1
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Soni H, Lako I, Placidi M, Cramer SM. Implications of AAV affinity column reuse and vector stability on product quality attributes. Biotechnol Bioeng 2024; 121:2449-2465. [PMID: 37485847 DOI: 10.1002/bit.28500] [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: 02/08/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
In this work, the implications of AAV9 capsid design and column reuse on AAV9 vector product quality were assessed with POROS CaptureSelect (PCS) AAVX and AAV9 resins using sf9 insect cell-derived model AAV9 vectors with varying viral protein (VP) ratios. Chromatographic experiments with purified drug substance AAV9 model feeds indicated consistent vector elution profiles, independent of adeno-associated virus (AAV) VP ratio, or cycle number. In contrast, the presence of process impurities in the clarified lysate feeds resulted in clear changes in the elution patterns. This included increased aggregate content in the vector eluates over multiple cycles as well as clear differences in the performance of these affinity resin systems. The AAV9-serotype specific PCS AAV9 column, with lower vector elution pH, resulted in higher aggregate content over multiple cycles as compared to the serotype-independent PCS AAVX column. Further, the results with vectors of varying VP ratio indicated that while one vector type eluate displayed higher aggregation in both affinity columns over column reuse, the eluate with the other vector type did not exhibit changes in the aggregation profile. Interestingly, vector aggregates in the affinity eluates also contained double-stranded DNA impurities and histone proteins, with similar trends to the aggregate levels. This behavior upon column reuse indicates that these host cell impurities are likely carried over to subsequent runs due to incomplete clean-in-place (CIP). These results indicate that feed impurities, affinity resin characteristics, elution pH, column CIP, and vector stability can impact the reusability of AAV affinity columns and product quality.
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Affiliation(s)
- Harshal Soni
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Ira Lako
- Voyager Therapeutics, Cambridge, Massachusetts, USA
| | | | - Steven M Cramer
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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2
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Nam YR, Ju HH, Lee J, Lee D, Kim Y, Lee SJ, Kim HK, Jang JH, Lee H. Distinguishing between DNA-Loaded Full and Empty Capsids of Adeno-Associated Virus with Atomic Force Microscopy Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:6740-6747. [PMID: 37130261 DOI: 10.1021/acs.langmuir.3c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Recently, miraculous therapy approaches involving adeno-associated virus (AAV) for incurable diseases such as spinal muscular atrophy and inherited retinal dysfunction have been introduced. Nonreplicative, nonpathogenic, low rates of chromosome insertional properties and the existence of neutralizing antibodies are main safety reasons why the FDA approved its use in gene delivery. To date, AAV production always results in a mixture of nontherapeutic (empty) and therapeutic (DNA-loaded) full capsids (10-98%). Such existence of empty viral particles inevitably increases viral doses to human. Thus, the rapid monitoring of empty capsids and reducing the empty-to-full ratio are critical in AAV science. However, transmission electron microscopy (TEM) is the primary tool for distinguishing between empty and full capsids, which creates a research bottleneck because of instrument accessibility and technical difficulty. Herein, we demonstrate that atomic force microscopy (AFM) can be an alternative tool to TEM. The simple, noncontact-mode imaging of AAV particles allows the distinct height difference between full capsids (∼22 nm) and empty capsids (∼16 nm). The sphere-to-ellipsoidal morphological distortion observed for empty AAV particles clearly distinguishes them from full AAV particles. Our study indicates that AFM imaging can be an extremely useful, quality-control tool in AAV particle monitoring, which is beneficial for the future development of AAV-based gene therapy.
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Affiliation(s)
- Yu Ri Nam
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Helen H Ju
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jeehee Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Daiheon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Yoojin Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sung Jin Lee
- R&D Center, GluGene Therapeutics Inc., Seoul 34028, Republic of Korea
| | - Hong Kee Kim
- R&D Center, GluGene Therapeutics Inc., Seoul 34028, Republic of Korea
| | - Jae-Hyung Jang
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
- R&D Center, GluGene Therapeutics Inc., Seoul 34028, Republic of Korea
| | - Haeshin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- R&D Center, GluGene Therapeutics Inc., Seoul 34028, Republic of Korea
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3
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Radiom M, Keys T, Turgay Y, Ali A, Preet S, Chesnov S, Lutz-Bueno V, Slack E, Mezzenga R. Mechanical tuning of virus-like particles. J Colloid Interface Sci 2023; 634:963-971. [PMID: 36571858 DOI: 10.1016/j.jcis.2022.12.090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/18/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
HYPOTHESIS Virus-like particles (VLPs) are promising scaffolds for developing mucosal vaccines. For their optimal performance, in addition to design parameters from an immunological perspective, biophysical properties may need to be considered. EXPERIMENTS We investigated the mechanical properties of VLPs scaffolded on the coat protein of Acinetobacter phage AP205 using atomic force microscopy and small angle X-ray scattering. FINDINGS Investigations showed that AP205 VLP is a tough nanoshell of stiffness 93 ± 23 pN/nm and elastic modulus 0.11 GPa. However, its mechanical properties are modulated by attaching muco-inert polyethylene glycol to 46 ± 10 pN/nm and 0.05 GPa. Addition of antigenic peptides derived from SARS-CoV2 spike protein by genetic fusion increased the stiffness to 146 ± 54 pN/nm although the elastic modulus remained unchanged. These results, which are interpreted in terms of shell thickness and coat protein net charge variations, demonstrate that surface conjugation can induce appreciable changes in the biophysical properties of VLP-scaffolded vaccines.
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Affiliation(s)
- Milad Radiom
- Laboratory of Food Immunology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland; Laboratory of Food and Soft Materials, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland.
| | - Tim Keys
- Laboratory of Food Immunology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Yagmur Turgay
- Laboratory of Food Immunology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Ahmed Ali
- Laboratory of Food Immunology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Swapan Preet
- Laboratory of Food Immunology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Serge Chesnov
- University of Zürich/ETH Zürich, Functional Genomics Centre Zürich, Zürich, Switzerland
| | | | - Emma Slack
- Laboratory of Food Immunology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland.
| | - Raffaele Mezzenga
- Laboratory of Food and Soft Materials, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland.
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4
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Contact force models for non-spherical particles with different surface properties: A review. POWDER TECHNOL 2023. [DOI: 10.1016/j.powtec.2023.118323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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5
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Menou L, Salas YC, Lecoq L, Salvetti A, Moskalenko CF, Castelnovo M. Stiffness heterogeneity of small viral capsids. Phys Rev E 2021; 104:064408. [PMID: 35030852 DOI: 10.1103/physreve.104.064408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/01/2021] [Indexed: 12/30/2022]
Abstract
Nanoindentation of viral capsids provides an efficient tool in order to probe their elastic properties. We investigate in the present work the various sources of stiffness heterogeneity as observed in atomic force microscopy experiments. By combining experimental results with both numerical and analytical modeling, we first show that for small viruses, a position-dependent stiffness is observed. This effect is strong and has not been properly taken into account previously. Moreover, we show that a geometrical model is able to reproduce this effect quantitatively. Our work suggests alternative ways of measuring stiffness heterogeneities on small viral capsids. This is illustrated on two different viral capsids: Adeno associated virus serotype 8 (AAV8) and hepatitis B virus (HBV with T=4). We discuss our results in light of continuous elasticity modeling.
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Affiliation(s)
- Lucas Menou
- Université de Lyon, Ens de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | | | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, University of Lyon 1, Lyon, France
| | - Anna Salvetti
- International Center for Research in Infectiology (CIRI), INSERM U111, CNRS UMR 5308, Lyon, France
| | | | - Martin Castelnovo
- Université de Lyon, Ens de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France
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6
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Zhang W, Jia Q, Teng Y, Yang M, Zhang H, Zhang XE, Wang P, Ge J, Cao S, Li F. An Ultrastable Virus-Like Particle with a Carbon Dot Core and Expanded Sequence Plasticity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101717. [PMID: 34302443 DOI: 10.1002/smll.202101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/06/2021] [Indexed: 06/13/2023]
Abstract
Ordered bio-inorganic hybridization has evolved for the generation of high-performance materials in living organisms and inspires novel strategies to design artificial hybrid materials. Virus-like particles (VLPs) are attracting extensive interest as self-assembling systems and platforms in the fields of biotechnology and nanotechnology. However, as soft nanomaterials, their structural stability remains a general and fundamental problem in various applications. Here, an ultrastable VLP assembled from the major capsid protein (VP1) of simian virus 40 is reported, which contains a carbon dot (C-dot) core. Co-assembly of VP1 with C-dots led to homogeneous T = 1 VLPs with a fourfold increase in VLP yields. The resultant hybrid VLPs showed markedly enhanced structural stability and sequence plasticity. C-dots and a polyhistidine tag fused to the inner-protruding N-terminus of VP1 contributed synergistically to these enhancements, where extensive and strong noncovalent interactions on the C-dot/VP1 interfaces are responsible according to cryo-EM 3D reconstruction, molecular simulation, and affinity measurements. C-dot-enhanced ultrastable VLPs can serve as a new platform, enabling the fabrication of new architectures for bioimaging, theranostics, nanovaccines, etc. The hybridization strategy is simple and can easily be extended to other VLPs and protein nanoparticle systems.
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Affiliation(s)
- Wenjing Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingyan Jia
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yibo Teng
- Wuhan Ready science and technology corporation Ltd, Wuhan, 430064, China
| | - Mengsi Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-En Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Pengfei Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiechao Ge
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Sheng Cao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Wright BW, Ruan J, Molloy MP, Jaschke PR. Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction. ACS Synth Biol 2020; 9:3079-3090. [PMID: 33044064 DOI: 10.1021/acssynbio.0c00323] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sequence overlap between two genes is common across all genomes, with viruses having high proportions of these gene overlaps. Genome modularization and refactoring is the process of disrupting natural gene overlaps to separate coding sequences to enable their individual manipulation. The biological function and fitness effects of gene overlaps are not fully understood, and their effects on gene cluster and genome-level refactoring are unknown. The bacteriophage φX174 genome has ∼26% of nucleotides involved in encoding more than one gene. In this study we use an engineered φX174 phage containing a genome with all gene overlaps removed to show that gene overlap is critical to maintaining optimal viral fecundity. Through detailed phenotypic measurements we reveal that genome modularization in φX174 causes virion replication, stability, and attachment deficiencies. Quantitation of the complete phage proteome across an infection cycle reveals 30% of proteins display abnormal expression patterns. Taken together, we have for the first time comprehensively demonstrated that gene modularization severely perturbs the coordinated functioning of a bacteriophage replication cycle. This work highlights the biological importance of gene overlap in natural genomes and that reducing gene overlap disruption should be an integral part of future genome engineering projects.
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Affiliation(s)
- Bradley W. Wright
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Juanfang Ruan
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Mark P. Molloy
- Kolling Institute, Northern Clinical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Paul R. Jaschke
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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8
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Single-particle chemical force microscopy to characterize virus surface chemistry. Biotechniques 2020; 69:363-370. [DOI: 10.2144/btn-2020-0085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Two important viral surface characteristics are the hydrophobicity and surface charge, which determine the viral colloidal behavior and mobility. Chemical force microscopy allows the detection of viral surface chemistry in liquid samples with small amounts of virus sample. This single-particle method requires the functionalization of an atomic force microscope (AFM) probe and covalent bonding of viruses to a surface. A hydrophobic methyl-modified AFM probe was used to study the viral surface hydrophobicity, and an AFM probe terminated with either negatively charged carboxyl acid or positively charged quaternary amine was used to study the viral surface charge. With an understanding of viral surface properties, the way in which viruses interact with the environment can be better predicted.
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9
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Mi X, Bromley EK, Joshi PU, Long F, Heldt CL. Virus Isoelectric Point Determination Using Single-Particle Chemical Force Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:370-378. [PMID: 31845814 DOI: 10.1021/acs.langmuir.9b03070] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Virus colloidal behavior is governed by the interaction of the viral surface and the surrounding environment. One method to characterize the virus surface charge is the isoelectric point (pI). Traditional determination of virus pI has focused on the bulk characterization of a viral solution. However, virus capsids are extremely heterogeneous, and a single-particle method may give more information on the range of surface charge observed across a population. One method to measure the virus pI is chemical force microscopy (CFM). CFM is a single-particle technique that measures the adhesion force of a functionalized atomic force microscope (AFM) probe and, in this case, a virus covalently bound to a surface. Non-enveloped porcine parvovirus (PPV) and enveloped bovine viral diarrhea virus (BVDV) were used to demonstrate the use of CFM for viral particles with different surface properties. We have validated the CFM to determine the pI of PPV to be 4.8-5.1, which has a known pI value of 5.0 in the literature, and to predict the unknown pI of BVDV to be 4.3-4.5. Bulk measurements, ζ-potential, and aqueous two-phase system (ATPS) cross-partitioning methods were also used to validate the new CFM method for the virus pI. Most methods were in good agreement. CFM can detect the surface charge of viral capsids at a single-particle level and enable the comparison of surface charge between different types of viruses.
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10
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Rodriguez-Estevez L, Asokan P, Borrás T. Transduction optimization of AAV vectors for human gene therapy of glaucoma and their reversed cell entry characteristics. Gene Ther 2019; 27:127-142. [PMID: 31611639 PMCID: PMC7153980 DOI: 10.1038/s41434-019-0105-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022]
Abstract
The trabecular meshwork (TM) of the eye is responsible for maintaining physiological intraocular pressure (IOP). Dysfunction of this tissue results in elevated IOP, subsequent optic nerve damage and glaucoma, the world’s leading cause of irreversible blindness. IOP regulation by delivering candidate TM genes would offer an enormous clinical advantage to the current daily-drops/surgery treatment. Initially, we showed that a double-stranded AAV2 (scAAV2) transduced the human TM very efficiently, while its single-stranded form (ssAAV2) did not. Here, we quantified transduction and entry of single- and double-strand serotypes 1, 2.5, 5, 6, 8, and 9 in primary, single individual-derived human TM cells (HTM). scAAV2 exhibited highest transduction in all individuals, distantly followed by scAAV2.5, scAAV6, and scAAV5. Transduction of scAAV1, scAAV8, and scAAV9 was negligible. None of the ssAAV serotypes transduced, but their cell entries were significantly higher than those of their corresponding scAAV. Tyrosine scAAV2 capsid mutants increased transduction in HTM cultured cells and all TM-outflow layers of perfused postmortem human eyes. These studies provide the first serotype optimization for gene therapy of glaucoma in humans. They further reveal biological differences between the AAV forms in HTM cells, whose understanding could contribute to the development of gene therapy of glaucoma.
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Affiliation(s)
- Laura Rodriguez-Estevez
- Department of Ophthalmology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Priyadarsini Asokan
- Department of Ophthalmology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Teresa Borrás
- Department of Ophthalmology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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11
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The application of atomic force microscopy for viruses and protein shells: Imaging and spectroscopy. Adv Virus Res 2019; 105:161-187. [PMID: 31522704 DOI: 10.1016/bs.aivir.2019.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atomic force microscopy (AFM) probes surface-adsorbed samples at the nanoscale by using a sharp stylus of nanometric size located at the end of a micro-cantilever. This technique can also work in a liquid environment and offers unique possibilities to study individual protein assemblies, such as viruses, under conditions that resemble their natural liquid milieu. Here, I show how AFM can be used to explore the topography of viruses and protein cages, including that of structures lacking a well-defined symmetry. AFM is not limited for imaging and allows the manipulation of individual viruses with force spectroscopy approaches, such as single indentation and mechanical fatigue assays. These pushing experiments deform the protein cages to obtain their mechanical information and can be used to monitor the structural changes induced by maturation or the exposure to different biochemical environments, such as pH variation. We discuss how studying capsid rupture and self-healing events offers insight into virus uncoating pathways. On the other hand, pulling tests can provide information about the virus-host interaction established between the viral fibers and the cell membrane.
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12
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Korayem MH, Khaksar H, Sharahi HJ. Modeling and simulation of contact parameters of elliptical and cubic nanoparticles to be used in nanomanipulation based on atomic force microscope. Ultramicroscopy 2019; 206:112808. [PMID: 31301606 DOI: 10.1016/j.ultramic.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 08/31/2018] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Abstract
Regarding the contact mechanics of smooth nanoparticles, two new geometries, specifically elliptical and cubic are chosen for nanoparticles. The results of elliptical contact simulation show that the JKR theory induces a greater indentation depth in both contact geometries since it includes the adhesion forces. Moreover, the Jamari theory shows a lesser indentation depth because it assumes larger contact area. The results of cubic nanoparticles simulation exhibit a significant difference between the contact of tip and nanoparticle compared to the contact of nanoparticle and surface. This can be attributed to the large contact area between the cubic nanoparticle and the reference surface. The JKR and DMT theories, however, show greater indentation depths in the tip contact with nanoparticle. Furthermore, the Lundberg theory yields the maximum indentation depth in the nanoparticle contact with reference surface. Finally, in order to validate the results, experimental and FEM approaches are incorporated. Concerning the experimental results, a certain number of silver nanoparticles are placed on a polystyrene surface. After obtaining the experimental force-displacement curves, the results of presented models are compared with them. The experimental results indicate that for silver nanoparticles and polystyrene surface, the Hertz theory with 1.11% of error and the JKR theory with 8.7% of error show the best output, respectively. Regarding rough nanoparticles contact, the geometry of roughness are taken as elliptical. Meanwhile, analytical relations are presented to solve force and contact area integrals while noting the problem dimensions. The results of simulation show that the JKR theory yields the highest roughness force, followed by the Hertz and Jamari theories, and regarding rough contact area, the Hertz theory creates the largest contact area, followed by the Jamari and JKR theories. The presented analytical method is compared with numerical results as a means of validation.
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Affiliation(s)
- M H Korayem
- Robotic Research Laboratory, Centre of Excellence in Experimental Solid Mechanics and Dynamics, School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran.
| | - H Khaksar
- Robotic Research Laboratory, Centre of Excellence in Experimental Solid Mechanics and Dynamics, School of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - H J Sharahi
- Department of Mechanical and Manufacturing Engineering, University of Calgary, AB, Canada
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13
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Korayem M, Khaksar H. Investigating the impact models for nanoparticles manipulation based on atomic force microscope (according to contact mechanics). POWDER TECHNOL 2019. [DOI: 10.1016/j.powtec.2018.11.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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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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15
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de Pablo PJ, Schaap IAT. Atomic Force Microscopy of Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:159-179. [PMID: 31317500 DOI: 10.1007/978-3-030-14741-9_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Atomic force microscopy employs a nanometric tip located at the end of a micro-cantilever to probe surface-mounted samples at nanometer resolution. Because the technique can also work in a liquid environment it offers unique possibilities to study individual viruses under conditions that mimic their natural milieu. Here, we review how AFM imaging can be used to study the surface structure of viruses including that of viruses lacking a well-defined symmetry. Beyond imaging, AFM enables the manipulation of single viruses by force spectroscopy experiments. Pulling experiments can provide information about the early events of virus-host interaction between the viral fibers and the cell membrane receptors. Pushing experiments measure the mechanical response of the viral capsid and its contents and can be used to show how virus maturation and exposure to different pH values change the mechanical response of the viruses and the interaction between the capsid and genome. Finally, we discuss how studying capsid rupture and self-healing events offers insight in virus uncoating pathways.
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Affiliation(s)
- P J de Pablo
- Department of Condensed Matter Physics and Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain.
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16
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Jiménez-Zaragoza M, Yubero MP, Martín-Forero E, Castón JR, Reguera D, Luque D, de Pablo PJ, Rodríguez JM. Biophysical properties of single rotavirus particles account for the functions of protein shells in a multilayered virus. eLife 2018; 7:37295. [PMID: 30201094 PMCID: PMC6133545 DOI: 10.7554/elife.37295] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/01/2018] [Indexed: 12/27/2022] Open
Abstract
The functions performed by the concentric shells of multilayered dsRNA viruses require specific protein interactions that can be directly explored through their mechanical properties. We studied the stiffness, breaking force, critical strain and mechanical fatigue of individual Triple, Double and Single layered rotavirus (RV) particles. Our results, in combination with Finite Element simulations, demonstrate that the mechanics of the external layer provides the resistance needed to counteract the stringent conditions of extracellular media. Our experiments, in combination with electrostatic analyses, reveal a strong interaction between the two outer layers and how it is suppressed by the removal of calcium ions, a key step for transcription initiation. The intermediate layer presents weak hydrophobic interactions with the inner layer that allow the assembly and favor the conformational dynamics needed for transcription. Our work shows how the biophysical properties of the three shells are finely tuned to produce an infective RV virion.
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Affiliation(s)
- Manuel Jiménez-Zaragoza
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Pl Yubero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Jose R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - David Reguera
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
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17
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Brunk NE, Lee LS, Glazier JA, Butske W, Zlotnick A. Molecular jenga: the percolation phase transition (collapse) in virus capsids. Phys Biol 2018; 15:056005. [PMID: 29714713 PMCID: PMC6004236 DOI: 10.1088/1478-3975/aac194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Virus capsids are polymeric protein shells that protect the viral cargo. About half of known virus families have icosahedral capsids that self-assemble from tens to thousands of subunits. Capsid disassembly is critical to the lifecycles of many viruses yet is poorly understood. Here, we apply a graph and percolation theory to examine the effect of removing capsid subunits on capsid stability and fragmentation. Based on the structure of the icosahedral capsid of hepatitis B virus (HBV), we constructed a graph of rhombic subunits arranged with icosahedral symmetry. Though our approach neglects dependence on energetics, time, and molecular detail, it quantitatively predicts a percolation phase transition consistent with recent in vitro studies of HBV capsid dissociation. While the stability of the capsid graph followed a gradual quadratic decay, the rhombic tiling abruptly fragmented when we removed more than 25% of the 120 subunits, near the percolation threshold observed experimentally. This threshold may also affect results of capsid assembly, which also experimentally produces a preponderance of 90 mer intermediates, as the intermediate steps in these reactions are reversible and can thus resemble dissociation. Application of percolation theory to understanding capsid association and dissociation may prove a general approach to relating virus biology to the underlying biophysics of the virus particle.
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Affiliation(s)
- Nicholas E Brunk
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, United States of America. Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States of America
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18
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Bernaud J, Rossi A, Fis A, Gardette L, Aillot L, Büning H, Castelnovo M, Salvetti A, Faivre-Moskalenko C. Characterization of AAV vector particle stability at the single-capsid level. J Biol Phys 2018; 44:181-194. [PMID: 29656365 DOI: 10.1007/s10867-018-9488-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/16/2018] [Indexed: 12/22/2022] Open
Abstract
Virus families have evolved different strategies for genome uncoating, which are also followed by recombinant vectors. Vectors derived from adeno-associated viruses (AAV) are considered as leading delivery tools for in vivo gene transfer, and in particular gene therapy. Using a combination of atomic force microscopy (AFM), biochemical experiments, and physical modeling, we investigated here the physical properties and stability of AAV vector particles. We first compared the morphological properties of AAV vectors derived from two different serotypes (AAV8 and AAV9). Furthermore, we triggered ssDNA uncoating by incubating vector particles to increasing controlled temperatures. Our analyses, performed at the single-particle level, indicate that genome release can occur in vitro via two alternative pathways: either the capsid remains intact and ejects linearly the ssDNA molecule, or the capsid is ruptured, leaving ssDNA in a compact entangled conformation. The analysis of the length distributions of ejected genomes further revealed a two-step ejection behavior. We propose a kinetic model aimed at quantitatively describing the evolution of capsids and genomes along the different pathways, as a function of time and temperature. This model allows quantifying the relative stability of AAV8 and AAV9 particles.
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Affiliation(s)
- Julien Bernaud
- Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France
| | - Axel Rossi
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, LabEx Ecofect, 69007, Lyon, France
| | - Anny Fis
- Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France
| | - Lara Gardette
- Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France
| | - Ludovic Aillot
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, LabEx Ecofect, 69007, Lyon, France
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, 30625, Hannover, Germany
| | - Martin Castelnovo
- Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.
| | - Anna Salvetti
- International Center for Infectiology Research (CIRI), Inserm U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, LabEx Ecofect, 69007, Lyon, France.
| | - Cendrine Faivre-Moskalenko
- Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.
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19
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Kant R, Rayaprolu V, McDonald K, Bothner B. Curating viscoelastic properties of icosahedral viruses, virus-based nanomaterials, and protein cages. J Biol Phys 2018; 44:211-224. [PMID: 29637472 DOI: 10.1007/s10867-018-9491-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/16/2018] [Indexed: 12/31/2022] Open
Abstract
The beauty, symmetry, and functionality of icosahedral virus capsids has attracted the attention of biologists, physicists, and mathematicians ever since they were first observed. Viruses and protein cages assemble into functional architectures in a range of sizes, shapes, and symmetries. To fulfill their biological roles, these structures must self-assemble, resist stress, and are often dynamic. The increasing use of icosahedral capsids and cages in materials science has driven the need to quantify them in terms of structural properties such as rigidity, stiffness, and viscoelasticity. In this study, we employed Quartz Crystal Microbalance with Dissipation technology (QCM-D) to characterize and compare the mechanical rigidity of different protein cages and viruses. We attempted to unveil the relationships between rigidity, radius, shell thickness, and triangulation number. We show that the rigidity and triangulation numbers are inversely related to each other and the comparison of rigidity and radius also follows the same trend. Our results suggest that subunit orientation, protein-protein interactions, and protein-nucleic acid interactions are important for the resistance to deformation of these complexes, however, the relationships are complex and need to be explored further. The QCM-D based viscoelastic measurements presented here help us elucidate these relationships and show the future prospect of this technique in the field of physical virology and nano-biotechnology.
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Affiliation(s)
- Ravi Kant
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Vamseedhar Rayaprolu
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, USA
| | - Kaitlyn McDonald
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
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20
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Bennett A, Patel S, Mietzsch M, Jose A, Lins-Austin B, Yu JC, Bothner B, McKenna R, Agbandje-McKenna M. Thermal Stability as a Determinant of AAV Serotype Identity. Mol Ther Methods Clin Dev 2017; 6:171-182. [PMID: 28828392 PMCID: PMC5552060 DOI: 10.1016/j.omtm.2017.07.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/18/2017] [Indexed: 12/11/2022]
Abstract
Currently, there are over 150 ongoing clinical trials utilizing adeno-associated viruses (AAVs) to target various genetic diseases, including hemophilia (AAV2 and AAV8), congenital heart failure (AAV1 and AAV6), cystic fibrosis (AAV2), rheumatoid arthritis (AAV2), and Batten disease (AAVrh.10). Prior to patient administration, AAV vectors must have their serotype, concentration, purity, and stability confirmed. Here, we report the application of differential scanning fluorimetry (DSF) as a good manufacturing practice (GMP) capable of determining the melting temperature (Tm) for AAV serotype identification. This is a simple, rapid, cost effective, and robust method utilizing small amounts of purified AAV capsids (∼25 μL of ∼1011 particles). AAV1-9 and AAVrh.10 exhibit specific Tms in buffer formulations commonly used in clinical trials. Notably, AAV2 and AAV3, which are the least stable, have varied Tms, whereas AAV5, the most stable, has a narrow Tm range in the different buffers, respectively. Vector stability was dictated by VP3 only, specifically, the ratio of basic/acidic amino acids, and was independent of VP1 and VP2 content or the genome packaged. Furthermore, stability of recombinant AAVs differing by a single basic or acidic amino acid residue are distinguishable. Hence, AAV DSF profiles can serve as a robust method for serotype identification of clinical vectors.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Saajan Patel
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ariana Jose
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Bridget Lins-Austin
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jennifer C. Yu
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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21
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In Situ Atomic Force Microscopy Studies on Nucleation and Self-Assembly of Biogenic and Bio-Inspired Materials. MINERALS 2017. [DOI: 10.3390/min7090158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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AFM nanoindentation of protein shells, expanding the approach beyond viruses. Semin Cell Dev Biol 2017; 73:145-152. [PMID: 28774579 DOI: 10.1016/j.semcdb.2017.07.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/26/2017] [Accepted: 07/28/2017] [Indexed: 02/01/2023]
Abstract
The archetypical protein nanoshell is the capsid that surrounds viral genomes. These capsids protect the viral RNA or DNA and function as transport vehicle for their nucleic acid. The material properties of a variety of viral capsids have been probed by Atomic Force Microscopy. In particular nanoindentation measurements revealed the complex mechanics of these shells and the intricate interplay of the capsid with its genomic content. Furthermore, effects of capsid protein mutations, capsid maturation and the effect of environmental changes have been probed. In addition, biological questions have been addressed by AFM nanoindentation of viruses and a direct link between mechanics and infectivity has been revealed. Recently, non-viral protein nanoshells have come under intense scrutiny and now the nanoindentation approach has been expanded to such particles as well. Both natural as well as engineered non-viral protein shells have been probed by this technique. Next to the material properties of viruses, therefor also the mechanics of encapsulins, carboxysomes, vault particles, lumazine synthase and artificial protein nanoshells is discussed here.
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23
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Zeng C, Hernando-Pérez M, Dragnea B, Ma X, van der Schoot P, Zandi R. Contact Mechanics of a Small Icosahedral Virus. PHYSICAL REVIEW LETTERS 2017; 119:038102. [PMID: 28777631 DOI: 10.1103/physrevlett.119.038102] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 06/07/2023]
Abstract
A virus binding to a surface causes stress of the virus cage near the contact area. Here, we investigate the potential role of substrate-induced structural perturbation in the mechanical response of virus particles to adsorption. This is particularly relevant to the broad category of viruses stabilized by weak noncovalent interactions. We utilize atomic force microscopy to measure height distributions of the brome mosaic virus upon adsorption from solution on atomically flat substrates and present a continuum model that captures our observations and provides estimates of elastic properties and of the interfacial energy of the virus, without recourse to indentation.
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Affiliation(s)
- Cheng Zeng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Xiang Ma
- Department of Chemistry, Idaho State University, Pocatello, Idaho 83209, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California at Riverside, 900 University Avenue, Riverside, California 92521, USA
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