1
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Garg A, González-Foutel NS, Gielnik MB, Kjaergaard M. Design of functional intrinsically disordered proteins. Protein Eng Des Sel 2024; 37:gzae004. [PMID: 38431892 DOI: 10.1093/protein/gzae004] [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: 10/02/2023] [Revised: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.
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Affiliation(s)
- Ankush Garg
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Maciej B Gielnik
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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2
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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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3
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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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4
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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
ConspectusThe 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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5
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Feng J, Gabryelczyk B, Tunn I, Osmekhina E, Linder MB. A Minispidroin Guides the Molecular Design for Cellular Condensation Mechanisms in S. cerevisiae. ACS Synth Biol 2023; 12:3050-3063. [PMID: 37688556 PMCID: PMC10594646 DOI: 10.1021/acssynbio.3c00374] [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: 06/18/2023] [Indexed: 09/11/2023]
Abstract
Structural engineering of molecules for condensation is an emerging technique within synthetic biology. Liquid-liquid phase separation of biomolecules leading to condensation is a central step in the assembly of biological materials into their functional forms. Intracellular condensates can also function within cells in a regulatory manner to facilitate reaction pathways and to compartmentalize interactions. We need to develop a strong understanding of how to design molecules for condensates and how their in vivo-in vitro properties are related. The spider silk protein NT2RepCT undergoes condensation during its fiber-forming process. Using parallel in vivo and in vitro characterization, in this study, we mapped the effects of intracellular conditions for NT2RepCT and its several structural variants. We found that intracellular conditions may suppress to some extent condensation whereas molecular crowding affects both condensate properties and their formation. Intracellular characterization of protein condensation allowed experiments on pH effects and solubilization to be performed within yeast cells. The growth of intracellular NT2RepCT condensates was restricted, and Ostwald ripening was not observed in yeast cells, in contrast to earlier observations in E. coli. Our results lead the way to using intracellular condensation to screen for properties of molecular assembly. For characterizing different structural variants, intracellular functional characterization can eliminate the need for time-consuming batch purification and in vitro condensation. Therefore, we suggest that the in vivo-in vitro understanding will become useful in, e.g., high-throughput screening for molecular functions and in strategies for designing tunable intracellular condensates.
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Affiliation(s)
- Jianhui Feng
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Bartosz Gabryelczyk
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Isabell Tunn
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Ekaterina Osmekhina
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Markus B. Linder
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
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6
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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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7
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Pokhrel P, Jonchhe S, Pan W, Mao H. Single-Molecular Dissection of Liquid-Liquid Phase Transitions. J Am Chem Soc 2023; 145:17143-17150. [PMID: 37494702 PMCID: PMC10528544 DOI: 10.1021/jacs.3c03812] [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: 07/28/2023]
Abstract
Interaction between peptides and nucleic acids is a ubiquitous process that drives many cellular functions, such as replications, transcriptions, and translations. Recently, this interaction has been found in liquid-liquid phase separation (LLPS), a process responsible for the formation of newly discovered membraneless organelles with a variety of biological functions inside cells. In this work, we studied the molecular interaction between the poly-l-lysine (PLL) peptide and nucleic acids during the early stage of an LLPS process at the single-molecule level using optical tweezers. By monitoring the mechanical tension of individual nucleic acid templates upon PLL addition, we revealed a multistage LLPS process mediated by the long-range interactions between nucleic acids and polyelectrolytes. By varying different types (ssDNA, ssRNA, and dsDNA) and sequences (A-, T-, G-, or U-rich) of nucleic acids, we pieced together transition diagrams of the PLL-nucleic acid condensates from which we concluded that the propensity to form rigid nucleic acid-PLL complexes reduces the condensate formation during the LLPS process. We anticipate that these results are instrumental in understanding the transition mechanism of LLPS condensates, which allows new strategies to interfere with the biological functions of LLPS condensates inside cells.
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Affiliation(s)
- Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Wei Pan
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
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8
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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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9
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Duarte B, Mamede R, Duarte IA, Caçador I, Reis-Santos P, Vasconcelos RP, Gameiro C, Rosa R, Tanner SE, Fonseca VF. Elemental and spectral chemometric analyses of Octopus vulgaris beaks as reliable markers of capture location. J Food Sci 2023; 88:1349-1364. [PMID: 36793205 DOI: 10.1111/1750-3841.16492] [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: 10/26/2022] [Revised: 12/21/2022] [Accepted: 01/20/2023] [Indexed: 02/17/2023]
Abstract
The high demand and economic relevance of cephalopods make them prone to food fraud, including related to harvest location. Therefore, there is a growing need to develop tools to unequivocally confirm their capture location. Cephalopod beaks are nonedible, making this material ideal for traceability studies as it can also be removed without a loss of commodity economic value. Within this context, common octopus (Octopus vulgaris) specimens were captured in five fishing areas along the Portuguese coast. Untargeted multi-elemental total X-ray fluorescence analysis of the octopus beaks revealed a high abundance of Ca, Cl, K, Na, S, and P, concomitant with the keratin and calcium phosphate nature of the material. We tested a suite of discrimination models on both elemental and spectral data, where the elements contributing most to discriminate capture location were typically associated with diet (As), human-related pressures (Zn, Se, and Mn), or geological features (P, S, Mn, and Zn). Among the six different chemometrics approaches used to classify individuals to their capture location according to their beaks' element concentration, classification trees attained a classification accuracy of 76.7%, whilst reducing the number of explanatory variables for sample classification and highlighting variable importance for group discrimination. However, using X-ray spectral features of the octopus beaks further improved classification accuracy, with the highest classification of 87.3% found with partial least-squares discriminant analysis. Ultimately, element and spectral analyses of nonedible structures such as octopus beaks can provide an important, complementary, and easily accessible means to support seafood provenance and traceability, whilst integrating anthropogenic and/or geological gradients.
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Affiliation(s)
- Bernardo Duarte
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.,Departamento de Biologia Vegetal da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Renato Mamede
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Irina A Duarte
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Caçador
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.,Departamento de Biologia Vegetal da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Patrick Reis-Santos
- Southern Seas Ecology Laboratories, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Carla Gameiro
- IPMA - Instituto Português do Mar e da Atmosfera, Algés, Portugal
| | - Rui Rosa
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia & ARNET - Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Cascais, Portugal.,Departamento de Biologia Animal da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Susanne E Tanner
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.,Departamento de Biologia Animal da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Vanessa F Fonseca
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.,Departamento de Biologia Animal da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
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10
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Otis JB, Sharpe S. Sequence Context and Complex Hofmeister Salt Interactions Dictate Phase Separation Propensity of Resilin-like Polypeptides. Biomacromolecules 2022; 23:5225-5238. [PMID: 36378745 DOI: 10.1021/acs.biomac.2c01027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Resilin is an elastic material found in insects with exceptional durability, resilience, and extensibility, making it a promising biomaterial for tissue engineering. The monomeric precursor, pro-resilin, undergoes thermo-responsive self-assembly through liquid-liquid phase separation (LLPS). Understanding the molecular details of this assembly process is critical to developing complex biomaterials. The present study investigates the interplay between the solvent, sequence syntax, structure, and dynamics in promoting LLPS of resilin-like-polypeptides (RLPs) derived from domains 1 and 3 of Drosophila melanogaster pro-resilin. NMR, UV-vis, and microscopy data demonstrate that while kosmotropic salts and low pH promote LLPS, the effects of chaotropic salts with increasing pH are more complex. Subtle variations between the repeating amino acid motifs of resilin domain 1 and domain 3 lead to significantly different salt and pH dependence of LLPS, with domain 3 sequence motifs more strongly favoring phase separation under most conditions. These findings provide new insight into the molecular drivers of RLP phase separation and the complex roles of both RLP sequence and solution composition in fine-tuning assembly conditions.
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Affiliation(s)
- James Brandt Otis
- Molecular Medicine, Hospital for Sick Children, 686 Bay St, Toronto, ONM5G 0A4, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ONM5S 1A8, Canada
| | - Simon Sharpe
- Molecular Medicine, Hospital for Sick Children, 686 Bay St, Toronto, ONM5G 0A4, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ONM5S 1A8, Canada
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11
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Gabryelczyk B, Sammalisto FE, Gandier JA, Feng J, Beaune G, Timonen JV, Linder MB. Recombinant protein condensation inside E. coli enables the development of building blocks for bioinspired materials engineering – Biomimetic spider silk protein as a case study. Mater Today Bio 2022; 17:100492. [DOI: 10.1016/j.mtbio.2022.100492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
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12
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Cai H, Vernon RM, Forman-Kay JD. An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions. Biomolecules 2022; 12:biom12081131. [PMID: 36009025 PMCID: PMC9405563 DOI: 10.3390/biom12081131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
Protein phase separation is increasingly understood to be an important mechanism of biological organization and biomaterial formation. Intrinsically disordered protein regions (IDRs) are often significant drivers of protein phase separation. A number of protein phase-separation-prediction algorithms are available, with many being specific for particular classes of proteins and others providing results that are not amenable to the interpretation of the contributing biophysical interactions. Here, we describe LLPhyScore, a new predictor of IDR-driven phase separation, based on a broad set of physical interactions or features. LLPhyScore uses sequence-based statistics from the RCSB PDB database of folded structures for these interactions, and is trained on a manually curated set of phase-separation-driving proteins with different negative training sets including the PDB and human proteome. Competitive training for a variety of physical chemical interactions shows the greatest contribution of solvent contacts, disorder, hydrogen bonds, pi–pi contacts, and kinked beta-structures to the score, with electrostatics, cation–pi contacts, and the absence of a helical secondary structure also contributing. LLPhyScore has strong phase-separation-prediction recall statistics and enables a breakdown of the contribution from each physical feature to a sequence’s phase-separation propensity, while recognizing the interdependence of many of these features. The tool should be a valuable resource for guiding experiments and providing hypotheses for protein function in normal and pathological states, as well as for understanding how specificity emerges in defining individual biomolecular condensates.
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Affiliation(s)
- Hao Cai
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Robert M. Vernon
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Julie D. Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence:
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13
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Taghizadeh A, Taghizadeh M, Khodadadi Yazdi M, Zarrintaj P, Ramsey JD, Seidi F, Stadler FJ, Lee H, Saeb MR, Mozafari M. Mussel‐Inspired
Biomaterials: From Chemistry to Clinic. Bioeng Transl Med 2022; 7:e10385. [PMID: 36176595 PMCID: PMC9472010 DOI: 10.1002/btm2.10385] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/25/2022] [Accepted: 07/16/2022] [Indexed: 11/18/2022] Open
Abstract
After several billions of years, nature still makes decisions on its own to identify, develop, and direct the most effective material for phenomena/challenges faced. Likewise, and inspired by the nature, we learned how to take steps in developing new technologies and materials innovations. Wet and strong adhesion by Mytilidae mussels (among which Mytilus edulis—blue mussel and Mytilus californianus—California mussel are the most well‐known species) has been an inspiration in developing advanced adhesives for the moist condition. The wet adhesion phenomenon is significant in designing tissue adhesives and surgical sealants. However, a deep understanding of engaged chemical moieties, microenvironmental conditions of secreted proteins, and other contributing mechanisms for outstanding wet adhesion mussels are essential for the optimal design of wet glues. In this review, all aspects of wet adhesion of Mytilidae mussels, as well as different strategies needed for designing and fabricating wet adhesives are discussed from a chemistry point of view. Developed muscle‐inspired chemistry is a versatile technique when designing not only wet adhesive, but also, in several more applications, especially in the bioengineering area. The applications of muscle‐inspired biomaterials in various medical applications are summarized for future developments in the field.
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Affiliation(s)
- Ali Taghizadeh
- Institute of Tissue Regeneration Engineering (ITREN) Dankook University Cheonan Republic of Korea
| | - Mohsen Taghizadeh
- Institute of Tissue Regeneration Engineering (ITREN) Dankook University Cheonan Republic of Korea
| | - Mohsen Khodadadi Yazdi
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science University of Tehran Tehran Iran
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University 420 Engineering North Stillwater OK United States
| | - Joshua D. Ramsey
- School of Chemical Engineering, Oklahoma State University 420 Engineering North Stillwater OK United States
| | - Farzad Seidi
- Jiangsu Co‐Innovation Center of Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials Nanjing Forestry University Nanjing China
| | - Florian J. Stadler
- College of Materials Science and Engineering, Shenzhen Key Laboratory of Polymer Science and Technology Guangdong China
| | - Haeshin Lee
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry Gdańsk University of Technology, G. Narutowicza 11 Gdańsk Poland
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative Medicine Iran University of Medical Sciences Tehran Iran
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14
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Lemetti L, Scacchi A, Yin Y, Shen M, Linder MB, Sammalkorpi M, Aranko AS. Liquid-Liquid Phase Separation and Assembly of Silk-like Proteins is Dependent on the Polymer Length. Biomacromolecules 2022; 23:3142-3153. [PMID: 35796676 PMCID: PMC9364312 DOI: 10.1021/acs.biomac.2c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Phase transitions
have an essential role in the assembly of nature’s
protein-based materials into hierarchically organized structures,
yet many of the underlying mechanisms and interactions remain to be
resolved. A central question for designing proteins for materials
is how the protein architecture and sequence affects the nature of
the phase transitions and resulting assembly. In this work, we produced
82 kDa (1×), 143 kDa (2×), and 204 kDa (3×) silk-mimicking
proteins by taking advantage of protein ligation by SpyCatcher/Tag
protein-peptide pair. We show that the three silk proteins all undergo
a phase transition from homogeneous solution to assembly formation.
In the assembly phase, a length- and concentration-dependent transition
between two distinct assembly morphologies, one forming aggregates
and another coacervates, exists. The coacervates showed properties
that were dependent on the protein size. Computational modeling of
the proteins by a bead-spring model supports the experimental results
and provides us a possible mechanistic origin for the assembly transitions
based on architectures and interactions.
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Affiliation(s)
- Laura Lemetti
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Alberto Scacchi
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland.,Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Department of Applied Physics, School of Science, Aalto University, Otakaari 1, Espoo 02150, Finland
| | - Yin Yin
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Mengjie Shen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
| | - Maria Sammalkorpi
- Department of Bioproducts and Biosystems, Department of Chemistry and Materials Science, and Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), School of Chemical Engineering, Aalto University, Espoo, 02150, Finland
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, Espoo 02150, Finland.,Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Kemistintie 1, Espoo 02150, Finland
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15
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Gabryelczyk B, Alag R, Philips M, Low K, Venkatraman A, Kannaian B, Shi X, Linder M, Pervushin K, Miserez A. In vivo liquid–liquid phase separation protects amyloidogenic and aggregation‐prone peptides during overexpression in
Escherichia coli
. Protein Sci 2022; 31:e4292. [PMID: 35481658 PMCID: PMC8994509 DOI: 10.1002/pro.4292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/03/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
Studying pathogenic effects of amyloids requires homogeneous amyloidogenic peptide samples. Recombinant production of these peptides is challenging due to their susceptibility to aggregation and chemical modifications. Thus, chemical synthesis is primarily used to produce amyloidogenic peptides suitable for high-resolution structural studies. Here, we exploited the shielded environment of protein condensates formed via liquid-liquid phase separation (LLPS) as a protective mechanism against premature aggregation. We designed a fusion protein tag undergoing LLPS in Escherichia coli and linked it to highly amyloidogenic peptides, including β amyloids. We find that the fusion proteins form membraneless organelles during overexpression and remain fluidic-like. We also developed a facile purification method of functional Aβ peptides free of chromatography steps. The strategy exploiting LLPS can be applied to other amyloidogenic, hydrophobic, and repetitive peptides that are otherwise difficult to produce.
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Affiliation(s)
- Bartosz Gabryelczyk
- Biological and Biomimetic Materials Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering Nanyang Technological University (NTU) Singapore
- Department of Bioproducts and Biosystems, School of Chemical Engineering Aalto University Espoo Finland
| | - Reema Alag
- School of Biological Sciences NTU Singapore
| | | | | | | | - Bhuvaneswari Kannaian
- Biological and Biomimetic Materials Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering Nanyang Technological University (NTU) Singapore
| | - Xiangyan Shi
- Department of Biology Shenzhen MSU‐BIT University Shenzhen China
| | - Markus Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering Aalto University Espoo Finland
| | | | - Ali Miserez
- Biological and Biomimetic Materials Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering Nanyang Technological University (NTU) Singapore
- School of Biological Sciences NTU Singapore
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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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Tardy BL, Mattos BD, Otoni CG, Beaumont M, Majoinen J, Kämäräinen T, Rojas OJ. Deconstruction and Reassembly of Renewable Polymers and Biocolloids into Next Generation Structured Materials. Chem Rev 2021; 121:14088-14188. [PMID: 34415732 PMCID: PMC8630709 DOI: 10.1021/acs.chemrev.0c01333] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Indexed: 12/12/2022]
Abstract
This review considers the most recent developments in supramolecular and supraparticle structures obtained from natural, renewable biopolymers as well as their disassembly and reassembly into engineered materials. We introduce the main interactions that control bottom-up synthesis and top-down design at different length scales, highlighting the promise of natural biopolymers and associated building blocks. The latter have become main actors in the recent surge of the scientific and patent literature related to the subject. Such developments make prominent use of multicomponent and hierarchical polymeric assemblies and structures that contain polysaccharides (cellulose, chitin, and others), polyphenols (lignins, tannins), and proteins (soy, whey, silk, and other proteins). We offer a comprehensive discussion about the interactions that exist in their native architectures (including multicomponent and composite forms), the chemical modification of polysaccharides and their deconstruction into high axial aspect nanofibers and nanorods. We reflect on the availability and suitability of the latter types of building blocks to enable superstructures and colloidal associations. As far as processing, we describe the most relevant transitions, from the solution to the gel state and the routes that can be used to arrive to consolidated materials with prescribed properties. We highlight the implementation of supramolecular and superstructures in different technological fields that exploit the synergies exhibited by renewable polymers and biocolloids integrated in structured materials.
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Affiliation(s)
- Blaise L. Tardy
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Bruno D. Mattos
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Caio G. Otoni
- Department
of Physical Chemistry, Institute of Chemistry, University of Campinas, P.O. Box 6154, Campinas, São Paulo 13083-970, Brazil
- Department
of Materials Engineering, Federal University
of São Carlos, Rod. Washington Luís, km 235, São
Carlos, São Paulo 13565-905, Brazil
| | - Marco Beaumont
- School
of Chemistry and Physics, Queensland University
of Technology, 2 George
Street, Brisbane, Queensland 4001, Australia
- Department
of Chemistry, Institute of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences, Vienna, A-3430 Tulln, Austria
| | - Johanna Majoinen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Tero Kämäräinen
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Orlando J. Rojas
- Department
of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
- Bioproducts
Institute, Department of Chemical and Biological Engineering, Department
of Chemistry and Department of Wood Science, University of British Columbia, 2360 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
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18
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Wanasingha N, Dutta NK, Choudhury NR. Emerging bioadhesives: from traditional bioactive and bioinert to a new biomimetic protein-based approach. Adv Colloid Interface Sci 2021; 296:102521. [PMID: 34534751 DOI: 10.1016/j.cis.2021.102521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/04/2021] [Accepted: 09/04/2021] [Indexed: 12/29/2022]
Abstract
Bioadhesives have reached significant milestones over the past two decades. Research has shown not only to produce adhesives capable of adhering to dry tissue but recently wet tissue as well. However, most bioadhesives developed have exhibited high adhesion strength yet lack other properties required for versatility in application, such as elasticity, biocompatibility and biodegradability. Adapting from limitations met from early bioadhesives and meeting the current demand allows novel bioadhesives to reach new milestones for the future. In this review, we overview the progression and variations of bioadhesives, current trends, characterisation techniques and conclude with future perspectives for bioadhesives for tissue engineering applications.
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Affiliation(s)
- Nisal Wanasingha
- School of Engineering, RMIT University, Melbourne, VIC 3000, Australia
| | - Naba K Dutta
- School of Engineering, RMIT University, Melbourne, VIC 3000, Australia
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19
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Lim J, Kumar A, Low K, Verma CS, Mu Y, Miserez A, Pervushin K. Liquid-Liquid Phase Separation of Short Histidine- and Tyrosine-Rich Peptides: Sequence Specificity and Molecular Topology. J Phys Chem B 2021; 125:6776-6790. [PMID: 34106723 DOI: 10.1021/acs.jpcb.0c11476] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The increasing realization of the prevalence of liquid-liquid phase separation (LLPS) across multiple length scales of biological constructs, from intracellular membraneless organelles to extracellular load-bearing tissues, has raised intriguing questions about intermolecular interactions regulating LLPS at the atomic level. Squid-beak derived histidine (His)- and tyrosine (Tyr)-rich peptides (HBpeps) have recently emerged as suitable short model peptides to precisely assess the roles of peptide motifs and single residues on the phase behavior and material properties of microdroplets obtained by LLPS. In this study, by systematically introducing single mutations in an HBpep, we have identified specific sticker residues that attract peptide chains together. We find that His and Tyr residues located near the sequence termini drive phase separation, forming interaction nodes that stabilize microdroplets. Combining quantum chemistry simulations with NMR studies, we predict atomic-level bond geometries and uncover inter-residue supramolecular interactions governing LLPS. These results are subsequently used to propose possible topological arrangements of the peptide chains, which upon expansion can help explain the three-dimensional network of microdroplets. The stability of the proposed topologies carried out through all-atom molecular dynamics simulations predicts chain topologies that are more likely to stabilize the microdroplets. Overall, this study provides useful guidelines for the de novo design of peptide coacervates with tunable phase behavior and material properties. In addition, the analysis of nanoscale topologies may pave the way to understand how client molecules can be trapped within microdroplets, with direct implications for the encapsulation and controlled release of therapeutics for drug delivery applications.
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Affiliation(s)
- Jessica Lim
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
| | - Akshita Kumar
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, NTU, 50 Nanyang Avenue, Singapore 637 553.,Bioinformatics Institute, A*STAR, 30 Biopolis Street, 07-01 Matrix, Singapore 138 671
| | - Kimberly Low
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
| | - Chandra S Verma
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551.,Bioinformatics Institute, A*STAR, 30 Biopolis Street, 07-01 Matrix, Singapore 138 671.,Department of Biological Sciences, National University of Singapore (NUS), 16 Science Drive 4, Singapore 117 558
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
| | - Ali Miserez
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551.,Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, NTU, 50 Nanyang Avenue, Singapore 637 553
| | - Konstantin Pervushin
- School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637 551
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20
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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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21
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Heymann D, Mohanram H, Kumar A, Verma CS, Lescar J, Miserez A. Structure of a consensus chitin-binding domain revealed by solution NMR. J Struct Biol 2021; 213:107725. [PMID: 33744410 DOI: 10.1016/j.jsb.2021.107725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/10/2021] [Accepted: 03/14/2021] [Indexed: 11/29/2022]
Abstract
Chitin-binding proteins (CBPs) are a versatile group of proteins found in almost every organism on earth. CBPs are involved in enzymatic carbohydrate degradation and also serve as templating scaffolds in the exoskeleton of crustaceans and insects. One specific chitin-binding motif found across a wide range of arthropods' exoskeletons is the "extended Rebers and Riddiford" consensus (R&R), whose mechanism of chitin binding remains unclear. Here, we report the 3D structure and molecular level interactions of a chitin-binding domain (CBD-γ) located in a CBP from the beak of the jumbo squid Dosidicus gigas. This CBP is one of four chitin-binding proteins identified in the beak mouthpart of D. gigas and is believed to interact with chitin to form a scaffold network that is infiltrated with a second set of structural proteins during beak maturation. We used solution state NMR spectroscopy to elucidate the molecular interactions between CBD-γ and the soluble chitin derivative pentaacetyl-chitopentaose (PCP), and find that folding of CBD-γ is triggered upon its interaction with PCP. To our knowledge, this is the first experimental 3D structure of a CBP containing the R&R consensus motif, which can be used as a template to understand in more details the role of the R&R motif found in a wide range of CBP-chitin complexes. The present structure also provides molecular information for biomimetic synthesis of graded biomaterials using aqueous-based chemistry and biopolymers.
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Affiliation(s)
- Dario Heymann
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore
| | - Harini Mohanram
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore
| | - Akshita Kumar
- Biological and Biomimetic Material Laboratory, Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore 637553, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra S Verma
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; Department of Biological Sciences, National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Julien Lescar
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore.
| | - 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 637553, Singapore; School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), 59 Nanyang Drive, Level 06-01, Singapore 636921, Singapore.
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22
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Abbas M, Lipiński WP, Wang J, Spruijt E. Peptide-based coacervates as biomimetic protocells. Chem Soc Rev 2021; 50:3690-3705. [PMID: 33616129 DOI: 10.1039/d0cs00307g] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coacervates are condensed liquid-like droplets formed by liquid-liquid phase separation of molecules through multiple weak associative interactions. In recent years it has emerged that not only long polymers, but also short peptides are capable of forming simple and complex coacervates. The coacervate droplets they form act as compartments that sequester and concentrate a wide range of solutes, and their spontaneous formation make coacervates attractive protocell models. The main advantage of peptides as building blocks lies in the functional diversity of the amino acid residues, which allows for tailoring of the peptide's phase separation propensity, their selectivity in guest molecule uptake and the physicochemical and catalytic properties of the compartments. The aim of this tutorial review is to illustrate the recent developments in the field of peptide-based coacervates in a systematic way and to deduce the basic requirements for both simple and complex coacervation of peptides. We review a selection of peptide coacervates that illustrates the essentials of phase separation, the limitations, and the properties that make peptide coacervates biomimetic protocells. Finally, we provide some perspectives of this novel research field in the direction of active droplets, moving away from thermodynamic equilibrium.
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Affiliation(s)
- Manzar Abbas
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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23
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Tiwari P, Bharti I, Bohidar HB, Quadir S, Joshi MC, Arfin N. Complex Coacervation and Overcharging during Interaction between Hydrophobic Zein and Hydrophilic Laponite in Aqueous Ethanol Solution. ACS OMEGA 2020; 5:33064-33074. [PMID: 33403268 PMCID: PMC7774070 DOI: 10.1021/acsomega.0c04647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
In this paper, for the first time, we have reported the formation of complex coacervate during interaction between hydrophobic protein, zein, and hydrophilic nanoclay, Laponite, in a 60% v/v ethanol solution at pH 4. Dynamic light scattering and viscosity measurements revealed the formation of zein-Laponite complexes during the interaction between zein at fixed concentration, C Z = 1 mg/mL, and varying concentrations of Laponite, C L (7.8 × 10-4 - 0.25% w/v). Further investigation of the zein-Laponite complexes using turbidity and zeta potential data showed that these complexes could be demarcated in three different regions: Region I, below the charge neutralization region (C Z = 1 mg/mL, C L ≤ 0.00625% w/v) where soluble complexes was formed during interaction between oppositely charged zein and Laponite; Region II, the charge neutralization region (C Z = 1 mg/mL, 0.00625 < C L ≤ 0.05% w/v) where zein-Laponite complexes form neutral coacervates; and Region III, the interesting overcharged coacervates region (C Z = 1 mg/mL, C L > 0.05% w/v). Investigation of coacervates using a fluorescence imaging technique showed that the size of neutral coacervates in region II was large (mean size = 1223.7 nm) owing to aggregation as compared to the small size of coacervates (mean size = 464.7 nm) in region III owing to repulsion between overcharged coacervates. Differential scanning calorimeter, DSC, revealed the presence of an ample amount of bound water in region III. The presence of bound water was evident from the presence of an additional peak at 107 °C in region III apart from normal enthalpy of evaporation of water from coacervates.
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Affiliation(s)
- Preeti Tiwari
- Soft
condense matter laboratory, Centre for Interdisciplinary Research
In Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Indu Bharti
- Soft
condense matter laboratory, Centre for Interdisciplinary Research
In Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Himadri B Bohidar
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shabina Quadir
- Multidisciplinary
Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohan C Joshi
- Multidisciplinary
Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Najmul Arfin
- Soft
condense matter laboratory, Centre for Interdisciplinary Research
In Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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24
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Chen N, Zhao Z, Wang Y, Dimova R. Resolving the Mechanisms of Soy Glycinin Self-Coacervation and Hollow-Condensate Formation. ACS Macro Lett 2020; 9:1844-1852. [PMID: 35653686 DOI: 10.1021/acsmacrolett.0c00709] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Self-coacervation of animal-derived proteins has been extensively investigated while that of plant proteins remains largely unexplored. Here, we study the process of soy glycinin self-coacervation and transformation into hollow condensates. The protein hexameric structure composed of hydrophilic and hydrophobic polypeptides is crucial for coacervation. The process is driven by charge screening of the intrinsically disordered region of acidic polypeptides, allowing for weak hydrophobic interactions between exposed hydrophobic polypeptides. We find that the coacervate surface exhibits order, which stabilizes the coacervate shape during hollow-condensate formation. The latter process occurs via nucleation and growth of protein-poor phase in the coacervate interior, during which another ordered layer at the inner surface is formed. Aging enhances the stability of both coacervates and hollow condensates. Understanding plant protein coacervation holds promises for fabricating novel functional materials.
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Affiliation(s)
- Nannan Chen
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, 510632 Guangzhou, China
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, 14424 Potsdam, Germany
| | - Ziliang Zhao
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, 14424 Potsdam, Germany
| | - Yong Wang
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, 510632 Guangzhou, China
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, 14424 Potsdam, Germany
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25
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Zhang Y, Pon N, Awaji A, Rowan SJ. Squid Beak Inspired Cross-Linked Cellulose Nanocrystal Composites. Biomacromolecules 2020; 22:201-212. [PMID: 32969223 DOI: 10.1021/acs.biomac.0c01051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioinspired cross-linked polymer nanocomposites that mimic the water-enhanced mechanical gradient properties of the squid beak have been prepared by embedding either carboxylic acid- or allyl-functionalized cellulose nanocrystals (CNC) into an alkene-containing polymer matrix (poly(vinyl acetate-co-vinyl pentenoate), P(VAc-co-VP)). Cross-linking is achieved by imbibing the composite with a tetrathiol cross-linker and carrying out a photoinduced thiol-ene reaction. Central to this study was an investigation on how the placement of cross-links (i.e., within matrix only or between the matrix and filler) impacts the wet mechanical properties of these materials. Through cross-linking both the CNCs and matrix, it is possible to access larger wet mechanical contrasts (E'stiff/E'soft = ca. 20) than can be obtained by just cross-linking the matrix alone (where contrast E'stiff/E'soft of up 11 are observed). For example, in nanocomposites fabricated with 15 wt % of allyl-functionalized tunicate CNCs and P(VAc-co-VP) with about 30 mol % of the alkene-containing VP units, an increase in the modulus of the wet composite from about 14 MPa to about 289 MPa at physiological temperature (37 °C) can be observed after UV irradiation. The water swelling of the nanocomposites is greatly reduced in the cross-linked materials as a result of the thiol-ene cross-linking network, which also contributes to the wet modulus increase. Given the mechanical turnability and the relatively simple approach that also allows photopatterning the material properties, these water-activated bioinspired nanocomposites have potential uses in a broad range of biomedical applications, such as mechanically compliant intracortical microelectrodes.
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Affiliation(s)
- Yefei Zhang
- Pritzker School of Molecular Engineering, University of Chicago, 5640 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Nanetta Pon
- Department of Chemistry, University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ahmed Awaji
- Department of Macromolecular Science and Engineering, Case Western Reserve University, 2100 Adelbert Road, Cleveland, Ohio 44106, United States
| | - Stuart J Rowan
- Pritzker School of Molecular Engineering, University of Chicago, 5640 S Ellis Avenue, Chicago, Illinois 60637, United States.,Department of Chemistry, University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States.,Chemical and Engineering Sciences, Argonne National Laboratory, 9700 Cass Avenue, Lemont, Illinois 60439, United States
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26
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Lim ZW, Varma VB, Ramanujan RV, Miserez A. Magnetically responsive peptide coacervates for dual hyperthermia and chemotherapy treatments of liver cancer. Acta Biomater 2020; 110:221-230. [PMID: 32422317 DOI: 10.1016/j.actbio.2020.04.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Liver cancer is an aggressive malignancy associated with high levels of mortality and morbidity. Doxorubicin (Dox) is often used to slow down liver cancer progression; however its efficacy is limited, and its severe side effects prevent its routine use at therapeutic concentrations. We present a biomimetic peptide that coacervates into micro-droplets, within which both Dox and magnetic nanoparticles (MNPs) can be sequestered. These Dox-loaded Magnetic Coacervates (DMCs) can be used for thermo-chemotherapy, with the controlled release of Dox triggered by an external Alternating Magnetic Field (AMF). The DMCs are internalized by the cells via an energy-independent mechanism which is not based on endocytosis. Application of AMF generates a temperature of 45 °C within the DMCs, triggering their disassembly and the simultaneous release of Dox, thereby resulting in dual hyperthermia and chemotherapy for more efficient cancer therapy. In vitro studies conducted under AMF reveal that DMCs are cytocompatible and effective in inducing HepG2 liver cancer cell death. Thermo-chemotherapy treatment against HepG2 cells is also shown to be more effective compared to either hyperthermia or chemotherapy treatments alone. Thus, our novel peptide DMCs can open avenues in theranostic strategies against liver cancer through programmable, wireless, and remote control of Dox release. STATEMENT OF SIGNIFICANCE: Simultaneous administration of chemical and thermal therapy (thermo-chemotherapy) is more effective in inducing liver cancer cell death and improving survival rate. Thus, there is a keen interest in developing suitable carriers for thermo-chemotherapy. Coacervate micro-droplets display significant advantages, including high loading capacity, fast self-assembly in aqueous environments, and liquid-like behavior. However, they have not yet been explored as carriers for thermo-chemotherapy. Here, we demonstrate that peptide coacervate micro-droplets can co-encapsulate Dox and magnetic nanoparticles and cross the cell membrane. Applying an alternating magnetic field to cells containing drug-loaded coacervates triggers the release of Dox as well as the localized heating by magnetic hyperthermia, resulting in efficient liver cancer cell death by dual thermo-chemotherapy.
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Affiliation(s)
- Zhi Wei Lim
- Biological and Biomimetic Materials Laboratory, Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 637553
| | - Vijaykumar B Varma
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Raju V Ramanujan
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Ali Miserez
- Biological and Biomimetic Materials Laboratory, Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 637553; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.
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27
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Zhou L, Shi H, Li Z, He C. Recent Advances in Complex Coacervation Design from Macromolecular Assemblies and Emerging Applications. Macromol Rapid Commun 2020; 41:e2000149. [DOI: 10.1002/marc.202000149] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/29/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lili Zhou
- Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117576 Singapore
| | - Huihui Shi
- Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117576 Singapore
| | - Zibiao Li
- Institute of Materials Research and Engineering A:STAR (Agency for Science, Technology and Research) 2 Fusionopolis Way, Innovis, #08‐03 Singapore 138634 Singapore
| | - Chaobin He
- Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117576 Singapore
- Institute of Materials Research and Engineering A:STAR (Agency for Science, Technology and Research) 2 Fusionopolis Way, Innovis, #08‐03 Singapore 138634 Singapore
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28
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Gleede T, Markwart JC, Huber N, Rieger E, Wurm FR. Competitive Copolymerization: Access to Aziridine Copolymers with Adjustable Gradient Strengths. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01623] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Tassilo Gleede
- Max-Planck-Institut für Polymerforschung (MPI-P), Ackermannweg 10, 55128 Mainz, Germany
| | - Jens C. Markwart
- Max-Planck-Institut für Polymerforschung (MPI-P), Ackermannweg 10, 55128 Mainz, Germany
| | - Niklas Huber
- Max-Planck-Institut für Polymerforschung (MPI-P), Ackermannweg 10, 55128 Mainz, Germany
| | - Elisabeth Rieger
- Max-Planck-Institut für Polymerforschung (MPI-P), Ackermannweg 10, 55128 Mainz, Germany
| | - Frederik R. Wurm
- Max-Planck-Institut für Polymerforschung (MPI-P), Ackermannweg 10, 55128 Mainz, Germany
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29
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Gabryelczyk B, Cai H, Shi X, Sun Y, Swinkels PJM, Salentinig S, Pervushin K, Miserez A. Hydrogen bond guidance and aromatic stacking drive liquid-liquid phase separation of intrinsically disordered histidine-rich peptides. Nat Commun 2019; 10:5465. [PMID: 31784535 PMCID: PMC6884462 DOI: 10.1038/s41467-019-13469-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/07/2019] [Indexed: 01/07/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) is involved in both intracellular membraneless organelles and extracellular tissues. Despite growing understanding of LLPS, molecular-level mechanisms behind this process are still not fully established. Here, we use histidine-rich squid beak proteins (HBPs) as model IDPs to shed light on molecular interactions governing LLPS. We show that LLPS of HBPs is mediated though specific modular repeats. The morphology of separated phases (liquid-like versus hydrogels) correlates with the repeats' hydrophobicity. Solution-state NMR indicates that LLPS is a multistep process initiated by deprotonation of histidine residues, followed by transient hydrogen bonding with tyrosine, and eventually by hydrophobic interactions. The microdroplets are stabilized by aromatic clustering of tyrosine residues exhibiting restricted molecular mobility in the nano-to-microsecond timescale according to solid-state NMR experiments. Our findings provide guidelines to rationally design pH-responsive peptides with LLPS ability for various applications, including bioinspired protocells and smart drug-delivery systems.
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Affiliation(s)
- Bartosz Gabryelczyk
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Hao Cai
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Xiangyan Shi
- School of Physical and Mathematical Sciences, NTU, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Yue Sun
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Piet J M Swinkels
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
- Physical Chemistry and Soft Matter, Wageningen University, 6708 WE, Wageningen, Netherlands
| | - Stefan Salentinig
- Laboratory for Biointerfaces, Department Materials Meet Life, EMPA, CH-9014, St-Gallen, Switzerland
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700, Fribourg, Switzerland
| | - Konstantin Pervushin
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Ali Miserez
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore.
- School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore.
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30
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Perro A, Giraud L, Coudon N, Shanmugathasan S, Lapeyre V, Goudeau B, Douliez JP, Ravaine V. Self-coacervation of ampholyte polymer chains as an efficient encapsulation strategy. J Colloid Interface Sci 2019; 548:275-283. [DOI: 10.1016/j.jcis.2019.04.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/09/2023]
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31
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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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32
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Lemetti L, Hirvonen SP, Fedorov D, Batys P, Sammalkorpi M, Tenhu H, Linder MB, Aranko AS. Molecular crowding facilitates assembly of spidroin-like proteins through phase separation. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2018.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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33
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Blackman LD, Gunatillake PA, Cass P, Locock KES. An introduction to zwitterionic polymer behavior and applications in solution and at surfaces. Chem Soc Rev 2019; 48:757-770. [PMID: 30548039 DOI: 10.1039/c8cs00508g] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Zwitterionic polymers, including polyampholytes and polybetaines, are polymers with both positive and negative charges incorporated into their structure. They are a unique class of smart materials with great potential in a broad range of applications in nanotechnology, biomaterials science, nanomedicine and healthcare, as additives for bulk construction materials and crude oil, and in water remediation. In this Tutorial Review, we aim to highlight their structural diversity and design criteria, and their preparation using modern techniques. Their behavior, both in solution and at surfaces, will be examined under a range of environmental conditions. Finally, we will exemplify how their unique behaviors give rise to specific properties tailored to a selection of their numerous applications.
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Affiliation(s)
- Lewis D Blackman
- Manufacturing Business Unit, Commonwealth Scientific and Industrial Research Organisation, Bayview Avenue, Clayton, VIC 3168, Australia.
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34
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Das S, Amin AN, Lin YH, Chan HS. Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters. Phys Chem Chem Phys 2018; 20:28558-28574. [PMID: 30397688 DOI: 10.1039/c8cp05095c] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biomolecular condensates undergirded by phase separations of proteins and nucleic acids serve crucial biological functions. To gain physical insights into their genetic basis, we study how liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) depends on their sequence charge patterns using a continuum Langevin chain model wherein each amino acid residue is represented by a single bead. Charge patterns are characterized by the "blockiness" measure κ and the "sequence charge decoration" (SCD) parameter. Consistent with random phase approximation (RPA) theory and lattice simulations, LLPS propensity as characterized by critical temperature Tcr* increases with increasingly negative SCD for a set of sequences showing a positive correlation between κ and -SCD. Relative to RPA, the simulated sequence-dependent variation in Tcr* is often-though not always-smaller, whereas the simulated critical volume fractions are higher. However, for a set of sequences exhibiting an anti-correlation between κ and -SCD, the simulated Tcr*'s are quite insensitive to either parameter. Additionally, we find that blocky sequences that allow for strong electrostatic repulsion can lead to coexistence curves with upward concavity as stipulated by RPA, but the LLPS propensity of a strictly alternating charge sequence was likely overestimated by RPA and lattice models because interchain stabilization of this sequence requires spatial alignments that are difficult to achieve in real space. These results help delineate the utility and limitations of the charge pattern parameters and of RPA, pointing to further efforts necessary for rationalizing the newly observed subtleties.
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Affiliation(s)
- Suman Das
- Department of Biochemistry, University of Toronto, Medical Sciences Building - 5th Fl., 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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35
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Mohammadi P, Beaune G, Stokke BT, Timonen JVI, Linder MB. Self-Coacervation of a Silk-Like Protein and Its Use As an Adhesive for Cellulosic Materials. ACS Macro Lett 2018; 7:1120-1125. [PMID: 30258700 PMCID: PMC6150716 DOI: 10.1021/acsmacrolett.8b00527] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/29/2018] [Indexed: 12/19/2022]
Abstract
![]()
Liquid–liquid
phase separation of biomacromolecules plays
a critical role in many of their functions, both as cellular components
and in structural assembly. Phase separation is also a key mechanism
in the assembly of engineered recombinant proteins for the general
aim to build new materials with unique structures and properties.
Here the phase separation process of an engineered protein with a
block-architecture was studied. As a central block, we used a modified
spider silk sequence, predicted to be unstructured. In each terminus,
folded globular blocks were used. We studied the kinetics and mechanisms
of phase formation and analyzed the evolving structures and their
viscoelastic properties. Individual droplets were studied with a micropipette
technique, showing both how properties vary between individual drops
and explaining overall bulk rheological properties. A very low surface
energy allowed easy deformation of droplets and led to efficient infiltration
into cellulosic fiber networks. Based on these findings, we demonstrated
an efficient use of the phase-separated material as an adhesive for
cellulose. We also conclude that the condensed state is metastable,
showing an ensemble of properties in individual droplets and that
an understanding of protein phase behavior will lead to developing
a wider use of proteins as structural polymers.
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Affiliation(s)
- Pezhman Mohammadi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150, Espoo, Finland
| | - Grégory Beaune
- Department of Applied Physics, School of Science, Aalto University, FI-02150, Espoo, Finland
| | - Bjørn Torger Stokke
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway
| | - Jaakko V. I. Timonen
- Department of Applied Physics, School of Science, Aalto University, FI-02150, Espoo, Finland
| | - Markus B. Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150, Espoo, Finland
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36
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Rumyantsev AM, Kramarenko EY, Borisov OV. Microphase Separation in Complex Coacervate Due to Incompatibility between Polyanion and Polycation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00721] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Artem M. Rumyantsev
- Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, UMR 5254 CNRS UPPA, Pau, France
| | | | - Oleg V. Borisov
- Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, UMR 5254 CNRS UPPA, Pau, France
- Institute of Macromolecular Compounds, Russian Academy of Sciences, 199004 St. Petersburg, Russia
- Peter the Great
St. Petersburg State Polytechnic University, 195251 St. Petersburg, Russia
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37
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Mohammadi P, Aranko AS, Lemetti L, Cenev Z, Zhou Q, Virtanen S, Landowski CP, Penttilä M, Fischer WJ, Wagermaier W, Linder MB. Phase transitions as intermediate steps in the formation of molecularly engineered protein fibers. Commun Biol 2018; 1:86. [PMID: 30271967 PMCID: PMC6123624 DOI: 10.1038/s42003-018-0090-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/08/2018] [Indexed: 12/19/2022] Open
Abstract
A central concept in molecular bioscience is how structure formation at different length scales is achieved. Here we use spider silk protein as a model to design new recombinant proteins that assemble into fibers. We made proteins with a three-block architecture with folded globular domains at each terminus of a truncated repetitive silk sequence. Aqueous solutions of these engineered proteins undergo liquid-liquid phase separation as an essential pre-assembly step before fibers can form by drawing in air. We show that two different forms of phase separation occur depending on solution conditions, but only one form leads to fiber assembly. Structural variants with one-block or two-block architectures do not lead to fibers. Fibers show strong adhesion to surfaces and self-fusing properties when placed into contact with each other. Our results show a link between protein architecture and phase separation behavior suggesting a general approach for understanding protein assembly from dilute solutions into functional structures.
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Affiliation(s)
- Pezhman Mohammadi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland.
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Laura Lemetti
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Zoran Cenev
- Department of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, 02150, Espoo, Finland
| | - Quan Zhou
- Department of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, 02150, Espoo, Finland
| | - Salla Virtanen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | | | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., 02150, Espoo, Finland
| | | | - Wolfgang Wagermaier
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland.
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38
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Lim ZW, Ping Y, Miserez A. Glucose-Responsive Peptide Coacervates with High Encapsulation Efficiency for Controlled Release of Insulin. Bioconjug Chem 2018; 29:2176-2180. [DOI: 10.1021/acs.bioconjchem.8b00369] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhi Wei Lim
- Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, 637553 Singapore
| | - Yuan Ping
- Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, 637553 Singapore
| | - Ali Miserez
- Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, 637553 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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39
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Affiliation(s)
- Skelte G. Anema
- Fonterra Research and Development Centre, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
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40
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Zhang B, Xiao Y, Fang H, Gao H, Wang F, Cheng X. Mesogenic D–A fluorophores based on cyanovinyl and benzothiadiazole. NEW J CHEM 2018. [DOI: 10.1039/c8nj02814a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesized cyanovinyl and BTD based fluorophores displayed LC, Gel as well as optical waveguide and chemosensor properties.
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Affiliation(s)
- Bei Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Chemistry Department
- Yunnan University
- Kunming
- P. R. China
| | - Yulong Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Chemistry Department
- Yunnan University
- Kunming
- P. R. China
| | - Haipeng Fang
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Chemistry Department
- Yunnan University
- Kunming
- P. R. China
| | - Hongfei Gao
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Chemistry Department
- Yunnan University
- Kunming
- P. R. China
| | - Fuke Wang
- Department of Sports Medicine
- First Affiliated Hospital of Kunming Medical University
- China
| | - Xiaohong Cheng
- Key Laboratory of Medicinal Chemistry for Natural Resources
- Chemistry Department
- Yunnan University
- Kunming
- P. R. China
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