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Kraj P, Hewagama ND, Douglas T. Diffusion and molecular partitioning in hierarchically complex virus-like particles. Virology 2023; 580:50-60. [PMID: 36764014 DOI: 10.1016/j.virol.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Viruses are diverse infectious agents found in virtually every type of natural environment. Due to the range of conditions in which viruses have evolved, they exhibit a wide range of structure and function which has been exploited for biotechnology. The self-assembly process of virus-like particles (VLPs), derived from structural virus components, allows for the assembly of a hierarchy of materials. Because VLPs are robust in both their assembly and the final product, functionality can be incorporated through design of their building blocks or chemical modification after their synthesis and assembly. In particular, encapsulation of active enzymes inside VLP results in macromolecular concentration approximating that of cells, introducing excluded volume effects on encapsulated cargo which are not present in traditional experiments done on dilute proteins. This work reviews the hierarchical assembly of VLPs, experiments investigating diffusion in VLP systems, and methods for partitioning of chemical species in VLPs as functional biomaterials.
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Affiliation(s)
- Pawel Kraj
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Nathasha D Hewagama
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave., Bloomington, IN, 47405, USA.
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2
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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: 4] [Impact Index Per Article: 4.0] [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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P Patterson D, Hjorth C, Hernandez Irias A, Hewagama N, Bird J. Delayed In Vivo Encapsulation of Enzymes Alters the Catalytic Activity of Virus-Like Particle Nanoreactors. ACS Synth Biol 2022; 11:2956-2968. [PMID: 36073831 DOI: 10.1021/acssynbio.1c00636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Encapsulation of enzymes inside protein cage structures, mimicking protein-based organelle structures found in nature, has great potential for the development of new catalytic materials with enhanced properties. In vitro and in vivo methodologies have been developed for the encapsulation of enzymes within protein cage structures of several types, particularly virus-like particles (VLPs), with the ability to retain the activity of the encapsulated enzymes. Here, we examine the in vivo encapsulation of enzymes within the bacteriophage P22 derived VLP and show that some enzymes may require a delay in encapsulation to allow proper folding and maturation before they can be encapsulated inside P22 as fully active enzymes. Using a sequential expression strategy, where enzyme cargoes are first expressed, allowed to fold, and later encapsulated by the expression of the P22 coat protein, altered enzymatic activities are obtained in comparison to enzymes encapsulated in P22 VLPs using a simultaneous coexpression strategy. The strategy and results discussed here highlight important considerations for researchers investigating the encapsulation of enzymes inside confined reaction environments via in vivo routes and provide a potential solution for those that have been unable to produce active enzymes upon encapsulation.
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Affiliation(s)
- Dustin P Patterson
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, 3900 University Blvd., Tyler, Texas 75799, United States
| | - Christy Hjorth
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, 3900 University Blvd., Tyler, Texas 75799, United States
| | - Andrea Hernandez Irias
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, 3900 University Blvd., Tyler, Texas 75799, United States
| | - Nathasha Hewagama
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Jessica Bird
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, 3900 University Blvd., Tyler, Texas 75799, United States
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Todd AR, Jarrold MF. Dynamic Calibration Enables High-Accuracy Charge Measurements on Individual Ions for Charge Detection Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1241-1248. [PMID: 32353231 DOI: 10.1021/jasms.0c00081] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. For high-accuracy charge measurements, the detection cylinder is embedded in an electrostatic linear ion trap (ELIT), and the ions oscillate back and forth through the cylinder so that multiple measurements are made. To assign the charge state with a low error rate, the charge of each ion must be determined with an uncertainty (root-mean-square deviation) of around 0.2 elementary charges. We show here that high-accuracy charge measurements can be achieved for large ions by dynamic calibration of the charge measurement using an internal standard. The internal standard is generated by irradiating the detection cylinder, by means of a small antenna, with a radiofrequency signal. Using this approach, we have obtained a relative charge uncertainty of around 5 × 10-4, allowing charge-state resolution to be achieved for single ions with up to 500 charges. In another application of this approach, the detection cylinder is irradiated with a signal that counteracts the transients generated when the potentials on the ELIT end-caps are switched to trapping mode. Using this approach, the dead time after switching (during which the signal cannot be analyzed) has been reduced by more than an order of magnitude. With charge-state resolution for ions with up to 500 charges, we were able to calibrate the charges precisely. The results show that the response of the charge-sensitive amplifier with dynamic calibration is linear to within a small fraction of an elementary charge.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department, Indiana University, Bloomington, Indiana 47405 United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, Indiana 47405 United States
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Todd AR, Alexander AW, Jarrold MF. Implementation of a Charge-Sensitive Amplifier without a Feedback Resistor for Charge Detection Mass Spectrometry Reduces Noise and Enables Detection of Individual Ions Carrying a Single Charge. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:146-154. [PMID: 32881508 DOI: 10.1021/jasms.9b00010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Charge detection mass spectrometry (CDMS) depends on the measurement of the charge induced on a cylinder by individual ions by means of a charge-sensitive amplifier. Electrical noise limits the accuracy of the charge measurement and the smallest charge that can be detected. Thermal noise in the feedback resistor is a major source of electrical noise. We describe the implementation of a charge-sensitive amplifier without a feedback resistor. The design has significantly reduced 1/f noise facilitating the detection of high m/z ions and substantially reducing the measurement time required to achieve almost perfect charge accuracy. With the new design we have been able to detect individual ions carrying a single charge. This is an important milestone in the development of CDMS.
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Affiliation(s)
- Aaron R Todd
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew W Alexander
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, Bloomington, Indiana 47405, United States
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Kondylis P, Schlicksup CJ, Zlotnick A, Jacobson SC. Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids. Anal Chem 2019; 91:622-636. [PMID: 30383361 PMCID: PMC6472978 DOI: 10.1021/acs.analchem.8b04824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Panagiotis Kondylis
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Christopher J. Schlicksup
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
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Zeng C, Rodriguez Lázaro G, Tsvetkova IB, Hagan MF, Dragnea B. Defects and Chirality in the Nanoparticle-Directed Assembly of Spherocylindrical Shells of Virus Coat Proteins. ACS NANO 2018; 12:5323-5332. [PMID: 29694012 PMCID: PMC6202266 DOI: 10.1021/acsnano.8b00069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Virus coat proteins of small isometric plant viruses readily assemble into symmetric, icosahedral cages encapsulating noncognate cargo, provided the cargo meets a minimal set of chemical and physical requirements. While this capability has been intensely explored for certain virus-enabled nanotechnologies, additional applications require lower symmetry than that of an icosahedron. Here, we show that the coat proteins of an icosahedral virus can efficiently assemble around metal nanorods into spherocylindrical closed shells with hexagonally close-packed bodies and icosahedral caps. Comparison of chiral angles and packing defects observed by in situ atomic force microscopy with those obtained from molecular dynamics models offers insight into the mechanism of growth, and the influence of stresses associated with intrinsic curvature and assembly pathways.
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Affiliation(s)
- Cheng Zeng
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | | | - Irina B Tsvetkova
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Michael F Hagan
- Department of Physics , Brandeis University , Waltham , Massachusetts 02453 , United States
| | - Bogdan Dragnea
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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Beyond icosahedral symmetry in packings of proteins in spherical shells. Proc Natl Acad Sci U S A 2017; 114:9014-9019. [PMID: 28790186 DOI: 10.1073/pnas.1706825114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.
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