1
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Dang M, Wu LJ, Zhang SR, Zhu JR, Hu YZ, Yang CX, Zhang XY. MS2 Virus-like Particles as a Versatile Peptide Presentation Platform: Insights into the Deterministic Abilities for Accommodating Heterologous Peptide Lengths. ACS Synth Biol 2023; 12:3704-3715. [PMID: 37946498 PMCID: PMC10729756 DOI: 10.1021/acssynbio.3c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Virus-like particles (VLPs) are nanostructures with the potential to present heterologous peptides at high density, thereby triggering heightened immunogenicity. RNA bacteriophage MS2 VLPs are a compelling delivery platform among them. However, a notable hurdle arises from the immune response toward MS2 coat protein, swiftly eliminating subsequent vaccinations via the same vector. Although larger inserts effectively mask carrier epitopes, current research predominantly focuses on displaying short conserved peptides (<30 aa). A systematic evaluation regarding the deterministic ability of MS2 VLPs as a platform for presenting heterologous peptides remains a gap. In light of this, we employed the "single-chain dimer" paradigm to scrutinize the tolerance of MS2 VLPs for peptide/protein insertions. The results unveiled functional MS2 VLP assembly solely for inserts smaller than 91 aa. Particularly noteworthy is the largest insertion achieved on the MS2 VLPs to date: the RNA helicase A (RHA) dsRNA-binding domains (dsRBD1). Attempts to introduce additional linkers or empty coat subunits fail to augment the expression level or assembly of the MS2 VLPs displaying dsRBD1, affirming 91 aa as the upper threshold for exogenous protein presentation. By illuminating the precise confines of MS2 VLPs in accommodating distinct peptide lengths, our study informs the selection of appropriate peptide and protein dimensions. This revelation not only underscores the scope of MS2 VLPs but also establishes a pivotal reference point, facilitating the strategic manipulation of MS2 VLPs to design next-generation epitope/antibody-based therapeutics.
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Affiliation(s)
- Mei Dang
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
- Department
of Biological Sciences, Faculty of Science, National University of Singapore, 10 Keng Ridge Crescent, 119260, Singapore
| | - Long J. Wu
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Si R. Zhang
- Xi’an
Middle School of Shaanxi Province, Fengcheng Wulu 69, Weiyang, Xi’an 710006, China
- Department
of Genetics, Stanford University, Palo Alto, California 94304, United States
- HSS,
Stanford University, Palo Alto, California 94305, United States
| | - Jian R. Zhu
- School of
Pharmacy, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yu Z. Hu
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Chen X. Yang
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Xiao Y. Zhang
- Qinba
State Key Laboratory of Biological Resources and Ecological Environment,
College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
- Centre
of Molecular & Environmental Biology, Department of Biology, University of Minho, 4710-057 Braga, Portugal
- Department
of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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2
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Hewagama ND, Uchida M, Wang Y, Kraj P, Lee B, Douglas T. Higher-Order VLP-Based Protein Macromolecular Framework Structures Assembled via Coiled-Coil Interactions. Biomacromolecules 2023; 24:3716-3728. [PMID: 37467146 DOI: 10.1021/acs.biomac.3c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Hierarchical organization is one of the fundamental features observed in biological systems that allows for efficient and effective functioning. Virus-like particles (VLPs) are elegant examples of a hierarchically organized supramolecular structure, where many subunits are self-assembled to generate the functional cage-like architecture. Utilizing VLPs as building blocks to construct two- and three-dimensional (3D) higher-order structures is an emerging research area in developing functional biomimetic materials. VLPs derived from P22 bacteriophages can be repurposed as nanoreactors by encapsulating enzymes and modular units to build higher-order catalytic materials via several techniques. In this study, we have used coiled-coil peptide interactions to mediate the P22 interparticle assembly into a highly stable, amorphous protein macromolecular framework (PMF) material, where the assembly does not depend on the VLP morphology, a limitation observed in previously reported P22 PMF assemblies. Many encapsulated enzymes lose their optimum functionalities under the harsh conditions that are required for the P22 VLP morphology transitions. Therefore, the coiled-coil-based PMF provides a fitting and versatile platform for constructing functional higher-order catalytic materials compatible with sensitive enzymes. We have characterized the material properties of the PMF and utilized the disordered PMF to construct a biocatalytic 3D material performing single- and multistep catalysis.
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Affiliation(s)
- Nathasha D Hewagama
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, California 93740, United States
| | - Yang Wang
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Pawel Kraj
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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3
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Essus VA, Souza Júnior GSE, Nunes GHP, Oliveira JDS, de Faria BM, Romão LF, Cortines JR. Bacteriophage P22 Capsid as a Pluripotent Nanotechnology Tool. Viruses 2023; 15:516. [PMID: 36851730 PMCID: PMC9962691 DOI: 10.3390/v15020516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
The Salmonella enterica bacteriophage P22 is one of the most promising models for the development of virus-like particle (VLP) nanocages. It possesses an icosahedral T = 7 capsid, assembled by the combination of two structural proteins: the coat protein (gp5) and the scaffold protein (gp8). The P22 capsid has the remarkable capability of undergoing structural transition into three morphologies with differing diameters and wall-pore sizes. These varied morphologies can be explored for the design of nanoplatforms, such as for the development of cargo internalization strategies. The capsid proteic nature allows for the extensive modification of its structure, enabling the addition of non-native structures to alter the VLP properties or confer them to diverse ends. Various molecules were added to the P22 VLP through genetic, chemical, and other means to both the capsid and the scaffold protein, permitting the encapsulation or the presentation of cargo. This allows the particle to be exploited for numerous purposes-for example, as a nanocarrier, nanoreactor, and vaccine model, among other applications. Therefore, the present review intends to give an overview of the literature on this amazing particle.
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Affiliation(s)
- Victor Alejandro Essus
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Getúlio Silva e Souza Júnior
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Gabriel Henrique Pereira Nunes
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Juliana dos Santos Oliveira
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Bruna Mafra de Faria
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CCS, Bl. F026, Rio de Janeiro 21941-590, Brazil
| | - Luciana Ferreira Romão
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CCS, Bl. F026, Rio de Janeiro 21941-590, Brazil
| | - Juliana Reis Cortines
- Laboratório de Virologia e Espectrometria de Massas (LAVEM), Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
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4
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Uchida M, Selivanovitch E, McCoy K, Douglas T. Fabrication of Protein Macromolecular Frameworks (PMFs) and Their Application in Catalytic Materials. Methods Mol Biol 2023; 2671:111-120. [PMID: 37308641 PMCID: PMC11034859 DOI: 10.1007/978-1-0716-3222-2_6] [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] [Indexed: 06/14/2023]
Abstract
The construction of three-dimensional (3D) array materials from nanoscale building blocks has drawn significant interest because of their potential to exhibit collective properties and functions arising from the interactions between individual building blocks. Protein cages such as virus-like particles (VLPs) have distinct advantages as building blocks for higher-order assemblies because they are extremely homogeneous in size and can be engineered with new functionalities by chemical and/or genetic modification. In this chapter, we describe a protocol for constructing a new class of protein-based superlattices, called protein macromolecular frameworks (PMFs). We also describe an exemplary method to evaluate the catalytic activity of enzyme-enclosed PMFs, which exhibit enhanced catalytic activity due to the preferential partitioning of charged substrates into the PMF.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, Fresno, CA, USA.
| | | | - Kimberly McCoy
- Department of Chemistry and Biochemistry, California State University, Fresno, Fresno, CA, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN, USA
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5
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McNeale D, Dashti N, Cheah LC, Sainsbury F. Protein cargo encapsulation by
virus‐like
particles: Strategies and applications. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 15:e1869. [PMID: 36345849 DOI: 10.1002/wnan.1869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022]
Abstract
Viruses and the recombinant protein cages assembled from their structural proteins, known as virus-like particles (VLPs), have gained wide interest as tools in biotechnology and nanotechnology. Detailed structural information and their amenability to genetic and chemical modification make them attractive systems for further engineering. This review describes the range of non-enveloped viruses that have been co-opted for heterologous protein cargo encapsulation and the strategies that have been developed to drive encapsulation. Spherical capsids of a range of sizes have been used as platforms for protein cargo encapsulation. Various approaches, based on native and non-native interactions between the cargo proteins and inner surface of VLP capsids, have been devised to drive encapsulation. Here, we outline the evolution of these approaches, discussing their benefits and limitations. Like the viruses from which they are derived, VLPs are of interest in both biomedical and materials applications. The encapsulation of protein cargo inside VLPs leads to numerous uses in both fundamental and applied biocatalysis and biomedicine, some of which are discussed herein. The applied science of protein-encapsulating VLPs is emerging as a research field with great potential. Developments in loading control, higher order assembly, and capsid optimization are poised to realize this potential in the near future. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Donna McNeale
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery Griffith University Nathan Queensland Australia
| | - Noor Dashti
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland St Lucia Queensland Australia
| | - Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland St Lucia Queensland Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery Griffith University Nathan Queensland Australia
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland St Lucia Queensland Australia
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6
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Wang Y, Douglas T. Bioinspired Approaches to Self-Assembly of Virus-like Particles: From Molecules to Materials. Acc Chem Res 2022; 55:1349-1359. [PMID: 35507643 DOI: 10.1021/acs.accounts.2c00056] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ConspectusWhen viewed through the lens of materials science, nature provides a vast library of hierarchically organized structures that serve as inspiration and raw materials for new synthetic materials. The structural organization of complex bioarchitectures with advanced functions arises from the association of building blocks and is strongly supported by ubiquitous mechanisms of self-assembly, where interactions among components result in spontaneous assembly into defined structures. Viruses are exemplary, where a capsid structure, often formed from the self-assembly of many individual protein subunits, serves as a vehicle for the transport and protection of the viral genome. Higher-order assemblies of viral particles are also found in nature with unexpected collective behaviors. When the infectious aspect of viruses is removed, the self-assembly of viral particles and their potential for hierarchical assembly become an inspiration for the design and construction of a new class of functional materials at a range of different length scales.Salmonella typhimurium bacteriophage P22 is a well-studied model for understanding viral self-assembly and the construction of virus-like particle (VLP)-based materials. The formation of cage-like P22 VLP structures results from scaffold protein (SP)-directed self-assembly of coat protein (CP) subunits into icosahedral capsids with encapsulation of SP inside the capsid. Employing the CP-SP interaction during self-assembly, the encapsulation of guest protein cargos inside P22 VLPs can be achieved with control over the composition and the number of guest cargos. The morphology of cargo-loaded VLPs can be altered, along with changes in both the physical properties of the capsid and the cargo-capsid interactions, by mimicking aspects of the infectious P22 viral maturation. The structure of the capsid differentiates the inside cavity from the outside environment and serves as a protecting layer for the encapsulated cargos. Pores in the capsid shell regulate molecular exchange between inside and outside, where small molecules can traverse the capsid freely while the diffusion of larger molecules is limited by the pores. The interior cavity of the P22 capsid can be packed with hundreds of copies of cargo proteins (especially enzymes), enforcing intermolecular proximity, making this an ideal model system in which to study enzymatic catalysis in crowded and confined environments. These aspects highlight the development of functional nanomaterials from individual P22 VLPs, through biomimetic design and self-assembly, resulting in fabrication of nanoreactors with controlled catalytic behaviors.Individual P22 VLPs have been used as building blocks for the self-assembly of higher-order structures. This relies on a balance between the intrinsic interparticle repulsion and a tunable interparticle attraction. The ordering of VLPs within three-dimensional assemblies is dependent on the balance between repulsive and attractive interactions: too strong an attraction results in kinetically trapped disordered structures, while decreasing the attraction can lead to more ordered arrays. These higher-order assemblies display collective behavior of high charge density beyond those of the individual VLPs.The development of synthetic nanomaterials based on P22 VLPs demonstrates how the potential for hierarchical self-assembly can be applied to other self-assembling capsid structures across multiple length scales toward future bioinspired functional materials.
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Affiliation(s)
- Yang Wang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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7
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Biela AP, Naskalska A, Fatehi F, Twarock R, Heddle JG. Programmable polymorphism of a virus-like particle. COMMUNICATIONS MATERIALS 2022; 3:7. [PMID: 35284827 PMCID: PMC7612486 DOI: 10.1038/s43246-022-00229-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Virus-like particles (VLPs) have significant potential as artificial vaccines and drug delivery systems. The ability to control their size has wide ranging utility but achieving such controlled polymorphism using a single protein subunit is challenging as it requires altering VLP geometry. Here we achieve size control of MS2 bacteriophage VLPs via insertion of amino acid sequences in an external loop to shift morphology to significantly larger forms. The resulting VLP size and geometry is controlled by altering the length and type of the insert. Cryo electron microscopy structures of the new VLPs, in combination with a kinetic model of their assembly, show that the abundance of wild type (T = 3), T = 4, D3 and D5 symmetrical VLPs can be biased in this way. We propose a mechanism whereby the insert leads to a change in the dynamic behavior of the capsid protein dimer, affecting the interconversion between the symmetric and asymmetric conformers and thus determining VLP size and morphology.
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Affiliation(s)
- Artur P. Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
| | - Antonina Naskalska
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
| | - Farzad Fatehi
- Departments of Mathematics, University of York, York YO10 5DD, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, UK
| | - Reidun Twarock
- Departments of Mathematics, University of York, York YO10 5DD, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York YO10 5GE, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-392 Krakow, Poland
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8
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Uchida M, Manzo E, Echeveria D, Jiménez S, Lovell L. Harnessing physicochemical properties of virus capsids for designing enzyme confined nanocompartments. Curr Opin Virol 2021; 52:250-257. [PMID: 34974380 PMCID: PMC8939255 DOI: 10.1016/j.coviro.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Viruses have drawn significant scientific interest from a wide variety of disciplines beyond virology because of their elegant architectures and delicately balanced activities. A virus-like particle (VLP), a noninfectious protein cage derived from viruses or other cage-forming proteins, has been exploited as a nano-scale platform for bioinspired engineering and synthetic manipulation with a range of applications. Encapsulation of functional proteins, especially enzymes, is an emerging use of VLPs that is promising not only for developing efficient and robust catalytic materials, but also for providing fundamental insights into the effects of enzyme compartmentalization commonly observed in cells. This review highlights recent advances in employing VLPs as a container for confining enzymes. To accomplish larger and more controlled enzyme loading, various different enzyme encapsulation strategies have been developed; many of these strategies are inspired from assembly and genome loading mechanisms of viral capsids. Characterization of VLPs’ physicochemical properties, such as porosity, could lead to rational manipulation and a better understanding of the catalytic behavior of the materials.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA.
| | - Elia Manzo
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
| | - Dustin Echeveria
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
| | - Sophie Jiménez
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
| | - Logan Lovell
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Ave., Fresno, CA 93740, USA
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9
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Selivanovitch E, Uchida M, Lee B, Douglas T. Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover. ACS NANO 2021; 15:15687-15699. [PMID: 34473481 PMCID: PMC9136710 DOI: 10.1021/acsnano.1c05004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). The highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.
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Affiliation(s)
- Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry and Biochemistry, California State University Fresno, Fresno, California 93740, Unites States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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10
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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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11
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Selivanovitch E, LaFrance B, Douglas T. Molecular exclusion limits for diffusion across a porous capsid. Nat Commun 2021; 12:2903. [PMID: 34006828 PMCID: PMC8131759 DOI: 10.1038/s41467-021-23200-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Molecular communication across physical barriers requires pores to connect the environments on either side and discriminate between the diffusants. Here we use porous virus-like particles (VLPs) derived from bacteriophage P22 to investigate the range of molecule sizes able to gain access to its interior. Although there are cryo-EM models of the VLP, they may not accurately depict the parameters of the molecules able to pass across the pores due to the dynamic nature of the P22 particles in the solution. After encapsulating the enzyme AdhD within the P22 VLPs, we use a redox reaction involving PAMAM dendrimer modified NADH/NAD+ to examine the size and charge limitations of molecules entering P22. Utilizing the three different accessible morphologies of the P22 particles, we determine the effective pore sizes of each and demonstrate that negatively charged substrates diffuse across more readily when compared to those that are neutral, despite the negatively charge exterior of the particles.
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Affiliation(s)
| | - Benjamin LaFrance
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, IN, USA.
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12
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Waghwani HK, Uchida M, Fu CY, LaFrance B, Sharma J, McCoy K, Douglas T. Virus-Like Particles (VLPs) as a Platform for Hierarchical Compartmentalization. Biomacromolecules 2020; 21:2060-2072. [PMID: 32319761 DOI: 10.1021/acs.biomac.0c00030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hierarchically self-assembled structures are common in biology, but it is often challenging to design and fabricate synthetic analogs. The archetypal cell is defined by hierarchically organized multicompartmentalized structures with boundaries that delineate the interior from exterior environments and is an inspiration for complex functional materials. Here, we have demonstrated an approach to the design and construction of a nested protein cage system that can additionally incorporate the packing of other functional macromolecules and exhibit some of the features of a minimal synthetic cell-like material. We have demonstrated a strategy for controlled co-packaging of subcompartments, ferritin (Fn) cages, together with active cellobiose-hydrolyzing β-glycosidase enzyme macromolecules, CelB, inside the sequestered volume of the bacteriophage P22 capsid. Using controlled in vitro assembly, we were able to modulate the stoichiometry of Fn cages and CelB encapsulated inside the P22 to control the degree of compartmentalization. The co-encapsulated enzyme CelB showed catalytic activity even when packaged at high total macromolecular concentrations comparable to an intracellular environment. This approach could be used as a model to create synthetic protein-based protocells that can confine smaller functionalized proto-organelles and additional macromolecules to support a range of biochemical reactions.
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Affiliation(s)
- Hitesh Kumar Waghwani
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.,Department of Chemistry, California State University Fresno, Fresno, California 93740, United States
| | - Chi-Yu Fu
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Benjamin LaFrance
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Jhanvi Sharma
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kimberly McCoy
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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