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van Stevendaal MME, Hazegh Nikroo A, Mason AF, Jansen J, Yewdall NA, van Hest JCM. Regulating Chemokine-Receptor Interactions through the Site-Specific Bioorthogonal Conjugation of Photoresponsive DNA Strands. Bioconjug Chem 2023; 34:2089-2095. [PMID: 37856672 PMCID: PMC10655040 DOI: 10.1021/acs.bioconjchem.3c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/30/2023] [Indexed: 10/21/2023]
Abstract
Oligonucleotide conjugation has emerged as a versatile molecular tool for regulating protein activity. A state-of-the-art labeling strategy includes the site-specific conjugation of DNA, by employing bioorthogonal groups genetically incorporated in proteins through unnatural amino acids (UAAs). The incorporation of UAAs in chemokines has to date, however, remained underexplored, probably due to their sometimes poor stability following recombinant expression. In this work, we designed a fluorescent stromal-derived factor-1β (SDF-1β) chemokine fusion protein with a bioorthogonal functionality amenable for click reactions. Using amber stop codon suppression, p-azido-L-phenylalanine was site-specifically incorporated in the fluorescent N-terminal fusion partner, superfolder green fluorescent protein (sfGFP). Conjugation to single-stranded DNAs (ssDNA), modified with a photocleavable spacer and a reactive bicyclononyne moiety, was performed to create a DNA-caged species that blocked the receptor binding ability. This inhibition was completely reversible by means of photocleavage of the ssDNA strands. The results described herein provide a versatile new direction for spatiotemporally regulating chemokine-receptor interactions, which is promising for tissue engineering purposes.
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Affiliation(s)
- Marleen
H. M. E. van Stevendaal
- Laboratory
of Bio-Organic Chemistry, Department of Biomedical Engineering, Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Arjan Hazegh Nikroo
- Laboratory
of Bio-Organic Chemistry, Department of Biomedical Engineering, Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Alexander F. Mason
- School
of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jitske Jansen
- Department
of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - N. Amy Yewdall
- School
of Biological Sciences, University of Canterbury, 8041 Christchurch, New Zealand
| | - Jan C. M. van Hest
- Laboratory
of Bio-Organic Chemistry, Department of Biomedical Engineering, Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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2
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Schoenmakers LLJ, Yewdall NA, Lu T, André AAM, Nelissen FHT, Spruijt E, Huck WTS. In Vitro Transcription-Translation in an Artificial Biomolecular Condensate. ACS Synth Biol 2023. [PMID: 37343188 PMCID: PMC10393115 DOI: 10.1021/acssynbio.3c00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Biomolecular condensates are a promising platform for synthetic cell formation and constitute a potential missing link between the chemical and cellular stage of the origins of life. However, it has proven challenging to integrate complex reaction networks into biomolecular condensates, such as a cell-free in vitro transcription-translation (IVTT) system. Integrating IVTT into biomolecular condensates successfully is one precondition for condensation-based synthetic cell formation. Moreover, it would provide a proof of concept that biomolecular condensates are in principle compatible with the central dogma, one of the hallmarks of cellular life. Here, we have systemically investigated the compatibility of eight different (bio)molecular condensates with IVTT incorporation. Of these eight candidates, we have found that a green fluorescent protein-labeled, intrinsically disordered cationic protein (GFP-K72) and single-stranded DNA (ssDNA) can form biomolecular condensates that are compatible with up to μM fluorescent protein expression. This shows that biomolecular condensates can indeed integrate complex reaction networks, confirming their use as synthetic cell platforms and hinting at a possible role in the origin of life.
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Affiliation(s)
- Ludo L J Schoenmakers
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Tiemei Lu
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Alain A M André
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
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3
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André AAM, Yewdall NA, Spruijt E. Crowding-induced phase separation and gelling by co-condensation of PEG in NPM1-rRNA condensates. Biophys J 2023; 122:397-407. [PMID: 36463407 PMCID: PMC9892608 DOI: 10.1016/j.bpj.2022.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The crowdedness of the cell calls for adequate intracellular organization. Biomolecular condensates, formed by liquid-liquid phase separation of intrinsically disordered proteins and nucleic acids, are important organizers of cellular fluids. To underpin the molecular mechanisms of protein condensation, cell-free studies are often used where the role of crowding is not investigated in detail. Here, we investigate the effects of macromolecular crowding on the formation and material properties of a model heterotypic biomolecular condensate, consisting of nucleophosmin (NPM1) and ribosomal RNA (rRNA). We studied the effect of the macromolecular crowding agent poly(ethylene glycol) (PEG), which is often considered an inert crowding agent. We observed that PEG could induce both homotypic and heterotypic phase separation of NPM1 and NPM1-rRNA, respectively. Crowding increases the condensed concentration of NPM1 and decreases its equilibrium dilute phase concentration, although no significant change in the concentration of rRNA in the dilute phase was observed. Interestingly, the crowder itself is concentrated in the condensates, suggesting that co-condensation rather than excluded volume interactions underlie the enhanced phase separation by PEG. Fluorescence recovery after photobleaching measurements indicated that both NPM1 and rRNA become immobile at high PEG concentrations, indicative of a liquid-to-gel transition. Together, these results provide more insight into the role of synthetic crowding agents in phase separation and demonstrate that condensate properties determined in vitro depend strongly on the addition of crowding agents.
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Affiliation(s)
- Alain A M André
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
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4
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Yewdall NA, André AAM, van Haren MHI, Nelissen FHT, Jonker A, Spruijt E. ATP:Mg 2+ shapes material properties of protein-RNA condensates and their partitioning of clients. Biophys J 2022; 121:3962-3974. [PMID: 36004782 PMCID: PMC9674983 DOI: 10.1016/j.bpj.2022.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/29/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022] Open
Abstract
Many cellular condensates are heterotypic mixtures of proteins and RNA formed in complex environments. Magnesium ions (Mg2+) and ATP can impact RNA folding, and local intracellular levels of these factors can vary significantly. However, the effect of ATP:Mg2+ on the material properties of protein-RNA condensates is largely unknown. Here, we use an in vitro condensate model of nucleoli, made from nucleophosmin 1 (NPM1) proteins and ribosomal RNA (rRNA), to study the effect of ATP:Mg2+. While NPM1 dynamics remain unchanged at increasing Mg2+ concentrations, the internal RNA dynamics dramatically slowed until a critical point, where gel-like states appeared, suggesting the RNA component alone forms a viscoelastic network that undergoes maturation driven by weak multivalent interactions. ATP reverses this arrest and liquefies the gel-like structures. ATP:Mg2+ also influenced the NPM1-rRNA composition of condensates and enhanced the partitioning of two clients: an arginine-rich peptide and a small nuclear RNA. By contrast, larger ribosome partitioning shows dependence on ATP:Mg2+ and can become reversibly trapped around NPM1-rRNA condensates. Lastly, we show that dissipative enzymatic reactions that deplete ATP can be used to control the shape, composition, and function of condensates. Our results illustrate how intracellular environments may regulate the state and client partitioning of RNA-containing condensates.
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Affiliation(s)
- N Amy Yewdall
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
| | - Alain A M André
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Aafke Jonker
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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5
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Song S, Mason AF, Post RAJ, De Corato M, Mestre R, Yewdall NA, Cao S, van der Hofstad RW, Sanchez S, Abdelmohsen LKEA, van Hest JCM. Author Correction: Engineering transient dynamics of artificial cells by stochastic distribution of enzymes. Nat Commun 2021; 12:7351. [PMID: 34916509 PMCID: PMC8677841 DOI: 10.1038/s41467-021-27682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Shidong Song
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Alexander F Mason
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Richard A J Post
- Department of Mathematics and Computer Science, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Marco De Corato
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.,Aragon Institute of Engineering Research (I3A), University of Zaragoza, 50009, Zaragoza, Spain
| | - Rafael Mestre
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - N Amy Yewdall
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Shoupeng Cao
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Remco W van der Hofstad
- Department of Mathematics and Computer Science, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
| | - Samuel Sanchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Loai K E A Abdelmohsen
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
| | - Jan C M van Hest
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
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6
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Song S, Mason AF, Post RAJ, De Corato M, Mestre R, Yewdall NA, Cao S, van der Hofstad RW, Sanchez S, Abdelmohsen LKEA, van Hest JCM. Engineering transient dynamics of artificial cells by stochastic distribution of enzymes. Nat Commun 2021; 12:6897. [PMID: 34824231 PMCID: PMC8617035 DOI: 10.1038/s41467-021-27229-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022] Open
Abstract
Random fluctuations are inherent to all complex molecular systems. Although nature has evolved mechanisms to control stochastic events to achieve the desired biological output, reproducing this in synthetic systems represents a significant challenge. Here we present an artificial platform that enables us to exploit stochasticity to direct motile behavior. We found that enzymes, when confined to the fluidic polymer membrane of a core-shell coacervate, were distributed stochastically in time and space. This resulted in a transient, asymmetric configuration of propulsive units, which imparted motility to such coacervates in presence of substrate. This mechanism was confirmed by stochastic modelling and simulations in silico. Furthermore, we showed that a deeper understanding of the mechanism of stochasticity could be utilized to modulate the motion output. Conceptually, this work represents a leap in design philosophy in the construction of synthetic systems with life-like behaviors. Here the authors develop a coacervate micromotor that can display autonomous motion as a result of stochastic distribution of propelling units. This stochastic-induced mobility is validated and explained through experiments and theory.
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Affiliation(s)
- Shidong Song
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Alexander F Mason
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Richard A J Post
- Department of Mathematics and Computer Science, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Marco De Corato
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.,Aragon Institute of Engineering Research (I3A), University of Zaragoza, 50009, Zaragoza, Spain
| | - Rafael Mestre
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - N Amy Yewdall
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Shoupeng Cao
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Remco W van der Hofstad
- Department of Mathematics and Computer Science, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
| | - Samuel Sanchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Loai K E A Abdelmohsen
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
| | - Jan C M van Hest
- Department of Bio-Organic Chemistry, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
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7
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8
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van Stevendaal MHME, Vasiukas L, Yewdall NA, Mason AF, van Hest JCM. Engineering of Biocompatible Coacervate-Based Synthetic Cells. ACS Appl Mater Interfaces 2021; 13:7879-7889. [PMID: 33587612 PMCID: PMC7908014 DOI: 10.1021/acsami.0c19052] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Polymer-stabilized complex coacervate microdroplets have emerged as a robust platform for synthetic cell research. Their unique core-shell properties enable the sequestration of high concentrations of biologically relevant macromolecules and their subsequent release through the semipermeable membrane. These unique properties render the synthetic cell platform highly suitable for a range of biomedical applications, as long as its biocompatibility upon interaction with biological cells is ensured. The purpose of this study is to investigate how the structure and formulation of these coacervate-based synthetic cells impact the viability of several different cell lines. Through careful examination of the individual synthetic cell components, it became evident that the presence of free polycation and membrane-forming polymer had to be prevented to ensure cell viability. After closely examining the structure-toxicity relationship, a set of conditions could be found whereby no detrimental effects were observed, when the artificial cells were cocultured with RAW264.7 cells. This opens up a range of possibilities to use this modular system for biomedical applications and creates design rules for the next generation of coacervate-based, biomedically relevant particles.
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Affiliation(s)
- Marleen H. M. E. van Stevendaal
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P. O. Box 513
(STO 3.41), 5600MB Eindhoven, The Netherlands
| | - Laurynas Vasiukas
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P. O. Box 513
(STO 3.41), 5600MB Eindhoven, The Netherlands
| | - N. Amy Yewdall
- Institute
for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Alexander F. Mason
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P. O. Box 513
(STO 3.41), 5600MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P. O. Box 513
(STO 3.41), 5600MB Eindhoven, The Netherlands
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9
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Altenburg WJ, Yewdall NA, Vervoort DFM, van Stevendaal MHME, Mason AF, van Hest JCM. Programmed spatial organization of biomacromolecules into discrete, coacervate-based protocells. Nat Commun 2020; 11:6282. [PMID: 33293610 PMCID: PMC7722712 DOI: 10.1038/s41467-020-20124-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
The cell cytosol is crowded with high concentrations of many different biomacromolecules, which is difficult to mimic in bottom-up synthetic cell research and limits the functionality of existing protocellular platforms. There is thus a clear need for a general, biocompatible, and accessible tool to more accurately emulate this environment. Herein, we describe the development of a discrete, membrane-bound coacervate-based protocellular platform that utilizes the well-known binding motif between Ni2+-nitrilotriacetic acid and His-tagged proteins to exercise a high level of control over the loading of biologically relevant macromolecules. This platform can accrete proteins in a controlled, efficient, and benign manner, culminating in the enhancement of an encapsulated two-enzyme cascade and protease-mediated cargo secretion, highlighting the potency of this methodology. This versatile approach for programmed spatial organization of biologically relevant proteins expands the protocellular toolbox, and paves the way for the development of the next generation of complex yet well-regulated synthetic cells.
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Affiliation(s)
- Wiggert J Altenburg
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - N Amy Yewdall
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Daan F M Vervoort
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Marleen H M E van Stevendaal
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Alexander F Mason
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
| | - Jan C M van Hest
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
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10
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De Martino MT, Tonin F, Yewdall NA, Abdelghani M, Williams DS, Hanefeld U, Rutjes FPJT, Abdelmohsen LKEA, van Hest JCM. Compartmentalized cross-linked enzymatic nano-aggregates ( c-CLE nA) for efficient in-flow biocatalysis. Chem Sci 2020; 11:2765-2769. [PMID: 34084336 PMCID: PMC8157641 DOI: 10.1039/c9sc05420k] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nano-sized enzyme aggregates, which preserve their catalytic activity are of great interest for flow processes, as these catalytic species show minimal diffusional issues, and are still sizeable enough to be effectively separated from the formed product. The realization of such catalysts is however far from trivial. The stable formation of a micro-to millimeter-sized enzyme aggregate is feasible via the formation of a cross-linked enzyme aggregate (CLEA); however, such a process leads to a rather broad size distribution, which is not always compatible with microflow conditions. Here, we present the design of a compartmentalized templated CLEA (c-CLEnA), inside the nano-cavity of bowl-shaped polymer vesicles, coined stomatocytes. Due to the enzyme preorganization and concentration in the cavity, cross-linking could be performed with substantially lower amount of cross-linking agents, which was highly beneficial for the residual enzyme activity. Our methodology is generally applicable, as demonstrated by using two different cross-linkers (glutaraldehyde and genipin). Moreover, c-CLEnA nanoreactors were designed with Candida antarctica Lipase B (CalB) and Porcine Liver Esterase (PLE), as well as a mixture of glucose oxidase (GOx) and horseradish peroxidase (HRP). Interestingly, when genipin was used as cross-linker, all enzymes preserved their initial activity. Furthermore, as proof of principle, we demonstrated the successful implementation of different c-CLEnAs in a flow reactor in which the c-CLEnA nanoreactors retained their full catalytic function even after ten runs. Such a c-CLEnA nanoreactor represents a significant step forward in the area of in-flow biocatalysis. c-CLEnA are obtained via cross-linking enzymes in the nanocavity of supramolecular stomatocytes. Such c-CLEnA can be recycled while retaining its activity – an excellent nanoreactors platform for in-flow bio-catalysis.![]()
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Affiliation(s)
- M Teresa De Martino
- Department of Bio-Organic Chemistry, Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology Het Kranenveld 14 5600 MB Eindhoven The Netherlands
| | - Fabio Tonin
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - N Amy Yewdall
- Department of Bio-Organic Chemistry, Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology Het Kranenveld 14 5600 MB Eindhoven The Netherlands
| | - Mona Abdelghani
- Department of Bio-Organic Chemistry, Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology Het Kranenveld 14 5600 MB Eindhoven The Netherlands
| | - David S Williams
- Department of Bio-Organic Chemistry, Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology Het Kranenveld 14 5600 MB Eindhoven The Netherlands
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Loai K E A Abdelmohsen
- Department of Bio-Organic Chemistry, Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology Het Kranenveld 14 5600 MB Eindhoven The Netherlands
| | - Jan C M van Hest
- Department of Bio-Organic Chemistry, Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology Het Kranenveld 14 5600 MB Eindhoven The Netherlands
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11
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Abstract
Peroxiredoxins are ubiquitous antioxidant proteins that exhibit a striking variety of quaternary structures, making them appealing building blocks with which nanoscale architectures are created for applications in nanotechnology. The solution environment of the protein, as well as protein sequence, influences the presentation of a particular structure, thereby enabling mesoscopic manipulations that affect arrangments at the nanoscale. This chapter will equip us with the knowledge necessary to not only produce and manipulate peroxiredoxin proteins into desired structures but also to characterize the different structures using dynamic light scattering, analytical centrifugation, and negative stain transmission electron microscopy, thereby setting the stage for us to use these proteins for applications in nanotechnology.
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Affiliation(s)
- Frankie Conroy
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - N Amy Yewdall
- Bio-Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
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12
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Yewdall NA, Buddingh BC, Altenburg WJ, Timmermans SBPE, Vervoort DFM, Abdelmohsen LKEA, Mason AF, van Hest JCM. Physicochemical Characterization of Polymer-Stabilized Coacervate Protocells. Chembiochem 2019; 20:2643-2652. [PMID: 31012235 PMCID: PMC6851677 DOI: 10.1002/cbic.201900195] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Indexed: 12/31/2022]
Abstract
The bottom-up construction of cell mimics has produced a range of membrane-bound protocells that have been endowed with functionality and biochemical processes reminiscent of living systems. The contents of these compartments, however, experience semidilute conditions, whereas macromolecules in the cytosol exist in protein-rich, crowded environments that affect their physicochemical properties, such as diffusion and catalytic activity. Recently, complex coacervates have emerged as attractive protocellular models because their condensed interiors would be expected to mimic this crowding better. Here we explore some relevant physicochemical properties of a recently developed polymer-stabilized coacervate system, such as the diffusion of macromolecules in the condensed coacervate phase, relative to in dilute solutions, the buffering capacity of the core, the molecular organization of the polymer membrane, the permeability characteristics of this membrane towards a wide range of compounds, and the behavior of a simple enzymatic reaction. In addition, either the coacervate charge or the cargo charge is engineered to allow the selective loading of protein cargo into the coacervate protocells. Our in-depth characterization has revealed that these polymer-stabilized coacervate protocells have many desirable properties, thus making them attractive candidates for the investigation of biochemical processes in stable, controlled, tunable, and increasingly cell-like environments.
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Affiliation(s)
- N. Amy Yewdall
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
| | - Bastiaan C. Buddingh
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
| | - Wiggert J. Altenburg
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
| | - Suzanne B. P. E. Timmermans
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
| | - Daan F. M. Vervoort
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
| | - Loai K. E. A. Abdelmohsen
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
| | - Alexander F. Mason
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
| | - Jan C. M. van Hest
- Department of Biomedical Engineering andDepartment of Chemical Engineering and ChemistryInstitute for Complex Molecular SystemsEindhoven University of TechnologyP. O. Box 5135600 MBEindhovenNetherlands
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13
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Mason A, Yewdall NA, Welzen PLW, Shao J, van Stevendaal M, van Hest JCM, Williams DS, Abdelmohsen LKEA. Mimicking Cellular Compartmentalization in a Hierarchical Protocell through Spontaneous Spatial Organization. ACS Cent Sci 2019; 5:1360-1365. [PMID: 31482118 PMCID: PMC6716124 DOI: 10.1021/acscentsci.9b00345] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Indexed: 05/19/2023]
Abstract
A systemic feature of eukaryotic cells is the spatial organization of functional components through compartmentalization. Developing protocells with compartmentalized synthetic organelles is, therefore, a critical milestone toward emulating one of the core characteristics of cellular life. Here we demonstrate the bottom-up, multistep, noncovalent, assembly of rudimentary subcompartmentalized protocells through the spontaneous encapsulation of semipermeable, polymersome proto-organelles inside cell-sized coacervates. The coacervate microdroplets are membranized using tailor-made terpolymers, to complete the hierarchical self-assembly of protocells, a system that mimics both the condensed cytosol and the structure of a cell membrane. In this way, the spatial organization of enzymes can be finely tuned, leading to an enhancement of functionality. Moreover, incompatible components can be sequestered in the same microenvironments without detrimental effect. The robust stability of the subcompartmentalized coacervate protocells in biocompatible milieu, such as in PBS or cell culture media, makes it a versatile platform to be extended toward studies in vitro, and perhaps, in vivo.
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Affiliation(s)
- Alexander
F. Mason
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - N. Amy Yewdall
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Pascal L. W. Welzen
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jingxin Shao
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Marleen van Stevendaal
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - David S. Williams
- Department
of Chemistry, College of Science, Swansea
University, Singleton Campus, Swansea, Wales SA2 8PP, United Kingdom
| | - Loai K. E. A. Abdelmohsen
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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14
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Abstract
Despite the astonishing diversity and complexity of living systems, they all share five common hallmarks: compartmentalization, growth and division, information processing, energy transduction and adaptability. In this review, we give not only examples of how cells satisfy these requirements for life and the ways in which it is possible to emulate these characteristics in engineered platforms, but also the gaps that remain to be bridged. The bottom-up synthesis of life-like systems continues to be driven forward by the advent of new technologies, by the discovery of biological phenomena through their transplantation to experimentally simpler constructs and by providing insights into one of the oldest questions posed by mankind, the origin of life on Earth.
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Affiliation(s)
| | | | - Jan C. M. van Hest
- Eindhoven University of Technology, PO Box 513 (STO 3.31), Eindhoven, MB, The Netherlands
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15
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Manuguri S, Webster K, Yewdall NA, An Y, Venugopal H, Bhugra V, Turner A, Domigan LJ, Gerrard JA, Williams DE, Malmström J. Assembly of Protein Stacks With in Situ Synthesized Nanoparticle Cargo. Nano Lett 2018; 18:5138-5145. [PMID: 30047268 DOI: 10.1021/acs.nanolett.8b02055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ability of proteins to form hierarchical structures through self-assembly provides an opportunity to synthesize and organize nanoparticles. Ordered nanoparticle assemblies are a subject of widespread interest due to the potential to harness their emergent functions. In this work, the toroidal-shaped form of the protein peroxiredoxin, which has a pore size of 7 nm, was used to organize iron oxyhydroxide nanoparticles. Iron in the form of Fe2+ was sequestered into the central cavity of the toroid ring using metal-binding sites engineered there and then hydrolyzed to form iron oxyhydroxide particles bound into the protein pore. By precise manipulation of the pH, the mineralized toroids were organized into stacks confining one-dimensional nanoparticle assemblies. We report the formation and the procedures leading to the formation of such nanostructures and their characterization by chromatography and microscopy. Electrostatic force microscopy clearly revealed the formation of iron-containing nanorods as a result of the self-assembly of the iron-loaded protein. This research bodes well for the use of peroxiredoxin as a template with which to form nanowires and structures for electronic and magnetic applications.
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Affiliation(s)
- Sesha Manuguri
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | | | - N Amy Yewdall
- Biomolecular Interaction Centre and School of Biological Sciences , University of Canterbury , Christchurch 8140 , New Zealand
| | | | | | - Vaibhav Bhugra
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | | | - Laura J Domigan
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | - Juliet A Gerrard
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | - David E Williams
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
| | - Jenny Malmström
- MacDiarmid Institute for Advanced Materials and Nanotechnology , 6140 Wellington , New Zealand
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16
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Yewdall NA, Allison TM, Pearce FG, Robinson CV, Gerrard JA. Self-assembly of toroidal proteins explored using native mass spectrometry. Chem Sci 2018; 9:6099-6106. [PMID: 30090298 PMCID: PMC6053953 DOI: 10.1039/c8sc01379a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022] Open
Abstract
The peroxiredoxins are a well characterised family of toroidal proteins which can self-assemble into a striking array of quaternary structures, including protein nanotubes, making them attractive as building blocks for nanotechnology.
The peroxiredoxins are a well characterised family of toroidal proteins which can self-assemble into a striking array of quaternary structures, including protein nanotubes, making them attractive as building blocks for nanotechnology. Tools to characterise these assemblies are currently scarce. Here, assemblies of peroxiredoxin proteins were examined using native mass spectrometry and complementary solution techniques. We demonstrated unequivocally that tube formation is fully reversible, a useful feature in a molecular switch. Simple assembly of individual toroids was shown to be tunable by pH and the presence of a histidine tag. Collision induced dissociation experiments on peroxiredoxin rings revealed a highly unusual symmetrical disassembly pathway, consistent with the structure disassembling as a hexamer of dimers. This study provides the foundation for the rational design and precise characterisation of peroxiredoxin protein structures where self-assembly can be harnessed as a key feature for applications in nanotechnology.
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Affiliation(s)
- N Amy Yewdall
- School of Biological Sciences , School of Chemical Sciences , University of Auckland , Auckland 1010 , New Zealand.,Biomolecular Interaction Centre , School of Biological Sciences , University of Canterbury , Christchurch 8140 , New Zealand
| | - Timothy M Allison
- Department of Chemistry , University of Oxford , Oxford OX1 5QY , UK
| | - F Grant Pearce
- School of Biological Sciences , School of Chemical Sciences , University of Auckland , Auckland 1010 , New Zealand
| | - Carol V Robinson
- Department of Chemistry , University of Oxford , Oxford OX1 5QY , UK
| | - Juliet A Gerrard
- Biomolecular Interaction Centre , School of Biological Sciences , University of Canterbury , Christchurch 8140 , New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology , Victoria University , Wellington 6140 , New Zealand
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17
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Yewdall NA, Peskin AV, Hampton MB, Goldstone DC, Pearce FG, Gerrard JA. Quaternary structure influences the peroxidase activity of peroxiredoxin 3. Biochem Biophys Res Commun 2018; 497:558-563. [PMID: 29438714 DOI: 10.1016/j.bbrc.2018.02.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/09/2018] [Indexed: 12/16/2022]
Abstract
Peroxiredoxins are abundant peroxidase enzymes that are key regulators of the cellular redox environment. A major subgroup of these proteins, the typical 2-Cys peroxiredoxins, can switch between dimers and decameric or dodecameric rings, during the catalytic cycle. The necessity of this change in quaternary structure for function as a peroxidase is not fully understood. In order to explore this, human peroxiredoxin 3 (Prx3) protein was engineered to form both obligate dimers (S75E Prx3) and stabilised dodecameric rings (S78C Prx3), uncoupling structural transformations from the catalytic cycle. The obligate dimer, S75E Prx3, retained catalytic activity towards hydrogen peroxide, albeit significantly lower than the wildtype and S78C proteins, suggesting an evolutionary advantage of having higher order self-assemblies.
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Affiliation(s)
- N Amy Yewdall
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand; Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Alexander V Peskin
- Centre for Free Radical Research, Department of Pathology, University of Otago Christchurch, Christchurch 8011, New Zealand
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology, University of Otago Christchurch, Christchurch 8011, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Juliet A Gerrard
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University, Wellington 6140, New Zealand; School of Chemical Sciences, University of Auckland, Auckland 1010, New Zealand.
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18
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Malmström J, Wason A, Roache F, Yewdall NA, Radjainia M, Wei S, Higgins MJ, Williams DE, Gerrard JA, Travas-Sejdic J. Protein nanorings organized by poly(styrene-block-ethylene oxide) self-assembled thin films. Nanoscale 2015; 7:19940-19948. [PMID: 26499391 DOI: 10.1039/c5nr05476a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This study explores the use of block copolymer self-assembly to organize Lsmα, a protein which forms stable doughnut-shaped heptameric structures. Here, we have explored the idea that 2-D crystalline arrays of protein filaments can be prepared by stacking doughnut shaped Lsmα protein into the poly(ethylene oxide) blocks of a hexagonal microphase-separated polystyrene-b-polyethylene oxide (PS-b-PEO) block copolymer. We were able to demonstrate the coordinated assembly of such a complex hierarchical nanostructure. The key to success was the choice of solvent systems and protein functionalization that achieved sufficient compatibility whilst still promoting assembly. Unambiguous characterisation of these structures is difficult; however AFM and TEM measurements confirmed that the protein was sequestered into the PEO blocks. The use of a protein that assembles into stackable doughnuts offers the possibility of assembling nanoscale optical, magnetic and electronic structures.
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Affiliation(s)
- Jenny Malmström
- MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand.
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19
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Phillips AJ, Littlejohn J, Yewdall NA, Zhu T, Valéry C, Pearce FG, Mitra AK, Radjainia M, Gerrard JA. Peroxiredoxin is a Versatile Self-Assembling Tecton for Protein Nanotechnology. Biomacromolecules 2014; 15:1871-81. [DOI: 10.1021/bm500261u] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Amy J. Phillips
- Biomolecular
Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Victoria University, Wellington, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jacob Littlejohn
- Biomolecular
Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - N. Amy Yewdall
- Biomolecular
Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Tong Zhu
- Biomolecular
Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Céline Valéry
- Biomolecular
Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - F. Grant Pearce
- Biomolecular
Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Alok K. Mitra
- School
of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mazdak Radjainia
- School
of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Juliet A. Gerrard
- Biomolecular
Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Victoria University, Wellington, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland, New Zealand
- Callaghan
Innovation
Research Limited, Lower Hutt, New Zealand
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