1
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Azuma Y, Gaweł S, Pasternak M, Woźnicka O, Pyza E, Heddle JG. Reengineering of an Artificial Protein Cage for Efficient Packaging of Active Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2312286. [PMID: 38738740 DOI: 10.1002/smll.202312286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/01/2024] [Indexed: 05/14/2024]
Abstract
Protein cages that readily encapsulate active enzymes of interest present useful nanotools for delivery and catalysis, wherein those with programmable disassembly characteristics serve as particularly attractive platforms. Here, a general guest packaging system based on an artificial protein cage, TRAP-cage, the disassembly of which can be induced by the addition of reducing agents, is established. In this system, TRAP-cage with SpyCatcher moieties in the lumen is prepared using genetic modification of the protein building block and assembled into a cage structure with either monovalent gold ions or molecular crosslinkers. The resulting protein cage can efficiently capture guest proteins equipped with a SpyTag by simply mixing them in an aqueous solution. This post-assembly loading system, which circumvents the exposure of guests to thiol-reactive crosslinkers, enables the packaging of enzymes possessing a catalytic cysteine or a metal cofactor while retaining their catalytic activity.
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Affiliation(s)
- Yusuke Azuma
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
| | - Szymon Gaweł
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, Krakow, 30-348, Poland
| | - Monika Pasternak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, Krakow, 30-348, Poland
| | - Olga Woźnicka
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, Krakow, 30-387, Poland
| | - Elżbieta Pyza
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, Krakow, 30-387, Poland
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
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2
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Hori M, Steinauer A, Tetter S, Hälg J, Manz EM, Hilvert D. Stimulus-responsive assembly of nonviral nucleocapsids. Nat Commun 2024; 15:3576. [PMID: 38678040 PMCID: PMC11055949 DOI: 10.1038/s41467-024-47808-1] [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: 02/17/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.
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Affiliation(s)
- Mao Hori
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LIBN, Lausanne, Switzerland
| | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Jamiro Hälg
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Eva-Maria Manz
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland.
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3
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Das D, Ainavarapu SRK. Protein engineering using circular permutation - structure, function, stability, and applications. FEBS J 2024. [PMID: 38676939 DOI: 10.1111/febs.17146] [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: 10/12/2023] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
Protein engineering is important for creating novel variants from natural proteins, enabling a wide range of applications. Approaches such as rational design and directed evolution are routinely used to make new protein variants. Computational tools like de novo design can introduce new protein folds. Expanding the amino acid repertoire to include unnatural amino acids with non-canonical side chains in vitro by native chemical ligation and in vivo via codon expansion methods broadens sequence and structural possibilities. Circular permutation (CP) is an invaluable approach to redesigning a protein by rearranging the amino acid sequence, where the connectivity of the secondary structural elements is altered without changing the overall structure of the protein. Artificial CP proteins (CPs) are employed in various applications such as biocatalysis, sensing of small molecules by fluorescence, genome editing, ligand-binding protein switches, and optogenetic engineering. Many studies have shown that CP can lead to either reduced or enhanced stability or catalytic efficiency. The effects of CP on a protein's energy landscape cannot be predicted a priori. Thus, it is important to understand how CP can affect the thermodynamic and kinetic stability of a protein. In this review, we discuss the discovery and advancement of techniques to create protein CP, and existing reviews on CP. We delve into the plethora of biological applications for designed CP proteins. We subsequently discuss the experimental and computational reports on the effects of CP on the thermodynamic and kinetic stabilities of proteins of various topologies. An understanding of the various aspects of CP will allow the reader to design robust CP proteins for their specific purposes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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4
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Ohara N, Kawakami N, Arai R, Adachi N, Ikeda A, Senda T, Miyamoto K. Fusion then fission: splitting and reassembly of an artificial fusion-protein nanocage. Chem Commun (Camb) 2024; 60:4605-4608. [PMID: 38586927 DOI: 10.1039/d4cc00115j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A split-protein system is a simple approach to introduce new termini which are useful as modification sites in protein engineering, but has been adapted mainly for monomeric proteins. Here we demonstrate the design of split subunits of the 60-mer artificial fusion-protein nanocage TIP60. The subunit fragments successfully reformed the cage structure in the same manner as prior to splitting. One of the newly introduced terminals at the interior surface can be modified using a tag peptide and green fluorescent protein. Therefore, the termini could serve as a versatile modification site for incorporating a wide variety of functional peptides and proteins.
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Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akihito Ikeda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
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5
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Fatehi F, Twarock R. An interaction network approach predicts protein cage architectures in bionanotechnology. Proc Natl Acad Sci U S A 2023; 120:e2303580120. [PMID: 38060565 PMCID: PMC10723117 DOI: 10.1073/pnas.2303580120] [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: 03/02/2023] [Accepted: 10/21/2023] [Indexed: 12/17/2023] Open
Abstract
Protein nanoparticles play pivotal roles in many areas of bionanotechnology, including drug delivery, vaccination, and diagnostics. These technologies require control over the distinct particle morphologies that protein nanocontainers can adopt during self-assembly from their constituent protein components. The geometric construction principle of virus-derived protein cages is by now fairly well understood by analogy to viral protein shells in terms of Caspar and Klug's quasi-equivalence principle. However, many artificial, or genetically modified, protein containers exhibit varying degrees of quasi-equivalence in the interactions between identical protein subunits. They can also contain a subset of protein subunits that do not participate in interactions with other assembly units, called capsomers, leading to gaps in the particle surface. We introduce a method that exploits information on the local interactions between the capsomers to infer the geometric construction principle of these nanoparticle architectures. The predictive power of this approach is demonstrated here for a prominent system in nanotechnology, the AaLS pentamer. Our method not only rationalises hitherto discovered cage structures but also predicts geometrically viable options that have not yet been observed. The classification of nanoparticle architecture based on the geometric properties of the interaction network closes a gap in our current understanding of protein container structure and can be widely applied in protein nanotechnology, paving the way to programmable control over particle polymorphism.
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Affiliation(s)
- Farzad Fatehi
- Departments of Mathematics, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Departments of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
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6
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Das D, Ainavarapu SRK. Circular permutation at azurin's active site slows down its folding. J Biol Inorg Chem 2023; 28:737-749. [PMID: 37957357 DOI: 10.1007/s00775-023-02023-z] [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: 05/08/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Circular permutation (CP) is a technique by which the primary sequence of a protein is rearranged to create new termini. The connectivity of the protein is altered but the overall protein structure generally remains unperturbed. Understanding the effect of CP can help design robust proteins for numerous applications such as in genetic engineering, optoelectronics, and improving catalytic activity. Studies on different protein topologies showed that CP usually affects protein stability as well as unfolding rates. Though a significant number of proteins contain metals or other cofactors, reports of metalloprotein CPs are rare. Thus, we chose a bacterial metalloprotein, azurin, and its CP within the metal-binding site (cpF114). We studied the stabilities, folding, and unfolding rates of apo- and Zn2+-bound CP azurin using fluorescence and circular dichroism. The introduced CP had destabilizing effects on the protein. Also, the folding of the Zn2+-CP protein was much slower than that of the Zn2+-WT or apo-protein. We compared this study to our previously reported azurin-cpN42, where we had observed an equilibrium and kinetic intermediate. cpF114 exhibits an apparent two-state equilibrium unfolding but has an off-pathway kinetic intermediate. Our study hinted at CP as a method to modify the energy landscape of proteins to alter their folding pathways. WT azurin, being a faster folder, may have evolved to optimize the folding rate of metal-bound protein compared to its CPs, albeit all of them have the same structure and function. Our study underscores that protein sequence and protein termini positions are crucial for metalloproteins. TOC Figure. (Top) Zn2+-azurin WT structure (PDB code: 1E67) and 2-D topology diagram of Zn2+-cpF114 azurin. (Bottom) Cartoon diagram representing folding (red arrows) and unfolding (blue arrows) of apo- and Zn2+- WT and cpF114 azurins. The width of the arrows represents the rate of the corresponding processes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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7
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Levasseur MD, Hofmann R, Edwardson TGW, Hehn S, Thanaburakorn M, Bode JW, Hilvert D. Post-Assembly Modification of Protein Cages by Ubc9-Mediated Lysine Acylation. Chembiochem 2022; 23:e202200332. [PMID: 35951442 PMCID: PMC9826087 DOI: 10.1002/cbic.202200332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/09/2022] [Indexed: 01/11/2023]
Abstract
Although viruses have been successfully repurposed as vaccines, antibiotics, and anticancer therapeutics, they also raise concerns regarding genome integration and immunogenicity. Virus-like particles and non-viral protein cages represent a potentially safer alternative but often lack desired functionality. Here, we investigated the utility of a new enzymatic bioconjugation method, called lysine acylation using conjugating enzymes (LACE), to chemoenzymatically modify protein cages. We equipped two structurally distinct protein capsules with a LACE-reactive peptide tag and demonstrated their modification with diverse ligands. This modular approach combines the advantages of chemical conjugation and genetic fusion and allows for site-specific modification with recombinant proteins as well as synthetic peptides with facile control of the extent of labeling. This strategy has the potential to fine-tune protein containers of different shape and size by providing them with new properties that go beyond their biologically native functions.
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Affiliation(s)
- Mikail D. Levasseur
- Laboratory of Organic ChemistryETH ZürichVladimir-Prelog-Weg 1–5/108093ZurichSwitzerland
| | - Raphael Hofmann
- Laboratory of Organic ChemistryETH ZürichVladimir-Prelog-Weg 1–5/108093ZurichSwitzerland
| | - Thomas G. W. Edwardson
- Laboratory of Organic ChemistryETH ZürichVladimir-Prelog-Weg 1–5/108093ZurichSwitzerland
| | - Svenja Hehn
- Laboratory of Organic ChemistryETH ZürichVladimir-Prelog-Weg 1–5/108093ZurichSwitzerland
| | | | - Jeffrey W. Bode
- Laboratory of Organic ChemistryETH ZürichVladimir-Prelog-Weg 1–5/108093ZurichSwitzerland
| | - Donald Hilvert
- Laboratory of Organic ChemistryETH ZürichVladimir-Prelog-Weg 1–5/108093ZurichSwitzerland
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8
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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9
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Kofoed C, Wu S, Sørensen KK, Treiberg T, Arnsdorf J, Bjørn SP, Jensen TL, Voldborg BG, Thygesen MB, Jensen KJ, Schoffelen S. Highly Selective Lysine Acylation in Proteins Using a Lys-His Tag Sequence. Chemistry 2022; 28:e202200147. [PMID: 35099088 DOI: 10.1002/chem.202200147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 11/07/2022]
Abstract
Chemical modification of proteins has numerous applications, but it has been challenging to achieve the required high degree of selectivity on lysine amino groups. Recently, we described the highly selective acylation of proteins with an N-terminal Gly-His6 segment. This tag promoted acylation of the N-terminal Nα -amine resulting in stable conjugates. Herein, we report the peptide sequences Hisn -Lys-Hism , which we term Lys-His tags. In combination with simple acylating agents, they facilitate the acylation of the designated Lys Nϵ -amine under mild conditions and with high selectivity over native Lys residues. We show that the Lys-His tags, which are 7 to 10 amino acids in length and still act as conventional His tags, can be inserted in proteins at the C-terminus or in loops, thus providing high flexibility regarding the site of modification. Finally, the selective and efficient acylation of the therapeutic antibody Rituximab, pure or mixed with other proteins, demonstrates the scope of the Lys-His tag acylation method.
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Affiliation(s)
- Christian Kofoed
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Present address: Frick Chemistry Laboratories, Princeton University, 08544, New Jersey, USA
| | - Shunliang Wu
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Kasper K Sørensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Tuule Treiberg
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Johnny Arnsdorf
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Tanja L Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Bjørn G Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Sanne Schoffelen
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
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10
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Stupka I, Azuma Y, Biela AP, Imamura M, Scheuring S, Pyza E, Woźnicka O, Maskell DP, Heddle JG. Chemically induced protein cage assembly with programmable opening and cargo release. SCIENCE ADVANCES 2022; 8:eabj9424. [PMID: 34985943 PMCID: PMC8730398 DOI: 10.1126/sciadv.abj9424] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Engineered protein cages are promising tools that can be customized for applications in medicine and nanotechnology. A major challenge is developing a straightforward strategy for endowing cages with bespoke, inducible disassembly. Such cages would allow release of encapsulated cargoes at desired timing and location. Here, we achieve such programmable disassembly using protein cages, in which the subunits are held together by different molecular cross-linkers. This modular system enables cage disassembly to be controlled in a condition-dependent manner. Structural details of the resulting cages were determined using cryo–electron microscopy, which allowed observation of bridging cross-linkers at intended positions. Triggered disassembly was demonstrated by high-speed atomic force microscopy and subsequent cargo release using an encapsulated Förster resonance energy transfer pair whose signal depends on the quaternary structure of the cage.
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Affiliation(s)
- Izabela Stupka
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Postgraduate School of Molecular Medicine, 02-091 Warsaw, Poland
| | - Yusuke Azuma
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Artur P. Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Motonori Imamura
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Elżbieta Pyza
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Olga Woźnicka
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Daniel P. Maskell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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11
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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12
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De novo peptide grafting to a self-assembling nanocapsule yields a hepatocyte growth factor receptor agonist. iScience 2021; 24:103302. [PMID: 34805784 PMCID: PMC8581506 DOI: 10.1016/j.isci.2021.103302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/29/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
Lasso-grafting (LG) technology is a method for generating de novo biologics (neobiologics) by genetically implanting macrocyclic peptide pharmacophores, which are selected in vitro against a protein of interest, into loops of arbitrary protein scaffolds. In this study, we have generated a neo-capsid that potently binds the hepatocyte growth factor receptor MET by LG of anti-MET peptide pharmacophores into a circularly permuted variant of Aquifex aeolicus lumazine synthase (AaLS), a self-assembling protein nanocapsule. By virtue of displaying multiple-pharmacophores on its surface, the neo-capsid can induce dimerization (or multimerization) of MET, resulting in phosphorylation and endosomal internalization of the MET-capsid complex. This work demonstrates the potential of the LG technology as a synthetic biology approach for generating capsid-based neobiologics capable of activating signaling receptors. Lasso-grafting enabled multiple display of peptide pharmacophore on protein capsid Engineered capsids induced dimerization of MET resulting in phosphorylation Engineered capsids were internalized into endosome via MET phosphorylation
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13
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Jones JA, Cristie-David AS, Andreas MP, Giessen TW. Triggered Reversible Disassembly of an Engineered Protein Nanocage*. Angew Chem Int Ed Engl 2021; 60:25034-25041. [PMID: 34532937 PMCID: PMC8578439 DOI: 10.1002/anie.202110318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Indexed: 01/13/2023]
Abstract
Protein nanocages play crucial roles in sub-cellular compartmentalization and spatial control in all domains of life and have been used as biomolecular tools for applications in biocatalysis, drug delivery, and bionanotechnology. The ability to control their assembly state under physiological conditions would further expand their practical utility. To gain such control, we introduced a peptide capable of triggering conformational change at a key structural position in the largest known encapsulin nanocompartment. We report the structure of the resulting engineered nanocage and demonstrate its ability to disassemble and reassemble on demand under physiological conditions. We demonstrate its capacity for in vivo encapsulation of proteins of choice while also demonstrating in vitro cargo loading capabilities. Our results represent a functionally robust addition to the nanocage toolbox and a novel approach for controlling protein nanocage disassembly and reassembly under mild conditions.
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
| | - Ajitha S Cristie-David
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
| | - Michael P Andreas
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, 1150 W. Medical Center Dr., MSRB2, Ann Arbor, MI, 48109-5622, USA
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14
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Jones JA, Cristie‐David AS, Andreas MP, Giessen TW. Triggered Reversible Disassembly of an Engineered Protein Nanocage**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jesse A. Jones
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
| | - Ajitha S. Cristie‐David
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
| | - Michael P. Andreas
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
| | - Tobias W. Giessen
- Department of Biomedical Engineering University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
- Department of Biological Chemistry University of Michigan Medical School, Ann Arbor 1150 W. Medical Center Dr., MSRB2 Ann Arbor MI 48109-5622 USA
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15
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Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
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Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
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16
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Honarmand Ebrahimi K. Ferritin as a Platform for Creating Antiviral Mosaic Nanocages: Prospects for Treating COVID-19. Chembiochem 2020; 22:1371-1378. [PMID: 33350032 DOI: 10.1002/cbic.202000728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/25/2020] [Indexed: 11/11/2022]
Abstract
Infectious diseases are a continues threat to human health and the economy worldwide. The latest example is the global pandemic of COVID-19 caused by SARS-CoV-2. Antibody therapy and vaccines are promising approaches to treat the disease; however, they have bottlenecks: they might have low efficacy or narrow breadth due to the continuous emergence of new strains of the virus or antibodies could cause antibody-dependent enhancement (ADE) of infection. To address these bottlenecks, I propose the use of 24-meric ferritin for the synthesis of mosaic nanocages to deliver a cocktail of antibodies or nanobodies alone or in combination with another therapeutic, like a nucleotide analogue, to mimic the viral entry process and deceive the virus, or to develop mosaic vaccines. I argue that available data showing the effectiveness of ferritin-antibody conjugates in targeting specific cells and ferritin-haemagglutinin nanocages in developing influenza vaccines strongly support my proposals.
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17
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Stupka I, Heddle JG. Artificial protein cages – inspiration, construction, and observation. Curr Opin Struct Biol 2020; 64:66-73. [DOI: 10.1016/j.sbi.2020.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/05/2020] [Accepted: 05/19/2020] [Indexed: 12/29/2022]
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18
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Lončar N, Rozeboom HJ, Franken LE, Stuart MC, Fraaije MW. Structure of a robust bacterial protein cage and its application as a versatile biocatalytic platform through enzyme encapsulation. Biochem Biophys Res Commun 2020; 529:548-553. [DOI: 10.1016/j.bbrc.2020.06.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 01/15/2023]
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19
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Majsterkiewicz K, Azuma Y, Heddle JG. Connectability of protein cages. NANOSCALE ADVANCES 2020; 2:2255-2264. [PMID: 36133365 PMCID: PMC9416917 DOI: 10.1039/d0na00227e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/27/2020] [Indexed: 06/14/2023]
Abstract
Regular, hollow proteinaceous nanoparticles are widespread in nature. The well-defined structures as well as diverse functions of naturally existing protein cages have inspired the development of new nanoarchitectures with desired capabilities. In such approaches, a key functionality is "connectability". Engineering of interfaces between cage building blocks to modulate intra-cage connectability leads to protein cages with new morphologies and assembly-disassembly properties. Modification of protein cage surfaces to control inter-cage connectability enables their arrangement into lattice-like nanomaterials. Here, we review the current progress in control of intra- and inter-cage connectability for protein cage-based nanotechnology development.
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Affiliation(s)
- Karolina Majsterkiewicz
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
- Postgraduate School of Molecular Medicine Trojdena 2a 02-091 Warsaw Poland
| | - Yusuke Azuma
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
| | - Jonathan G Heddle
- Małopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A 30-387 Krakow Poland
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20
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Steinmetz NF, Lim S, Sainsbury F. Protein cages and virus-like particles: from fundamental insight to biomimetic therapeutics. Biomater Sci 2020; 8:2771-2777. [PMID: 32352101 PMCID: PMC8085892 DOI: 10.1039/d0bm00159g] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein cages (viral and non-viral) found in nature have evolved for a variety of purposes and are found in all kingdoms of life. The main functions of these nanoscale compartments are the protection and delivery of nucleic acids e.g. virus capsids, or the enrichment and sequestration of metabolons e.g. bacterial microcompartments. This review focuses on recent developments of protein cages for use in immunotherapy and therapeutic delivery. In doing so, we highlight the unique ways in which protein cages have informed on fundamental principles governing bio-nano interactions. With the enormous existing design space among naturally occurring protein cages, there is still much to learn from studying them as biomimetic particles.
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Affiliation(s)
- Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, CA 92093, USA and Department of Bioengineering, University of California, San Diego, CA 92093, USA and Department of Radiology, University of California, San Diego, CA 92093, USA and Moores Cancer Center, University of California, San Diego, CA 92093, USA and Center for Nano-ImmunoEngineering, University of California, San Diego, CA 92093, USA
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457, Singapore and NTU-Northwestern Institute for Nanomedicine, Nanyang Technological University, Singapore 637457, Singapore
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia. and Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD 4001, Australia
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21
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Chakraborti S, Lin TY, Glatt S, Heddle JG. Enzyme encapsulation by protein cages. RSC Adv 2020; 10:13293-13301. [PMID: 35492120 PMCID: PMC9051456 DOI: 10.1039/c9ra10983h] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 03/10/2020] [Indexed: 01/04/2023] Open
Abstract
Protein cages are hollow protein shells with a nanometric cavity that can be filled with useful materials. The encapsulating nature of the cages means that they are particularly attractive for loading with biological macromolecules, affording the guests protection in conditions where they may be degraded. Given the importance of proteins in both industrial and all cellular processes, encapsulation of functional protein cargoes, particularly enzymes, are of high interest both for in vivo diagnostic and therapeutic use as well as for ex vivo applications. Increasing knowledge of protein cage structures at high resolution along with recent advances in producing artificial protein cages means that they can now be designed with various attachment chemistries on their internal surfaces - a useful tool for cargo capture. Here we review the different available attachment strategies that have recently been successfully demonstrated for enzyme encapsulation in protein cages and consider their future potential.
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Affiliation(s)
- Soumyananda Chakraborti
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University Krakow 30-387 Poland
| | - Ting-Yu Lin
- Max Planck Research Group, Malopolska Centre of Biotechnology, Jagiellonian University Krakow 30-387 Poland
| | - Sebastian Glatt
- Max Planck Research Group, Malopolska Centre of Biotechnology, Jagiellonian University Krakow 30-387 Poland
| | - Jonathan G Heddle
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University Krakow 30-387 Poland
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22
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Abstract
The use of proteins and peptides as nanoscale components to generate new-to-nature physical entities holds great promise in biocatalysis, therapeutic or diagnostic delivery, and materials templating. The majority of functionalized particles have been based on existing structures found in nature. Developing biomimetic particles in this way takes advantage of highly evolved platforms for organization or encapsulation of functional moieties, offering significant advantages in stoichiometry, multivalency, and sequestration. However, novel assembly paradigms for the modular construction of macromolecular structures are now greatly expanding the functional diversity of protein-based nanoparticles in health and manufacturing. In the February issue of ACS Nano, Kepiro et al. demonstrate the refinement of this concept, engineering the capacity for self-assembly such that it is integral to pore-forming peptide motifs, resulting in superior antibiotic activity of the self-assembled particle. Nature encodes multiple functions in proteins with exquisite efficiency, and emulating this multiplicity may be the ultimate goal of biomimetic nanotechnologies.
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Affiliation(s)
- Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
- Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Queensland 4001, Australia
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23
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Li LL, Qiao ZY, Wang L, Wang H. Programmable Construction of Peptide-Based Materials in Living Subjects: From Modular Design and Morphological Control to Theranostics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1804971. [PMID: 30450607 DOI: 10.1002/adma.201804971] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/30/2018] [Indexed: 06/09/2023]
Abstract
Self-assembled nanomaterials show potential high efficiency as theranostics for high-performance bioimaging and disease treatment. However, the superstructures of pre-assembled nanomaterials may change in the complicated physiological conditions, resulting in compromised properties and/or biofunctions. Taking advantage of chemical self-assembly and biomedicine, a new strategy of "in vivo self-assembly" is proposed to in situ construct functional nanomaterials in living subjects to explore new biological effects. Herein, recent advances on peptide-based nanomaterials constructed by the in vivo self-assembly strategy are summarized. Modular peptide building blocks with various functions, such as targeting, self-assembly, tailoring, and biofunctional motifs, are employed for the construction of nanomaterials. Then, self-assembly of these building blocks in living systems to construct various morphologies of nanostructures and corresponding unique biological effects, such as assembly/aggregation-induced retention (AIR), are introduced, followed by their applications in high-performance drug delivery and bioimaging. Finally, an outlook and perspective toward future developments of in vivo self-assembled peptide-based nanomaterials for translational medicine are concluded.
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Affiliation(s)
- Li-Li Li
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Zeng-Ying Qiao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
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24
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Edwardson TGW, Hilvert D. Virus-Inspired Function in Engineered Protein Cages. J Am Chem Soc 2019; 141:9432-9443. [PMID: 31117660 DOI: 10.1021/jacs.9b03705] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The structural and functional diversity of proteins combined with their genetic programmability has made them indispensable modern materials. Well-defined, hollow protein capsules have proven to be particularly useful due to their ability to compartmentalize macromolecules and chemical processes. To this end, viral capsids are common scaffolds and have been successfully repurposed to produce a suite of practical protein-based nanotechnologies. Recently, the recapitulation of viromimetic function in protein cages of nonviral origin has emerged as a strategy to both complement physical studies of natural viruses and produce useful scaffolds for diverse applications. In this perspective, we review recent progress toward generation of virus-like behavior in nonviral protein cages through rational engineering and directed evolution. These artificial systems can aid our understanding of the emergence of viruses from existing cellular components, as well as provide alternative approaches to tackle current problems, and open up new opportunities, in medicine and biotechnology.
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Affiliation(s)
| | - Donald Hilvert
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
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25
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Ross JF, Wildsmith GC, Johnson M, Hurdiss DL, Hollingsworth K, Thompson RF, Mosayebi M, Trinh CH, Paci E, Pearson AR, Webb ME, Turnbull WB. Directed Assembly of Homopentameric Cholera Toxin B-Subunit Proteins into Higher-Order Structures Using Coiled-Coil Appendages. J Am Chem Soc 2019; 141:5211-5219. [PMID: 30856321 PMCID: PMC6449800 DOI: 10.1021/jacs.8b11480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The self-assembly
of proteins into higher order structures is ubiquitous
in living systems. It is also an essential process for the bottom-up
creation of novel molecular architectures and devices for synthetic
biology. However, the complexity of protein–protein interaction
surfaces makes it challenging to mimic natural assembly processes
in artificial systems. Indeed, many successful computationally designed
protein assemblies are prescreened for “designability”,
limiting the choice of components. Here, we report a simple and pragmatic
strategy to assemble chosen multisubunit proteins into more complex
structures. A coiled-coil domain appended to one face of the pentameric
cholera toxin B-subunit (CTB) enabled the ordered assembly of tubular
supra-molecular complexes. Analysis of a tubular structure determined
by X-ray crystallography has revealed a hierarchical assembly process
that displays features reminiscent of the polymorphic assembly of
polyomavirus proteins. The approach provides a simple and straightforward
method to direct the assembly of protein building blocks which present
either termini on a single face of an oligomer. This scaffolding approach
can be used to generate bespoke supramolecular assemblies of functional
proteins. Additionally, structural resolution of the scaffolded assemblies
highlight “native-state” forced protein–protein
interfaces, which may prove useful as starting conformations for future
computational design.
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Affiliation(s)
- James F Ross
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Gemma C Wildsmith
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Michael Johnson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Daniel L Hurdiss
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Kristian Hollingsworth
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Majid Mosayebi
- School of Mathematics , University of Bristol , Bristol BS8 1TW , United Kingdom.,BrisSynBio, Life Sciences Building , University of Bristol , Bristol BS8 1TQ , United Kingdom
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics , Universität Hamburg , Hamburg D-22761 , Germany
| | - Michael E Webb
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - W Bruce Turnbull
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom.,School of Chemistry , University of Leeds , Leeds LS2 9JT , United Kingdom
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26
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Herrera-Morande A, Castro-Fernández V, Merino F, Ramírez-Sarmiento CA, Fernández FJ, Vega MC, Guixé V. Protein topology determines substrate-binding mechanism in homologous enzymes. Biochim Biophys Acta Gen Subj 2018; 1862:2869-2878. [PMID: 30251675 DOI: 10.1016/j.bbagen.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/21/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
Abstract
During evolution, some homologs proteins appear with different connectivity between secondary structures (different topology) but conserving the tridimensional arrangement of them (same architecture). These events can produce two types of arrangements; circular permutation or non-cyclic permutations. The first one results in the N and C terminus transferring to a different position on a protein sequence while the second refers to a more complex arrangement of the structural elements. In ribokinase superfamily, two different topologies can be identified, which are related to each other as a non-cyclic permutation occurred during the evolution. Interestingly, this change in topology is correlated with the nucleotide specificity of its members. Thereby, the connectivity of the secondary elements allows us to distinguish an ATP-dependent and an ADP-dependent topology. Here we address the impact of introducing the topology of a homologous ATP-dependent kinase in an ADP-dependent kinase (Thermococcus litoralis glucokinase) in the structure, nucleotide specificity, and substrate binding order of the engineered enzyme. Structural evidence demonstrates that rewiring the topology of TlGK leads to an active and soluble enzyme without modifications on its three-dimensional architecture. The permuted enzyme (PerGK) retains the nucleotide preference of the parent TlGK enzyme but shows a change in the substrate binding order. Our results illustrate how the rearrangement of the protein folding topology during the evolution of the ribokinase superfamily enzymes may have dictated the substrate-binding order in homologous enzymes of this superfamily.
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Affiliation(s)
| | | | - Felipe Merino
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Francisco J Fernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain.
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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27
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Choi H, Choi B, Kim GJ, Kim HU, Kim H, Jung HS, Kang S. Fabrication of Nanoreaction Clusters with Dual-Functionalized Protein Cage Nanobuilding Blocks. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1801488. [PMID: 30066359 DOI: 10.1002/smll.201801488] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/08/2018] [Indexed: 06/08/2023]
Abstract
Fabrication of functional nanostructures is a prominent issue in nanotechnology, because they often exhibit unique properties that are different from the individual building blocks. Protein cage nanoparticles are attractive nanobuilding blocks for constructing nanostructures due to their well-defined symmetric spherical structures, polyvalent nature, and functional plasticity. Here, a lumazine synthase protein cage nanoparticle is genetically modified to be used as a template to generate functional nanobuilding blocks and covalently display enzymes (β-lactamase) and protein ligands (FKBP12/FRB) on its surface, making dual-functional nanobuilding blocks. Nanoreaction clusters are subsequently created by ligand-mediated alternate deposition of two complementary building blocks using layer-by-layer (LbL) assemblies. 3D nanoreaction clusters provide enhanced enzymatic activity compared with monolayered building block arrays. The approaches described here may provide new opportunities for fabricating functional nanostructures and nanoreaction clusters, leading to the development of new protein nanoparticle-based nanostructured biosensor devices.
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Affiliation(s)
- Hyukjun Choi
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Bongseo Choi
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Gwang Joong Kim
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Han-Ul Kim
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Hansol Kim
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, South Korea
| | - Sebyung Kang
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
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28
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Laboratory evolution of virus-like nucleocapsids from nonviral protein cages. Proc Natl Acad Sci U S A 2018; 115:5432-5437. [PMID: 29735682 DOI: 10.1073/pnas.1800527115] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viruses are remarkable nanomachines that efficiently hijack cellular functions to replicate and self-assemble their components within a complex biological environment. As all steps of the viral life cycle depend on formation of a protective proteinaceous shell that packages the DNA or RNA genome, bottom-up construction of virus-like nucleocapsids from nonviral materials could provide valuable insights into virion assembly and evolution. Such constructs could also serve as safe alternatives to natural viruses for diverse nano- and biotechnological applications. Here we show that artificial virus-like nucleocapsids can be generated-rapidly and surprisingly easily-by engineering and laboratory evolution of a nonviral protein cage formed by Aquifex aeolicus lumazine synthase (AaLS) and its encoding mRNA. Cationic peptides were appended to the engineered capsid proteins to enable specific recognition of packaging signals on cognate mRNAs, and subsequent evolutionary optimization afforded nucleocapsids with expanded spherical structures that encapsulate their own full-length RNA genome in vivo and protect the cargo molecules from nucleases. These findings provide strong experimental support for the hypothesis that subcellular protein-bounded compartments may have facilitated the emergence of ancient viruses.
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Azuma Y, Edwardson TGW, Terasaka N, Hilvert D. Modular Protein Cages for Size-Selective RNA Packaging in Vivo. J Am Chem Soc 2018; 140:566-569. [DOI: 10.1021/jacs.7b10798] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yusuke Azuma
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Naohiro Terasaka
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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Abstract
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Compartmentalization of proteases
enables spatially and temporally
controlled protein degradation in cells. Here we show that an engineered
lumazine synthase protein cage, which possesses a negatively supercharged
lumen, can exploit electrostatic effects to sort substrates for an
encapsulated protease. This proteasome-like nanoreactor preferentially
cleaves positively charged polypeptides over both anionic and zwitterionic
substrates, inverting the inherent substrate specificity of the guest
enzyme approximately 480 fold. Our results suggest that supercharged
nanochambers could provide a simple and potentially general means
of conferring substrate specificity to diverse encapsulated catalysts.
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Affiliation(s)
- Yusuke Azuma
- Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Daniel L V Bader
- Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
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31
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Azuma Y, Edwardson TGW, Hilvert D. Tailoring lumazine synthase assemblies for bionanotechnology. Chem Soc Rev 2018; 47:3543-3557. [DOI: 10.1039/c8cs00154e] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The cage-forming protein lumazine synthase is readily modified, evolved and assembled with other components.
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Affiliation(s)
- Yusuke Azuma
- Laboratory of Organic Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | | | - Donald Hilvert
- Laboratory of Organic Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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