- Department of Infectious and Parasitic Diseases, Immunology-Vaccinology, University of Liège, Liège B-4000, Belgium,Department of Aquaculture, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Hisao Saneyoshi
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yan Xu
- Department of Medical Sciences, Division of Chemistry, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussel B-1050, Belgium
| | - Joel L Sussman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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16
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Ramos R, Bernard J, Ganachaud F, Miserez A. Protein‐Based Encapsulation Strategies: Toward Micro‐ and Nanoscale Carriers with Increased Functionality. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202100095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Ricardo Ramos
- Université de Lyon INSA Lyon CNRS IMP 5223 Villeurbanne Cedex 69621 France
- INSA-Lyon, IMP Villeurbanne F-69621 France
- CNRS, UMR 5223 Ingénierie des Matériaux Polymères Villeurbanne F-69621 France
| | - Julien Bernard
- Université de Lyon INSA Lyon CNRS IMP 5223 Villeurbanne Cedex 69621 France
- INSA-Lyon, IMP Villeurbanne F-69621 France
- CNRS, UMR 5223 Ingénierie des Matériaux Polymères Villeurbanne F-69621 France
| | - François Ganachaud
- Université de Lyon INSA Lyon CNRS IMP 5223 Villeurbanne Cedex 69621 France
- INSA-Lyon, IMP Villeurbanne F-69621 France
- CNRS, UMR 5223 Ingénierie des Matériaux Polymères Villeurbanne F-69621 France
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory Center for Sustainable Materials (SusMat), School of Materials Science and Engineering Nanyang Technological University (NTU) 50 Nanyang Avenue Singapore 637 553 Singapore
- School of Biological Sciences NTU 59 Nanyang Drive Singapore 636921 Singapore
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17
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Keating CD, Pappu RV. Liquid-Liquid Phase Separation: A Widespread and Versatile Way to Organize Aqueous Solutions. J Phys Chem B 2021; 125:12399-12400. [PMID: 34788996 DOI: 10.1021/acs.jpcb.1c08831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christine D Keating
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biolgical Systems Engineering Campus, Washington University in Saint Louis, Box 1097, One Brookings Drive, St. Louis, Missouri 63130, United States
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18
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Keating CD, Pappu RV. Liquid-Liquid Phase Separation: A Widespread and Versatile Way to Organize Aqueous Solutions. J Phys Chem Lett 2021; 12:10994-10995. [PMID: 34788997 DOI: 10.1021/acs.jpclett.1c03352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Christine D Keating
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biolgical Systems Engineering Campus, Washington University in Saint Louis, Box 1097, One Brookings Drive, St. Louis, Missouri 63130, United States
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