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López-Astacio RA, Adu OF, Lee H, Hafenstein SL, Parrish CR. The Structures and Functions of Parvovirus Capsids and Missing Pieces: the Viral DNA and Its Packaging, Asymmetrical Features, Nonprotein Components, and Receptor or Antibody Binding and Interactions. J Virol 2023; 97:e0016123. [PMID: 37367301 PMCID: PMC10373561 DOI: 10.1128/jvi.00161-23] [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: 06/28/2023] Open
Abstract
Parvoviruses are among the smallest and superficially simplest animal viruses, infecting a broad range of hosts, including humans, and causing some deadly infections. In 1990, the first atomic structure of the canine parvovirus (CPV) capsid revealed a 26-nm-diameter T=1 particle made up of two or three versions of a single protein, and packaging about 5,100 nucleotides of single-stranded DNA. Our structural and functional understanding of parvovirus capsids and their ligands has increased as imaging and molecular techniques have advanced, and capsid structures for most groups within the Parvoviridae family have now been determined. Despite those advances, significant questions remain unanswered about the functioning of those viral capsids and their roles in release, transmission, or cellular infection. In addition, the interactions of capsids with host receptors, antibodies, or other biological components are also still incompletely understood. The parvovirus capsid's apparent simplicity likely conceals important functions carried out by small, transient, or asymmetric structures. Here, we highlight some remaining open questions that may need to be answered to provide a more thorough understanding of how these viruses carry out their various functions. The many different members of the family Parvoviridae share a capsid architecture, and while many functions are likely similar, others may differ in detail. Many of those parvoviruses have not been experimentally examined in detail (or at all in some cases), so we, therefore, focus this minireview on the widely studied protoparvoviruses, as well as the most thoroughly investigated examples of adeno-associated viruses.
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Affiliation(s)
- Robert A. López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Oluwafemi F. Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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2
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Yuan B, Liu Y, Lv M, Sui Y, Hou S, Yang T, Belhadj Z, Zhou Y, Chang N, Ren Y, Sun C. Virus-like particle-based nanocarriers as an emerging platform for drug delivery. J Drug Target 2023; 31:433-455. [PMID: 36940208 DOI: 10.1080/1061186x.2023.2193358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
New nanocarrier technologies are emerging, and they have great potential for improving drug delivery, targeting efficiency, and bioavailability. Virus-like particles (VLPs) are natural nanoparticles from animal and plant viruses and bacteriophages. Hence, VLPs present several great advantages, such as morphological uniformity, biocompatibility, reduced toxicity, and easy functionalisation. VLPs can deliver many active ingredients to the target tissue and have great potential as a nanocarrier to overcome the limitations associated with other nanoparticles. This review will focus primarily on the construction and applications of VLPs, particularly as a novel nanocarrier to deliver active ingredients. Herein, the main methods for the construction, purification, and characterisation of VLPs, as well as various VLP-based materials used in delivery systems are summarised. The biological distribution of VLPs in drug delivery, phagocyte-mediated clearance, and toxicity are also discussed.
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Affiliation(s)
| | - Yang Liu
- School of Pharmaceutical Sciences, Zhengzhou University, No.100, Kexue Avenue, Zhengzhou 450001, China
| | - Meilin Lv
- Harbin Medical University-Daqing, Daqing 163319, China
| | - Yilei Sui
- Harbin Medical University-Daqing, Daqing 163319, China
| | - Shenghua Hou
- Harbin Medical University-Daqing, Daqing 163319, China
| | - Tinghui Yang
- Harbin Medical University-Daqing, Daqing 163319, China
| | - Zakia Belhadj
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yulong Zhou
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Naidan Chang
- Harbin Medical University-Daqing, Daqing 163319, China
| | - Yachao Ren
- Harbin Medical University-Daqing, Daqing 163319, China.,School of Chemistry and Chemical Engineering, Tianjin University of Technology, tianjin, 300000, China
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Moreno-Gutierrez DS, Del Toro-Ríos X, Martinez-Sulvaran NJ, Perez-Altamirano MB, Hernandez-Garcia A. Programming the Cellular Uptake of Protein-Based Viromimetic Nanoparticles for Enhanced Delivery. Biomacromolecules 2023; 24:1563-1573. [PMID: 36877960 DOI: 10.1021/acs.biomac.2c01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Viral mimetics is a noteworthy strategy to design efficient delivery systems without the safety drawbacks and engineering difficulties of modifying viral vectors. The triblock polypeptide CSB was previously designed de novo to self-assemble with DNA into nanocomplexes called artificial virus-like particles (AVLPs) due to their similarities to viral particles. Here, we show how we can incorporate new blocks into the CSB polypeptide to enhance its transfection without altering its self-assembly capabilities and the stability and morphology of the AVLPs. The addition of a short peptide (aurein) and/or a large protein (transferrin) to the AVLPs improved their internalization and specific targeting to cells by up to 11 times. Overall, these results show how we can further program the cellular uptake of the AVLPs with a wide range of bioactive blocks. This can pave the way to develop programmable and efficient gene delivery systems.
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Affiliation(s)
- David S Moreno-Gutierrez
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Ximena Del Toro-Ríos
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Natalia J Martinez-Sulvaran
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Mayra B Perez-Altamirano
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
| | - Armando Hernandez-Garcia
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, UNAM, 04510 Mexico City, Mexico
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Calvo-López T, Grueso E, Sánchez-Martínez C, Almendral JM. Intracellular virion traffic to the endosome driven by cell type specific sialic acid receptors determines parvovirus tropism. Front Microbiol 2023; 13:1063706. [PMID: 36756201 PMCID: PMC9899843 DOI: 10.3389/fmicb.2022.1063706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Parvoviruses are promising anticancer and gene therapy agents, but a deep knowledge of the entry process is crucial to exploit their therapeutic potential. We addressed this issue while attempting to retarget the oncolytic parvovirus minute virus of mice (MVMp) to the tumor vasculature. Residues at three functional domains of the icosahedral capsid were substituted by rational design with peptides competing with the vascular endothelial growth factor. Most substitutions impaired virus maturation, though some yielded infectious chimeric virions, and substitutions in a dimple at the twofold axis that allocates sialic acid (SIA) receptors altered viral tropism. One dimple-modified chimeric virion was efficiently attached as MVMp to α2-linked SIA moieties, but the infection was impaired by the binding to some inhibitory α2-3,-6,-8 SIA pseudoreceptors, which hampers intracellular virus traffic to the endosome in a cell type-dependent manner. Infectious from nonproductive traffic could be mechanistically discriminated by an endosomal drastic capsid structural transition comprising the cleavage of some VP2-Nt sequences and its associated VP1-Nt exposure. Correspondingly, neuraminidase removal of inhibitory SIA moieties enhanced the infection quantitatively, correlating to the restored virus traffic to the endosome and the extent of VP2-Nt cleavage/VP1-Nt exposure. This study illustrates (i) structural constraints to retarget parvoviruses with evolutionary adopted narrow grooves allocating small SIA receptors, (ii) the possibility to enhance parvovirus oncolysis by relaxing the glycan network on the cancer cell surface, and (iii) the major role played by the attachment to cell type-specific SIAs in the intracellular virus traffic to the endosome, which may determine parvovirus tropism and host range.
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Affiliation(s)
- Tania Calvo-López
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - Esther Grueso
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - Cristina Sánchez-Martínez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
| | - José M. Almendral
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain,*Correspondence: José M. Almendral ✉
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Pathak AK, Bandyopadhyay T. Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation. J Biomol Struct Dyn 2022; 40:11900-11913. [PMID: 34459706 DOI: 10.1080/07391102.2021.1969283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The capsid-like structure of the virus-based protein nanoparticles (NPs) can serve as bionanomaterials, with applications in biomedicines and nanotechnology. Release of packaged material from these nanocontainers is associated with subtle conformational changes of the NP structure, which in vitro, is readily accomplished by heating. Characterizing the structural changes as a function of temperature may provide fresh insights into nanomaterial/antiviral strategies. Here, we have calculated heat induced changes in the properties of an empty minute virus of mice particle using large-scale ≈ 3.0 × 106 all-atom molecular dynamics simulations. We focus on two heat induced structural changes of the NP, namely, dynamical transition (DT) and breathing transition (BT), both characterized by sudden and sharp change of measured parameters at temperatures, TDT and TBT, respectively. While DT is assessed by mean-square fluctuation of hydrogen atoms of the NP, BT is monitored through internal volume and permeation rate of water molecules through the NP. Both the transitions, resulting primarily from collective atomistic motion, are found to occur at temperatures widely separated from one another (TBT>TDT). The breathing motions, responsible for the translocation events of the packaged materials through the NP to kick off, are further probed by computing atomic resolution stresses from NVE simulations. Distribution of equilibrium atomistic stresses on the NP reveals a largely asymmetric nature and suggests structural breathing may actually represent large dynamic changes in the hotspot regions, far from the NP pores, which is in remarkable resemblance with recently conducted hydrogen-deuterium exchange coupled to mass spectrometry experiment. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
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Hillebrandt N, Vormittag P, Dietrich A, Hubbuch J. Process Monitoring Framework for Cross‐flow Diafiltration‐based Virus‐like Particle Disassembly: Tracing Product Properties and Filtration Performance. Biotechnol Bioeng 2022; 119:1522-1538. [DOI: 10.1002/bit.28063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Nils Hillebrandt
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 2 76131 Karlsruhe Baden‐Württemberg Germany
| | - Philipp Vormittag
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 2 76131 Karlsruhe Baden‐Württemberg Germany
| | - Annabelle Dietrich
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 2 76131 Karlsruhe Baden‐Württemberg Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 2 76131 Karlsruhe Baden‐Württemberg Germany
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7
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Capsid assembly is regulated by amino acid residues asparagine 47 and 48 in the VP2 protein of porcine parvovirus. Vet Microbiol 2020; 253:108974. [PMID: 33433338 DOI: 10.1016/j.vetmic.2020.108974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/26/2020] [Indexed: 11/20/2022]
Abstract
Porcine parvovirus (PPV) is a major cause of reproductive failure in swine and has caused substantial losses throughout the world. Viral protein 2 (VP2) of PPV is a major structural protein that can self-assemble into virus-like particles (VLP) with hemagglutination (HA) activity. In order to identify the essential residues involved in the mechanism of capsid assembly and to further understand the function of HA, we analyzed a series of deletion mutants and site-directed mutations within the N-terminal of VP2 using the Escherichia coli system. Our results showed that deletion of the first 47 amino acids from the N-terminal of the VP2 protein did not affect capsid assembly, and further truncation to residue 48 Asparagine (Asn, N) caused detrimental effects. Site-directed mutagenesis experiments demonstrated that residue 47Asn reduced the assembly efficiency of PPV VLP, while residue 48Asn destroyed the stability, hemagglutination, and self-assembly characteristics of the PPV VP2 protein. Results from native PAGE inferred that macromolecular polymers were critical intermediates of the VP2 protein during the capsid assembly process. Site-directed mutation at 48Asn did not affect the ability of monomers to form into oligomers, but destroyed the ability of oligomers to assemble into macromolecular particles, influencing both capsid assembly and HA activity. Our findings provide valuable information on the mechanisms of PPV capsid assembly and the possibility of chimeric VLP vaccine development by replacing the first 47 amino acids at the N-terminal of the VP2 protein.
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Thadani NN, Zhou Q, Reyes Gamas K, Butler S, Bueno C, Schafer NP, Morcos F, Wolynes PG, Suh J. Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus. Biophys J 2020; 120:489-503. [PMID: 33359833 DOI: 10.1016/j.bpj.2020.12.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/08/2020] [Accepted: 12/08/2020] [Indexed: 01/03/2023] Open
Abstract
Adeno-associated virus (AAV) is a promising gene therapy vector because of its efficient gene delivery and relatively mild immunogenicity. To improve delivery target specificity, researchers use combinatorial and rational library design strategies to generate novel AAV capsid variants. These approaches frequently propose high proportions of nonforming or noninfective capsid protein sequences that reduce the effective depth of synthesized vector DNA libraries, thereby raising the discovery cost of novel vectors. We evaluated two computational techniques for their ability to estimate the impact of residue mutations on AAV capsid protein-protein interactions and thus predict changes in vector fitness, reasoning that these approaches might inform the design of functionally enriched AAV libraries and accelerate therapeutic candidate identification. The Frustratometer computes an energy function derived from the energy landscape theory of protein folding. Direct-coupling analysis (DCA) is a statistical framework that captures residue coevolution within proteins. We applied the Frustratometer to select candidate protein residues predicted to favor assembled or disassembled capsid states, then predicted mutation effects at these sites using the Frustratometer and DCA. Capsid mutants were experimentally assessed for changes in virus formation, stability, and transduction ability. The Frustratometer-based metric showed a counterintuitive correlation with viral stability, whereas a DCA-derived metric was highly correlated with virus transduction ability in the small population of residues studied. Our results suggest that coevolutionary models may be able to elucidate complex capsid residue-residue interaction networks essential for viral function, but further study is needed to understand the relationship between protein energy simulations and viral capsid metastability.
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Affiliation(s)
| | - Qin Zhou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas
| | | | - Susan Butler
- Department of Bioengineering, Rice University, Houston, Texas
| | - Carlos Bueno
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas; Center for Systems Biology, University of Texas at Dallas, Richardson, Texas; Department of Bioengineering, University of Texas at Dallas, Richardson, Texas
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, Rice University, Houston, Texas; Department of Biosciences, Rice University, Houston, Texas; Department of Physics, Rice University, Houston, Texas
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, Texas; Department of Biosciences, Rice University, Houston, Texas; Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas; Systems, Synthetic, and Physical Biology Program, Rice University, Houston, Texas.
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Adeno-Associated Virus (AAV) Capsid Stability and Liposome Remodeling During Endo/Lysosomal pH Trafficking. Viruses 2020; 12:v12060668. [PMID: 32575696 PMCID: PMC7354436 DOI: 10.3390/v12060668] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Adeno-associated viruses (AAVs) are small, non-pathogenic ssDNA viruses being used as therapeutic gene delivery vectors for the treatment of a variety of monogenic diseases. An obstacle to successful gene delivery is inefficient capsid trafficking through the endo/lysosomal pathway. This study aimed to characterize the AAV capsid stability and dynamics associated with this process for a select number of AAV serotypes, AAV1, AAV2, AAV5, and AAV8, at pHs representative of the early and late endosome, and the lysosome (6.0, 5.5, and 4.0, respectively). All AAV serotypes displayed thermal melt temperatures that varied with pH. The stability of AAV1, AAV2, and AAV8 increased in response to acidic conditions and then decreased at pH 4.0. In contrast, AAV5 demonstrated a consistent decrease in thermostability in response to acidification. Negative-stain EM visualization of liposomes in the presence of capsids at pH 5.5 or when heat shocked showed induced remodeling consistent with the externalization of the PLA2 domain of VP1u. These observations provide clues to the AAV capsid dynamics that facilitate successful infection. Finally, transduction assays revealed a pH and temperature dependence with low acidity and temperatures > 4 °C as detrimental factors.
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Rieser R, Penaud-Budloo M, Bouzelha M, Rossi A, Menzen T, Biel M, Büning H, Ayuso E, Winter G, Michalakis S. Intrinsic Differential Scanning Fluorimetry for Fast and Easy Identification of Adeno-Associated Virus Serotypes. J Pharm Sci 2020; 109:854-862. [DOI: 10.1016/j.xphs.2019.10.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/23/2019] [Accepted: 10/11/2019] [Indexed: 12/14/2022]
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Antiangiogenic Vascular Endothelial Growth Factor-Blocking Peptides Displayed on the Capsid of an Infectious Oncolytic Parvovirus: Assembly and Immune Interactions. J Virol 2019; 93:JVI.00798-19. [PMID: 31315994 DOI: 10.1128/jvi.00798-19] [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: 05/10/2019] [Accepted: 07/10/2019] [Indexed: 11/20/2022] Open
Abstract
As many tumor cells synthetize vascular endothelial growth factors (VEGF) that promote neo-vascularization and metastasis, frontline cancer therapies often administer anti-VEGF (α-VEGF) antibodies. To target the oncolytic parvovirus minute virus of mice (MVM) to the tumor vasculature, we studied the functional tolerance, evasion of neutralization, and induction of α-VEGF antibodies of chimeric viruses in which the footprint of a neutralizing monoclonal antibody within the 3-fold capsid spike was replaced by VEGF-blocking peptides: P6L (PQPRPL) and A7R (ATWLPPR). Both peptides allowed viral genome replication and nuclear translocation of chimeric capsid subunits. MVM-P6L efficiently propagated in culture, exposing the heterologous peptide on the capsid surface, and evaded neutralization by the anti-spike monoclonal antibody. In contrast, MVM-A7R yielded low infectious titers and was poorly recognized by an α-A7R monoclonal antibody. MVM-A7R showed a deficient assembly pattern, suggesting that A7R impaired a transitional configuration that the subunits must undergo in the 3-fold axis to close up the capsid shell. The MVM-A7R chimeric virus consistently evolved in culture into a mutant carrying the P6Q amino acid substitution within the A7R sequence, which restored normal capsid assembly and infectivity. Consistent with this finding, anti-native VEGF antibodies were induced in mice by a single injection of MVM-A7R empty capsids, but not by MVM-A7R virions. This fundamental study provides insights to endow an infectious parvovirus with immune antineovascularization and evasion capacities by replacing an antibody footprint in the capsid 3-fold axis with VEGF-blocking peptides, and it also illustrates the evolutionary capacity of single-stranded DNA (ssDNA) viruses to overcome engineered capsid structural restrictions.IMPORTANCE Targeting the VEGF signaling required for neovascularization by vaccination with chimeric capsids of oncolytic viruses may boost therapy for solid tumors. VEGF-blocking peptides (VEbp) engineered in the capsid 3-fold axis endowed the infectious parvovirus MVM with the ability to induce α-VEGF antibodies without adjuvant and to evade neutralization by MVM-specific antibodies. However, these properties may be compromised by structural restraints that the capsid imposes on the peptide configuration and by misassembly caused by the heterologous peptides. Significantly, chimeric MVM-VEbp resolved the structural restrictions by selecting mutations within the engineered peptides that restored efficient capsid assembly. These data show the promise of antineovascularization vaccines using chimeric VEbp-icosahedral capsids of oncolytic viruses but also raise safety concerns regarding the genetic stability of manipulated infectious parvoviruses in cancer and gene therapies.
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Medrano M, Valbuena A, Rodríguez-Huete A, Mateu MG. Structural determinants of mechanical resistance against breakage of a virus-based protein nanoparticle at a resolution of single amino acids. NANOSCALE 2019; 11:9369-9383. [PMID: 31041970 DOI: 10.1039/c9nr01935a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Virus particles and other protein-based supramolecular complexes have a vast nanotechnological potential. However, protein nanostructures are "soft" materials prone to disruption by force. Whereas some non-biological nanoparticles (NPs) may be stronger, for certain applications protein- and virus-based NPs have potential advantages related to their structure, self-assembly, production, engineering, and/or inbuilt functions. Thus, it may be desirable to acquire the knowledge needed to engineer protein-based nanomaterials with a higher strength against mechanical breakage. Here we have used the capsid of the minute virus of mice to experimentally identify individual chemical groups that determine breakage-related properties of a virus particle. Individual amino acid side chains that establish interactions between building blocks in the viral particle were truncated using protein engineering. Indentation experiments using atomic force microscopy were carried out to investigate the role of each targeted side chain in determining capsid strength and brittleness, by comparing the maximum force and deformation each modified capsid withstood before breaking apart. Side chains with major roles in determining capsid strength against breakage included polar groups located in solvent-exposed positions, and did not generally correspond with those previously identified as determinants of mechanical stiffness. In contrast, apolar side chains buried along the intersubunit interfaces that generally determined capsid stiffness had, at most, a minor influence on strength against disruption. Whereas no correlated variations between strength and either stiffness or brittleness were found, brittleness and stiffness were quantitatively correlated. Implications for developing robust protein-based NPs and for acquiring a deeper physics-based perspective of viruses are discussed.
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Affiliation(s)
- María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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Systematic analysis of biological roles of charged amino acid residues located throughout the structured inner wall of a virus capsid. Sci Rep 2018; 8:9543. [PMID: 29934575 PMCID: PMC6015035 DOI: 10.1038/s41598-018-27749-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/01/2018] [Indexed: 12/31/2022] Open
Abstract
Structure-based mutational analysis of viruses is providing many insights into the relationship between structure and biological function of macromolecular complexes. We have systematically investigated the individual biological roles of charged residues located throughout the structured capsid inner wall (outside disordered peptide segments) of a model spherical virus, the minute virus of mice (MVM). The functional effects of point mutations that altered the electrical charge at 16 different positions at the capsid inner wall were analyzed. The results revealed that MVM capsid self-assembly is rather tolerant to point mutations that alter the number and distribution of charged residues at the capsid inner wall. However, mutations that either increased or decreased the number of positive charges around capsid-bound DNA segments reduced the thermal resistance of the virion. Moreover, mutations that either removed or changed the positions of negatively charged carboxylates in rings of acidic residues around capsid pores were deleterious by precluding a capsid conformational transition associated to through-pore translocation events. The results suggest that number, distribution and specific position of electrically charged residues across the inner wall of a spherical virus may have been selected through evolution as a compromise between several different biological requirements.
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Gil-Ranedo J, Hernando E, Valle N, Riolobos L, Maroto B, Almendral JM. Differential phosphorylation and n-terminal configuration of capsid subunits in parvovirus assembly and viral trafficking. Virology 2018. [PMID: 29524834 DOI: 10.1016/j.virol.2018.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The T1 parvovirus Minute Virus of Mice (MVM) was used to study the roles that phosphorylation and N-terminal domains (Nt) configuration of capsid subunits may play in icosahedral nuclear viruses assembly. In synchronous MVM infection, capsid subunits newly assembled as two types of cytoplasmic trimeric intermediates (3VP2, and 1VP1:2VP2) harbored a VP1 phosphorylation level fivefold higher than that of VP2, and hidden Nt. Upon nuclear translocation at S phase, VP1-Nt became exposed in the heterotrimer and subsequent subviral assembly intermediates. Empty capsid subunits showed a phosphorylation level restored to VP1:VP2 stoichiometry, and the Nt concealed in their interior. However ssDNA-filled virus maturing at S/G2 lacked VP1 phosphorylation and one major VP2 phosphopeptide, and exposed VP2-Nt. Endosomal VP2-Nt cleavage resulted in VP3 subunits devoid of any phospholabel, implying that incoming viral particles specifically harbor a low phosphorylation status. Phosphorylation provides a mechanistic coupling of parvovirus nuclear assembly to the cell cycle.
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Affiliation(s)
- Jon Gil-Ranedo
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
| | - Eva Hernando
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
| | - Noelia Valle
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
| | - Laura Riolobos
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
| | - Beatriz Maroto
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
| | - José M Almendral
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain.
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15
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Ilyas M, Mietzsch M, Kailasan S, Väisänen E, Luo M, Chipman P, Smith JK, Kurian J, Sousa D, McKenna R, Söderlund-Venermo M, Agbandje-McKenna M. Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy. Viruses 2018; 10:E22. [PMID: 29300333 PMCID: PMC5795435 DOI: 10.3390/v10010022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/18/2017] [Accepted: 12/28/2017] [Indexed: 11/29/2022] Open
Abstract
Bufavirus strain 1 (BuV1), a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65-73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI), α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.
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Affiliation(s)
- Maria Ilyas
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Shweta Kailasan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Elina Väisänen
- Department of Virology, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), University of Helsinki, FIN-00014 Helsinki, Finland.
| | - Mengxiao Luo
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - J Kennon Smith
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Justin Kurian
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Duncan Sousa
- Biological Science Imaging Resource, Department of Biological Sciences, The Florida State University, 89 Chieftan Way, Rm 119, Tallahassee, FL 32306, USA.
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Maria Söderlund-Venermo
- Department of Virology, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), University of Helsinki, FIN-00014 Helsinki, Finland.
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
- Center for Structural Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
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16
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Guerra P, Valbuena A, Querol-Audí J, Silva C, Castellanos M, Rodríguez-Huete A, Garriga D, Mateu MG, Verdaguer N. Structural basis for biologically relevant mechanical stiffening of a virus capsid by cavity-creating or spacefilling mutations. Sci Rep 2017; 7:4101. [PMID: 28642465 PMCID: PMC5481337 DOI: 10.1038/s41598-017-04345-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/12/2017] [Indexed: 11/26/2022] Open
Abstract
Recent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics. To provide atomic-resolution insights into biologically relevant changes in virus capsid mechanics, we have determined by X-ray crystallography the structural effects of deleterious, mechanically stiffening mutations around the capsid pores. Data show that the cavity-creating N170A mutation at the pore wall does not induce any dramatic structural change around the pores, but instead generates subtle rearrangements that propagate throughout the capsid, resulting in a more compact, less flexible structure. Analysis of the spacefilling L172W mutation revealed the same relationship between increased stiffness and compacted capsid structure. Implications for understanding connections between virus mechanics, structure, dynamics and infectivity, and for engineering modified virus-based nanoparticles, are discussed.
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Affiliation(s)
- Pablo Guerra
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Jordi Querol-Audí
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Cristina Silva
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Damià Garriga
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain.
| | - Nuria Verdaguer
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (CSIC). Parc Científic de Barcelona, Baldiri i Reixac 15, E-08028, Barcelona, Spain.
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17
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Pacouret S, Bouzelha M, Shelke R, Andres-Mateos E, Xiao R, Maurer A, Mevel M, Turunen H, Barungi T, Penaud-Budloo M, Broucque F, Blouin V, Moullier P, Ayuso E, Vandenberghe LH. AAV-ID: A Rapid and Robust Assay for Batch-to-Batch Consistency Evaluation of AAV Preparations. Mol Ther 2017; 25:1375-1386. [PMID: 28427840 DOI: 10.1016/j.ymthe.2017.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are promising clinical candidates for therapeutic gene transfer, and a number of AAV-based drugs may emerge on the market over the coming years. To insure the consistency in efficacy and safety of any drug vial that reaches the patient, regulatory agencies require extensive characterization of the final product. Identity is a key characteristic of a therapeutic product, as it ensures its proper labeling and batch-to-batch consistency. Currently, there is no facile, fast, and robust characterization assay enabling to probe the identity of AAV products at the protein level. Here, we investigated whether the thermostability of AAV particles could inform us on the composition of vector preparations. AAV-ID, an assay based on differential scanning fluorimetry (DSF), was evaluated in two AAV research laboratories for specificity, sensitivity, and reproducibility, for six different serotypes (AAV1, 2, 5, 6.2, 8, and 9), using 67 randomly selected AAV preparations. In addition to enabling discrimination of AAV serotypes based on their melting temperatures, the obtained fluorescent fingerprints also provided information on sample homogeneity, particle concentration, and buffer composition. Our data support the use of AAV-ID as a reproducible, fast, and low-cost method to ensure batch-to-batch consistency in manufacturing facilities and academic laboratories.
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Affiliation(s)
- Simon Pacouret
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA; Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Mohammed Bouzelha
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Rajani Shelke
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Eva Andres-Mateos
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Ru Xiao
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Anna Maurer
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA; Biological and Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Mathieu Mevel
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Heikki Turunen
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Trisha Barungi
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Magalie Penaud-Budloo
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Frédéric Broucque
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Véronique Blouin
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Philippe Moullier
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Eduard Ayuso
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA; Department of Ophthalmology, Ocular Genomics Institute, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA; Schepens Eye Research Institute, 20 Staniford Street, Boston MA 02114, USA; Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
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18
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van de Waterbeemd M, Llauró A, Snijder J, Valbuena A, Rodríguez-Huete A, Fuertes MA, de Pablo PJ, Mateu MG, Heck AJR. Structural Analysis of a Temperature-Induced Transition in a Viral Capsid Probed by HDX-MS. Biophys J 2017; 112:1157-1165. [PMID: 28355543 PMCID: PMC5375139 DOI: 10.1016/j.bpj.2017.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 01/30/2023] Open
Abstract
Icosahedral viral capsids are made of a large number of symmetrically organized protein subunits whose local movements can be essential for infection. In the capsid of the minute virus of mice, events required for infection that involve translocation of peptides through capsid pores are associated with a subtle conformational change. In vitro, this change can be reversibly induced by overcoming the energy barrier through mild heating of the capsid, but little is known about the capsid regions involved in the process. Here, we use hydrogen-deuterium exchange coupled to mass spectrometry to analyze the dynamics of the minute virus of mice capsid at increasing temperatures. Our results indicate that the transition associated with peptide translocation involves the structural rearrangement of regions distant from the capsid pores. These alterations are reflected in an increased dynamics of some secondary-structure elements in the capsid shell from which spikes protrude, and a decreased dynamics in the long intertwined loops that form the large capsid spikes. Thus, the translocation events through capsid pores involve a global conformational rearrangement of the capsid and a complex alteration of its equilibrium dynamics. This study additionally demonstrates the potential of hydrogen-deuterium exchange coupled to mass spectrometry to explore in detail temperature-dependent structural dynamics in large macromolecular protein assemblies. Most importantly, it paves the way for undertaking novel studies of the relationship between structure, dynamics, and biological function in virus particles and other large protein cages.
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Affiliation(s)
- Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Centre, Utrecht, the Netherlands
| | - Aida Llauró
- Department of Physics of the Condensed Matter, Universidad Autónoma de Madrid, Madrid, Spain
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Centre, Utrecht, the Netherlands
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Angel Fuertes
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Pedro J de Pablo
- Department of Physics of the Condensed Matter, Universidad Autónoma de Madrid, Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Netherlands Proteomics Centre, Utrecht, the Netherlands.
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19
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Carrillo PJP, Medrano M, Valbuena A, Rodríguez-Huete A, Castellanos M, Pérez R, Mateu MG. Amino Acid Side Chains Buried along Intersubunit Interfaces in a Viral Capsid Preserve Low Mechanical Stiffness Associated with Virus Infectivity. ACS NANO 2017; 11:2194-2208. [PMID: 28117975 DOI: 10.1021/acsnano.6b08549] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule experimental techniques and theoretical approaches reveal that important aspects of virus biology can be understood in biomechanical terms at the nanoscale. A detailed knowledge of the relationship in virus capsids between small structural changes caused by single-point mutations and changes in mechanical properties may provide further physics-based insights into virus function; it may also facilitate the engineering of viral nanoparticles with improved mechanical behavior. Here, we used the minute virus of mice to undertake a systematic experimental study on the contribution to capsid stiffness of amino acid side chains at interprotein interfaces and the specific noncovalent interactions they establish. Selected side chains were individually truncated by introducing point mutations to alanine, and the effects on local and global capsid stiffness were determined using atomic force microscopy. The results revealed that, in the natural virus capsid, multiple, mostly hydrophobic, side chains buried along the interfaces between subunits preserve a comparatively low stiffness of most (S2 and S3) regions. Virtually no point mutation tested substantially reduced stiffness, whereas most mutations increased stiffness of the S2/S3 regions. This stiffening was invariably associated with reduced virus yields during cell infection. The experimental evidence suggests that a comparatively low stiffness at S3/S2 capsid regions may have been biologically selected because it facilitates capsid assembly, increasing infectious virus yields. This study demonstrated also that knowledge of individual amino acid side chains and biological pressures that determine the physical behavior of a protein nanoparticle may be used for engineering its mechanical properties.
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Affiliation(s)
- Pablo José P Carrillo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Rebeca Pérez
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , c/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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20
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Parvovirus Capsid Structures Required for Infection: Mutations Controlling Receptor Recognition and Protease Cleavages. J Virol 2017; 91:JVI.01871-16. [PMID: 27847360 DOI: 10.1128/jvi.01871-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/01/2016] [Indexed: 01/11/2023] Open
Abstract
Parvovirus capsids are small but complex molecular machines responsible for undertaking many of the steps of cell infection, genome packing, and cell-to-cell as well as host-to-host transfer. The details of parvovirus infection of cells are still not fully understood, but the processes must involve small changes in the capsid structure that allow the endocytosed virus to escape from the endosome, pass through the cell cytoplasm, and deliver the single-stranded DNA (ssDNA) genome to the nucleus, where viral replication occurs. Here, we examine capsid substitutions that eliminate canine parvovirus (CPV) infectivity and identify how those mutations changed the capsid structure or altered interactions with the infectious pathway. Amino acid substitutions on the exterior surface of the capsid (Gly299Lys/Ala300Lys) altered the binding of the capsid to transferrin receptor type 1 (TfR), particularly during virus dissociation from the receptor, but still allowed efficient entry into both feline and canine cells without successful infection. These substitutions likely control specific capsid structural changes resulting from TfR binding required for infection. A second set of changes on the interior surface of the capsid reduced viral infectivity by >100-fold and included two cysteine residues and neighboring residues. One of these substitutions, Cys270Ser, modulates a VP2 cleavage event found in ∼10% of the capsid proteins that also was shown to alter capsid stability. A neighboring substitution, Pro272Lys, significantly reduced capsid assembly, while a Cys273Ser change appeared to alter capsid transport from the nucleus. These mutants reveal additional structural details that explain cell infection processes of parvovirus capsids. IMPORTANCE Parvoviruses are commonly found in both vertebrate and invertebrate animals and cause widespread disease. They are also being developed as oncolytic therapeutics and as gene therapy vectors. Most functions involved in infection or transduction are mediated by the viral capsid, but the structure-function correlates of the capsids and their constituent proteins are still incompletely understood, especially in relation to identifying capsid processes responsible for infection and release from the cell. Here, we characterize the functional effects of capsid protein mutations that result in the loss of virus infectivity, giving a better understanding of the portions of the capsid that mediate essential steps in successful infection pathways and how they contribute to viral infectivity.
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21
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Medrano M, Fuertes MÁ, Valbuena A, Carrillo PJP, Rodríguez-Huete A, Mateu MG. Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid. J Am Chem Soc 2016; 138:15385-15396. [PMID: 27933931 DOI: 10.1021/jacs.6b07663] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.
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Affiliation(s)
- María Medrano
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Miguel Ángel Fuertes
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Pablo J P Carrillo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Alicia Rodríguez-Huete
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid , 28049 Madrid, Spain
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22
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Castellanos M, Carrillo PJP, Mateu MG. Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis. NANOSCALE 2015; 7:5654-5664. [PMID: 25744136 DOI: 10.1039/c4nr07046a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.
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Affiliation(s)
- Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid 28049, Spain.
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23
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A slender tract of glycine residues is required for translocation of the VP2 protein N-terminal domain through the parvovirus MVM capsid channel to initiate infection. Biochem J 2013; 455:87-94. [PMID: 23875612 DOI: 10.1042/bj20130503] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Viruses constitute paradigms to study conformational dynamics in biomacromolecular assemblies. Infection by the parvovirus MVM (minute virus of mice) requires a conformational rearrangement that involves the intracellular externalization through capsid channels of the 2Nt (N-terminal region of VP2). We have investigated the role in this process of conserved glycine residues in an extended glycine-rich tract located immediately after 2Nt. Based on the virus structure, residues with hydrophobic side chains of increasing volume were substituted for glycine residues 31 or 33. Mutations had no effect on capsid assembly or stability, but inhibited virus infectivity. All mutations, except those to alanine residues which had minor effects, impaired 2Nt externalization in nuclear maturing virions and in purified virions, to an extent that correlated with the side chain size. Different biochemical and biophysical analyses were consistent with this result. Importantly, all of the tested glycine residue replacements impaired the capacity of the virion to initiate infection, at ratios correlating with their restrictive effects on 2Nt externalization. Thus small residues within the evolutionarily conserved glycine-rich tract facilitate 2Nt externalization through the capsid channel, as required by this virus to initiate cell entry. The results demonstrate the exquisite dependence on geometric constraints of a biologically relevant translocation event in a biomolecular complex.
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Reduction of porcine parvovirus infectivity in the presence of protecting osmolytes. Antiviral Res 2013; 99:27-33. [DOI: 10.1016/j.antiviral.2013.04.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/21/2013] [Accepted: 04/24/2013] [Indexed: 11/19/2022]
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Neira JL. Fluorescence, circular dichroism and mass spectrometry as tools to study virus structure. Subcell Biochem 2013; 68:177-202. [PMID: 23737052 DOI: 10.1007/978-94-007-6552-8_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fluorescence and circular dichroism, as analytical spectroscopic techniques, and mass spectrometry as an analytical tool to determine the molecular mass, provide important biophysical approaches in structural virology. Although they do not provide atomic, or near-atomic, details as electron microscopy, X-ray crystallography or nuclear magnetic resonance spectroscopy can do, they do provide important insights into virus particle composition, structure, conformational stability and dynamics, assembly and maturation, and interactions with other viral and cellular biomolecules. They can be used also to investigate the molecular determinants of virus particle structure and properties, and the changes induced in them by external factors. In this chapter, I describe the physical bases of these three techniques, and some examples on how they have helped us to understand virus particle structure and physicochemical properties.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain,
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Bustamante N, Rico-Lastres P, García E, García P, Menéndez M. Thermal stability of Cpl-7 endolysin from the streptococcus pneumoniae bacteriophage Cp-7; cell wall-targeting of its CW_7 motifs. PLoS One 2012; 7:e46654. [PMID: 23056389 PMCID: PMC3466307 DOI: 10.1371/journal.pone.0046654] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/02/2012] [Indexed: 11/28/2022] Open
Abstract
Endolysins comprise a novel class of selective antibacterials refractory to develop resistances. The Cpl-7 endolysin, encoded by the Streptococcus pneumoniae bacteriophage Cp-7, consists of a catalytic module (CM) with muramidase activity and a cell wall-binding module (CWBM) made of three fully conserved CW_7 repeats essential for activity. Firstly identified in the Cpl-7 endolysin, CW_7 motifs are also present in a great variety of cell wall hydrolases encoded, among others, by human and live-stock pathogens. However, the nature of CW_7 receptors on the bacterial envelope remains unknown. In the present study, the structural stability of Cpl-7 and the target recognized by CW_7 repeats, relevant for exploitation of Cpl-7 as antimicrobial, have been analyzed, and transitions from the CM and the CWBM assigned, using circular dichroism and differential scanning calorimetry. Cpl-7 stability is maximum around 6.0-6.5, near the optimal pH for activity. Above pH 8.0 the CM becomes extremely unstable, probably due to deprotonation of the N-terminal amino-group, whereas the CWBM is rather insensitive to pH variation and its structural stabilization by GlcNAc-MurNAc-l-Ala-d-isoGln points to the cell wall muropeptide as the cell wall target recognized by the CW_7 repeats. Denaturation data also revealed that Cpl-7 is organized into two essentially independent folding units, which will facilitate the recombination of the CM and the CWBM with other catalytic domains and/or cell wall-binding motifs to yield new tailored chimeric lysins with higher bactericidal activities or new pathogen specificities.
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Affiliation(s)
- Noemí Bustamante
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Palma Rico-Lastres
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ernesto García
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Pedro García
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Mateu MG. Mechanical properties of viruses analyzed by atomic force microscopy: A virological perspective. Virus Res 2012; 168:1-22. [DOI: 10.1016/j.virusres.2012.06.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/05/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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Pérez-Berná AJ, Ortega-Esteban A, Menéndez-Conejero R, Winkler DC, Menéndez M, Steven AC, Flint SJ, de Pablo PJ, San Martín C. The role of capsid maturation on adenovirus priming for sequential uncoating. J Biol Chem 2012; 287:31582-95. [PMID: 22791715 DOI: 10.1074/jbc.m112.389957] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Adenovirus assembly concludes with proteolytic processing of several capsid and core proteins. Immature virions containing precursor proteins lack infectivity because they cannot properly uncoat, becoming trapped in early endosomes. Structural studies have shown that precursors increase the network of interactions maintaining virion integrity. Using different biophysical techniques to analyze capsid disruption in vitro, we show that immature virions are more stable than the mature ones under a variety of stress conditions and that maturation primes adenovirus for highly cooperative DNA release. Cryoelectron tomography reveals that under mildly acidic conditions mimicking the early endosome, mature virions release pentons and peripheral core contents. At higher stress levels, both mature and immature capsids crack open. The virus core is completely released from cracked capsids in mature virions, but it remains connected to shell fragments in the immature particle. The extra stability of immature adenovirus does not equate with greater rigidity, because in nanoindentation assays immature virions exhibit greater elasticity than the mature particles. Our results have implications for the role of proteolytic maturation in adenovirus assembly and uncoating. Precursor proteins favor assembly by establishing stable interactions with the appropriate curvature and preventing premature ejection of contents by tightly sealing the capsid vertices. Upon maturation, core organization is looser, particularly at the periphery, and interactions preserving capsid curvature are weakened. The capsid becomes brittle, and pentons are more easily released. Based on these results, we hypothesize that changes in core compaction during maturation may increase capsid internal pressure to trigger proper uncoating of adenovirus.
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Affiliation(s)
- Ana J Pérez-Berná
- Department of Macromolecular Structure, Centro Nacional de Biotecnología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Mechanical elasticity as a physical signature of conformational dynamics in a virus particle. Proc Natl Acad Sci U S A 2012; 109:12028-33. [PMID: 22797893 DOI: 10.1073/pnas.1207437109] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this study we test the hypothesis that mechanically elastic regions in a virus particle (or large biomolecular complex) must coincide with conformationally dynamic regions, because both properties are intrinsically correlated. Hypothesis-derived predictions were subjected to verification by using 19 variants of the minute virus of mice capsid. The structural modifications in these variants reduced, preserved, or restored the conformational dynamism of regions surrounding capsid pores that are involved in molecular translocation events required for virus infectivity. The mechanical elasticity of the modified capsids was analyzed by atomic force microscopy, and the results corroborated every prediction tested: Any mutation (or chemical cross-linking) that impaired a conformational rearrangement of the pore regions increased their mechanical stiffness. On the contrary, any mutation that preserved the dynamics of the pore regions also preserved their elasticity. Moreover, any pseudo-reversion that restored the dynamics of the pore regions (lost through previous mutation) also restored their elasticity. Finally, no correlation was observed between dynamics of the pore regions and mechanical elasticity of other capsid regions. This study (i) corroborates the hypothesis that local mechanical elasticity and conformational dynamics in a viral particle are intrinsically correlated; (ii) proposes that determination by atomic force microscopy of local mechanical elasticity, combined with mutational analysis, may be used to identify and study conformationally dynamic regions in virus particles and large biomolecular complexes; (iii) supports a connection between mechanical properties and biological function in a virus; (iv) shows that viral capsids can be greatly stiffened by protein engineering for nanotechnological applications.
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Sánchez-Martínez C, Grueso E, Carroll M, Rommelaere J, Almendral JM. Essential role of the unordered VP2 n-terminal domain of the parvovirus MVM capsid in nuclear assembly and endosomal enlargement of the virion fivefold channel for cell entry. Virology 2012; 432:45-56. [PMID: 22727830 DOI: 10.1016/j.virol.2012.05.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 04/24/2012] [Accepted: 05/24/2012] [Indexed: 11/29/2022]
Abstract
The unordered N-termini of parvovirus capsid proteins (Nt) are translocated through a channel at the icosahedral five-fold axis to serve for virus traffick. Heterologous peptides were genetically inserted at the Nt of MVM to study their functional tolerance to manipulations. Insertion of a 5T4-single-chain antibody at VP2-Nt (2Nt) yielded chimeric capsid subunits failing to enter the nucleus. The VEGFR2-binding peptide (V1) inserted at both 2Nt and VP1-Nt efficiently assembled in virions, but V1 disrupted VP1 and VP2 entry functions. The VP2 defect correlated with restricted externalization of V1-2Nt out of the coat. The specific infectivity of MVM and wtVP-pseudotyped mosaic MVM-V1 virions, upon heating and/or partial 2Nt cleavage, demonstrated that some 2Nt domains become intracellularly translocated out of the virus shell and cleaved to initiate entry. The V1 insertion defines a VP2-driven endosomal enlargement of the channel as an essential structural rearrangement performed by the MVM virion to infect.
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Affiliation(s)
- Cristina Sánchez-Martínez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
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Castellanos M, Pérez R, Carrillo PJP, de Pablo PJ, Mateu MG. Mechanical disassembly of single virus particles reveals kinetic intermediates predicted by theory. Biophys J 2012; 102:2615-24. [PMID: 22713577 DOI: 10.1016/j.bpj.2012.04.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/30/2012] [Accepted: 04/17/2012] [Indexed: 01/22/2023] Open
Abstract
New experimental approaches are required to detect the elusive transient intermediates predicted by simulations of virus assembly or disassembly. Here, an atomic force microscope (AFM) was used to mechanically induce partial disassembly of single icosahedral T=1 capsids and virions of the minute virus of mice. The kinetic intermediates formed were imaged by AFM. The results revealed that induced disassembly of single minute-virus-of-mice particles is frequently initiated by loss of one of the 20 equivalent capsomers (trimers of capsid protein subunits) leading to a stable, nearly complete particle that does not readily lose further capsomers. With lower frequency, a fairly stable, three-fourths-complete capsid lacking one pentamer of capsomers and a free, stable pentamer were obtained. The intermediates most frequently identified (capsids missing one capsomer, capsids missing one pentamer of capsomers, and free pentamers of capsomers) had been predicted in theoretical studies of reversible capsid assembly based on thermodynamic-kinetic models, molecular dynamics, or oligomerization energies. We conclude that mechanical manipulation and imaging of simple virus particles by AFM can be used to experimentally identify kinetic intermediates predicted by simulations of assembly or disassembly.
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Affiliation(s)
- Milagros Castellanos
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Departamento de Física de la Materia Condensada C-III, Universidad Autónoma de Madrid, Madrid, Spain
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32
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Sánchez-Rodríguez SP, Münch-Anguiano L, Echeverría O, Vázquez-Nin G, Mora-Pale M, Dordick JS, Bustos-Jaimes I. Human parvovirus B19 virus-like particles: In vitro assembly and stability. Biochimie 2012; 94:870-8. [DOI: 10.1016/j.biochi.2011.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 12/07/2011] [Indexed: 12/29/2022]
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33
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Pérez R, Castellanos M, Rodríguez-Huete A, Mateu MG. Molecular Determinants of Self-Association and Rearrangement of a Trimeric Intermediate during the Assembly of a Parvovirus Capsid. J Mol Biol 2011; 413:32-40. [DOI: 10.1016/j.jmb.2011.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/26/2011] [Accepted: 08/09/2011] [Indexed: 10/17/2022]
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34
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Caldeira JC, Peabody DS. Thermal stability of RNA phage virus-like particles displaying foreign peptides. J Nanobiotechnology 2011; 9:22. [PMID: 21609437 PMCID: PMC3118325 DOI: 10.1186/1477-3155-9-22] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/24/2011] [Indexed: 02/01/2023] Open
Abstract
Background To be useful for genetic display of foreign peptides a viral coat protein must tolerate peptide insertions without major disruption of subunit folding and capsid assembly. The folding of the coat protein of RNA phage MS2 does not normally tolerate insertions in its AB-loop, but an engineered single-chain dimer readily accepts them as long as they are restricted to one of its two halves. Results Here we characterize the effects of peptide insertions on the thermal stabilities of MS2 virus-like particles (VLPs) displaying a variety of different peptides in one AB-loop of the coat protein single-chain dimer. These particles typically denature at temperatures around 5-10°C lower than unmodified VLPs. Even so, they are generally stable up to about 50°C. VLPs of the related RNA phage PP7 are cross-linked with intersubunit disulfide bonds and are therefore significantly more stable. An AB-loop insertion also reduces the stability of PP7 VLPs, but they only begin to denature above about 70°C. Conclusions VLPs assembled from MS2 single-chain dimer coat proteins with peptide insertions in one of their AB-loops are somewhat less stable than the wild-type particle, but still resist heating up to about 50°C. Because they possess disulfide cross-links, PP7-derived VLPs provide an alternate platform with even higher stability.
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Affiliation(s)
- Jerri C Caldeira
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, USA
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35
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Mateu MG. Virus engineering: functionalization and stabilization. Protein Eng Des Sel 2010; 24:53-63. [PMID: 20923881 DOI: 10.1093/protein/gzq069] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chemically and/or genetically engineered viruses, viral capsids and viral-like particles carry the promise of important and diverse applications in biomedicine, biotechnology and nanotechnology. Potential uses include new vaccines, vectors for gene therapy and targeted drug delivery, contrast agents for molecular imaging and building blocks for the construction of nanostructured materials and electronic nanodevices. For many of the contemplated applications, the improvement of the physical stability of viral particles may be critical to adequately meet the demanding physicochemical conditions they may encounter during production, storage and/or medical or industrial use. The first part of this review attempts to provide an updated general overview of the fast-moving, interdisciplinary virus engineering field; the second part focuses specifically on the modification of the physical stability of viral particles by protein engineering, an emerging subject that has not been reviewed before.
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Affiliation(s)
- Mauricio G Mateu
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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36
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Johnston IG, Louis AA, Doye JPK. Modelling the self-assembly of virus capsids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:104101. [PMID: 21389435 DOI: 10.1088/0953-8984/22/10/104101] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We use computer simulations to study a model, first proposed by Wales (2005 Phil. Trans. R. Soc. A 363 357), for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy landscape structure of the assembling system. Even though the model is strongly coarse-grained, it exhibits a number of features also observed in experiments, such as sigmoidal assembly dynamics, hysteresis in capsid formation and numerous kinetic traps. We also investigate the effect of macromolecular crowding on the assembly dynamics. Crowding agents generally reduce capsid yields at optimal conditions for non-crowded assembly, but may increase yields for parameter regimes away from the optimum. Finally, we generalize the model to a larger triangulation number T = 3, and observe assembly dynamics more complex than that seen for the original T = 1 model.
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Affiliation(s)
- Iain G Johnston
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK
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Abstract
The central role of Raf protein kinase isoforms in human cancer demands specific anti-Raf therapeutic inhibitors. Parvoviruses are currently used in experimental cancer therapy due to their natural oncotropism and lytic life cycle. In searching for mechanisms underlying parvovirus oncolysis, we found that trimers of the major structural protein (VP) of the parvovirus minute virus of mice (MVM), which have to be imported into the nucleus for capsid assembly, undergo phosphorylation by the Raf-1 kinase. Purified Raf-1 phosphorylated the capsid subunits in vitro to the two-dimensional pattern found in natural MVM infections. VP trimers isolated from mammalian cells translocated into the nucleus of digitonin-permeabilized human cells. In contrast, VP trimers isolated from insect cells, which are devoid of Raf-1, were neither phosphorylated nor imported into the mammalian nucleus. However, the coexpression of a constitutively active Raf-1 kinase in insect cells restored VP trimer phosphorylation and nuclear transport competence. In MVM-infected normal and transformed cells, Raf-1 inhibition resulted in cytoplasmic retention of capsid proteins, preventing their nuclear assembly and progeny virus maturation. The level of Raf-1 activity in cancer cells was consistent with the extent of VP specific phosphorylation and with the permissiveness to MVM infection. Thus, Raf-1 control of nuclear translocation of MVM capsid assembly intermediates provides a novel target for viral oncolysis. MVM may reinforce specific therapies against frequent human cancers with deregulated Raf signaling.
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Mellado MCM, Mena JA, Lopes A, Ramírez OT, Carrondo MJT, Palomares LA, Alves PM. Impact of physicochemical parameters on in vitro assembly and disassembly kinetics of recombinant triple-layered rotavirus-like particles. Biotechnol Bioeng 2009; 104:674-86. [PMID: 19623564 DOI: 10.1002/bit.22430] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Virus-like particles constitute potentially relevant vaccine candidates. Nevertheless, their behavior in vitro and assembly process needs to be understood in order to improve their yield and quality. In this study we aimed at addressing these issues and for that purpose triple- and double-layered rotavirus-like particles (TLP 2/6/7 and DLP 2/6, respectively) size and zeta potential were measured using dynamic light scattering at different physicochemical conditions, namely pH, ionic strength, and temperature. Both TLP and DLP were stable within a pH range of 3-7 and at 5-25 degrees C. Aggregation occurred at 35-45 degrees C and their disassembly became evident at 65 degrees C. The isoelectric points of TLP and DLP were 3.0 and 3.8, respectively. In vitro kinetics of TLP disassembly was monitored. Ionic strength, temperature, and the chelating agent employed determined disassembly kinetics. Glycerol (10%) stabilized TLP by preventing its disassembly. Disassembled TLP was able to reassemble by dialysis at high calcium conditions. VP7 monomers were added to DLP in the presence of calcium to follow in vitro TLP assembly kinetics; its assembly rate being mostly affected by pH. Finally, DLP and TLP were found to coexist under certain conditions as determined from all reaction products analyzed by capillary electrophoresis. Overall, these results contribute to the design of new strategies for the improvement of TLP yield and quality by reducing the VP7 detachment from TLP.
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Kinns H, Badelt-Lichtblau H, Egelseer EM, Sleytr UB, Howorka S. Identifying assembly-inhibiting and assembly-tolerant sites in the SbsB S-layer protein from Geobacillus stearothermophilus. J Mol Biol 2009; 395:742-53. [PMID: 19836402 DOI: 10.1016/j.jmb.2009.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Revised: 10/07/2009] [Accepted: 10/08/2009] [Indexed: 10/20/2022]
Abstract
Surface layer (S-layer) proteins self-assemble into two-dimensional crystalline lattices that cover the cell wall of all archaea and many bacteria. We have generated assembly-negative protein variants of high solubility that will facilitate high-resolution structure determination. Assembly-negative versions of the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2 were obtained using an insertion mutagenesis screen. The haemagglutinin epitope tag was inserted at 23 amino acid positions known to be located on the monomer protein surface from a previous cysteine accessibility screen. Limited proteolysis, circular dichroism, and fluorescence were used to probe whether the epitope insertion affected the secondary and tertiary structures of the monomer, while electron microscopy and size-exclusion chromatography were employed to examine proteins' ability to self-assemble. The screen not only identified assembly-compromised mutants with native fold but also yielded correctly folded, self-assembling mutants suitable for displaying epitopes for biomedical and biophysical applications, as well as cryo-electron microscopy imaging. Our study marks an important step in the analysis of the S-layer structure. In addition, the approach of concerted insertion and cysteine mutagenesis can likely be applied for other supramolecular assemblies.
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Affiliation(s)
- Helen Kinns
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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40
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Detecting small changes and additional peptides in the canine parvovirus capsid structure. J Virol 2008; 82:10397-407. [PMID: 18701590 DOI: 10.1128/jvi.00972-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Parvovirus capsids are assembled from multiple forms of a single protein and are quite stable structurally. However, in order to infect cells, conformational plasticity of the capsid is required and this likely involves the exposure of structures that are buried within the structural models. The presence of functional asymmetry in the otherwise icosahedral capsid has also been proposed. Here we examined the protein composition of canine parvovirus capsids and evaluated their structural variation and permeability by protease sensitivity, spectrofluorometry, and negative staining electron microscopy. Additional protein forms identified included an apparent smaller variant of the virus protein 1 (VP1) and a small proportion of a cleaved form of VP2. Only a small percentage of the proteins in intact capsids were cleaved by any of the proteases tested. The capsid susceptibility to proteolysis varied with temperature but new cleavages were not revealed. No global change in the capsid structure was observed by analysis of Trp fluorescence when capsids were heated between 40 degrees C and 60 degrees C. However, increased polarity of empty capsids was indicated by bis-ANS binding, something not seen for DNA-containing capsids. Removal of calcium with EGTA or exposure to pHs as low as 5.0 had little effect on the structure, but at pH 4.0 changes were revealed by proteinase K digestion. Exposure of viral DNA to the external environment started above 50 degrees C. Some negative stains showed increased permeability of empty capsids at higher temperatures, but no effects were seen after EGTA treatment.
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Abstract
The plant-infecting geminiviruses encapsidate their single-stranded DNA genome in characteristic twinned particles that are unique among viruses. These particles are formed by joining two incomplete T=1 icosahedra. African cassava mosaic virions were purified by density-gradient centrifugation from infected Nicotiana benthamiana plants and analysed for their stability with respect to pH changes and heat treatment by using electron microscopy. Negative staining and rotary shadowing revealed stable virions as well as isolated capsomeres between pH 4.0 and 8.5. At pH 9.0 and above, particles disintegrated, whereas they mainly aggregated at a pH below 6.0. Heating the preparations to 55 degrees C and above resulted in the complete loss of any discernible structure. A low proportion (approx. 10 %) of particles ejected their DNA within the pH range of 6.0-8.5. Most virions released their DNA at the top (15.9 %) or the shoulder (71.4 %) of the twin particles and only 12.7 % at the waist. Compared with the expected numbers of pentameric capsomeres at the top (9 %), the shoulder (45.5 %) or the waist (45.5 %), the results revealed a preferential DNA release from the top and shoulder of the geminate particle.
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Affiliation(s)
- Katharina Kittelmann
- Universität Stuttgart, Institute of Biology, Department of Molecular Biology and Plant Virology, Pfaffenwaldring 57, 70550 Stuttgart, Germany
| | - Holger Jeske
- Universität Stuttgart, Institute of Biology, Department of Molecular Biology and Plant Virology, Pfaffenwaldring 57, 70550 Stuttgart, Germany
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42
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Manipulation of the mechanical properties of a virus by protein engineering. Proc Natl Acad Sci U S A 2008; 105:4150-5. [PMID: 18334651 DOI: 10.1073/pnas.0708017105] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In a previous study, we showed that the DNA molecule within a spherical virus (the minute virus of mice) plays an architectural role by anisotropically increasing the mechanical stiffness of the virus. A finite element model predicted that this mechanical reinforcement is a consequence of the interaction between crystallographically visible, short DNA patches and the inner capsid wall. We have now tested this model by using protein engineering. Selected amino acid side chains have been truncated to specifically remove major interactions between the capsid and the visible DNA patches, and the effect of the mutations on the stiffness of virus particles has been measured using atomic force microscopy. The mutations do not affect the stiffness of the empty capsid; however, they significantly reduce the difference in stiffness between the DNA-filled virion and the empty capsid. The results (i) reveal that intermolecular interactions between individual chemical groups contribute to the mechanical properties of a supramolecular assembly and (ii) identify specific protein-DNA interactions as the origin of the anisotropic increase in the rigidity of a virus. This study also demonstrates that it is possible to control the mechanical properties of a protein nanoparticle by the rational application of protein engineering based on a mechanical model.
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Li Z, He J, Huang X, Dai A, Cheng L, Shao D, Zhang J. The truncated virus-like particles of C6/36 cell densovirus: implications for the assembly mechanism of brevidensovirus. Virus Res 2008; 132:248-52. [PMID: 18201787 DOI: 10.1016/j.virusres.2007.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 12/03/2007] [Accepted: 12/03/2007] [Indexed: 10/22/2022]
Abstract
The brevidensovirus is one of the smallest viruses in the world and the capsid of Aedes albopictus C6/36 cell densovirus (C6/36DNV) is the simplest and most compact capsid in brevidensovirus. To understand the assembly mechanism of icosahedral-virus capsid from this simplest model, we tried to express various lengths of virus proteins (VPs) of C6/36DNV in Bac-to-Bac system and evaluate their self-assembly capacities in insect Spodoptera frugiperda 9 (Sf9) cells. The result showed that the N-terminal GGSG sequence (residue 23-26), highly conserved glycine-rich region in Parvoviridae, and C-terminal GTGGVVTCMP (residue 344-353) were essential for capsid assembly, while the N-terminal nuclear localization signal, GTKRKR sequence (residue 15-20), was nonessential for the virus-like particles (VLPs) assembly, but did effect the formation of crystalline arrays in infected Sf9 cells. These information provided clues for how icosahedral-virus capsids formed and showed the potential of C6/36DNV-VLPs becoming a powerful nanoparticle vector.
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Affiliation(s)
- Zhihong Li
- Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
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Kaufmann B, López-Bueno A, Mateu MG, Chipman PR, Nelson CDS, Parrish CR, Almendral JM, Rossmann MG. Minute virus of mice, a parvovirus, in complex with the Fab fragment of a neutralizing monoclonal antibody. J Virol 2007; 81:9851-8. [PMID: 17626084 PMCID: PMC2045413 DOI: 10.1128/jvi.00775-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of virus-like particles of the lymphotropic, immunosuppressive strain of minute virus of mice (MVMi) in complex with the neutralizing Fab fragment of the mouse monoclonal antibody (MAb) B7 was determined by cryo-electron microscopy to 7-A resolution. The Fab molecule recognizes a conformational epitope at the vertex of a three-fold protrusion on the viral surface, thereby simultaneously engaging three symmetry-related viral proteins in binding. The location of the epitope close to the three-fold axis is consistent with the previous analysis of MVMi mutants able to escape from the B7 antibody. The binding site close to the symmetry axes sterically forbids the binding of more than one Fab molecule per spike. MAb as well as the Fab molecules inhibits the binding of the minute virus of mice (MVM) to permissive cells but can also neutralize MVM postattachment. This finding suggests that the interaction of B7 with three symmetry-related viral subunits at each spike hinders structural transitions in the viral capsid essential during viral entry.
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Affiliation(s)
- Bärbel Kaufmann
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA
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Grieger JC, Snowdy S, Samulski RJ. Separate basic region motifs within the adeno-associated virus capsid proteins are essential for infectivity and assembly. J Virol 2007; 80:5199-210. [PMID: 16699000 PMCID: PMC1472161 DOI: 10.1128/jvi.02723-05] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adeno-associated virus (AAV) is gaining momentum as a gene therapy vector for human applications. However, there remain impediments to the development of this virus as a vector. One of these is the incomplete understanding of the biology of the virus, including nuclear targeting of the incoming virion during initial infection, as well as assembly of progeny virions from structural components in the nucleus. Toward this end, we have identified four basic regions (BR) on the AAV2 capsid that represent possible nuclear localization sequence (NLS) motifs. Mutagenesis of BR1 ((120)QAKKRVL(126)) and BR2 ((140)PGKKRPV(146)) had minor effects on viral infectivity ( approximately 4- and approximately 10-fold, respectively), whereas BR3 ((166)PARKRLN(172)) and BR4 ((307)RPKRLN(312)) were found to be essential for infectivity and virion assembly, respectively. Mutagenesis of BR3, which is located in Vp1 and Vp2 capsid proteins, does not interfere with viral production or trafficking of intact AAV capsids to the nuclear periphery but does inhibit transfer of encapsidated DNA into the nucleus. Substitution of the canine parvovirus NLS rescued the BR3 mutant to wild-type (wt) levels, supporting the role of an AAV NLS motif. In addition, rAAV2 containing a mutant form of BR3 in Vp1 and a wt BR3 in Vp2 was found to be infectious, suggesting that the function of BR3 is redundant between Vp1 and Vp2 and that Vp2 may play a role in infectivity. Mutagenesis of BR4 was found to inhibit virion assembly in the nucleus of transfected cells. This affect was not completely due to the inefficient nuclear import of capsid subunits based on Western blot analysis. In fact, aberrant capsid foci were observed in the cytoplasm of transfected cells, compared to the wild type, suggesting a defect in early viral assembly or trafficking. Using three-dimensional structural analysis, the lysine- and arginine-to-asparagine change disrupts hydrogen bonding between these basic residues and adjacent beta strand glutamine residues that may prevent assembly of intact virions. Taken together, these data support that the BR4 domain is essential for virion assembly. Each BR was also found to be conserved in serotypes 1 to 11, suggesting that these regions are significant and function similarly in each serotype. This study establishes the importance of two BR motifs on the AAV2 capsid that are essential for infectivity and virion assembly.
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Affiliation(s)
- Joshua C Grieger
- Curriculum in Genetics and Molecular Biology, Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7352, USA
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Grieger JC, Johnson JS, Gurda-Whitaker B, Agbandje-McKenna M, Samulski RJ. Surface-exposed adeno-associated virus Vp1-NLS capsid fusion protein rescues infectivity of noninfectious wild-type Vp2/Vp3 and Vp3-only capsids but not that of fivefold pore mutant virions. J Virol 2007; 81:7833-43. [PMID: 17507473 PMCID: PMC1951316 DOI: 10.1128/jvi.00580-07] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the past 2 decades, significant effort has been dedicated to the development of adeno-associated virus (AAV) as a vector for human gene therapy. However, understanding of the virus with respect to the functional domains of the capsid remains incomplete. In this study, the goal was to further examine the role of the unique Vp1 N terminus, the N terminus plus the recently identified nuclear localization signal (NLS) (J. C. Grieger, S. Snowdy, and R. J. Samulski, J. Virol 80:5199-5210, 2006), and the virion pore at the fivefold axis in infection. We generated two Vp1 fusion proteins (Vp1 and Vp1NLS) linked to the 8-kDa chemokine domain of rat fractalkine (FKN) for the purpose of surface exposure upon assembly of the virion, as previously described (K. H. Warrington, Jr., O. S. Gorbatyuk, J. K. Harrison, S. R. Opie, S. Zolotukhin, and N. Muzyczka, J. Virol 78:6595-6609, 2004). The unique Vp1 N termini were found to be exposed on the surfaces of these capsids and maintained their phospholipase A2 (PLA2) activity, as determined by native dot blot Western and PLA2 assays, respectively. Incorporation of the fusions into AAV type 2 capsids lacking a wild-type Vp1, i.e., Vp2/Vp3 and Vp3 capsid only, increased infectivity by 3- to 5-fold (Vp1FKN) and 10- to 100-fold (Vp1NLSFKN), respectively. However, the surface-exposed fusions did not restore infectivity to AAV virions containing mutations at a conserved leucine (Leu336Ala, Leu336Cys, or Leu336Trp) located at the base of the fivefold pore. EM analyses suggest that Leu336 may play a role in global structural changes to the virion directly impacting downstream conformational changes essential for infectivity and not only have local effects within the pore, as previously suggested.
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Affiliation(s)
- Joshua C Grieger
- Gene Therapy Center, University of North Carolina at Chapel Hill, 7119 Thurston Bowles, CB 7352, Chapel Hill, NC 27599-7352, USA
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Ausar SF, Foubert TR, Hudson MH, Vedvick TS, Middaugh CR. Conformational Stability and Disassembly of Norwalk Virus-like Particles. J Biol Chem 2006; 281:19478-88. [PMID: 16675449 DOI: 10.1074/jbc.m603313200] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Greater than 99% of the Norwalk virus (NV) capsid consists of 180 copies of a single 58-kDa protein. Recombinantly expressed monomers self-assemble into virus-like particles (VLPs) with a well defined icosahedral structure. NV-VLPs are an appropriate vaccine antigen since the antigenic determinants of the parent virion are preserved. They also constitute very simple models to study the mechanisms of assembly and disassembly of viral capsids. This work examines the inherent stability of NV-VLPs over a range of pH and temperature values and provides detailed insight into structural perturbations that accompany disassembly. The NV-VLP structure was monitored using a variety of biophysical techniques including intrinsic and extrinsic fluorescence, high resolution second-derivative UV absorption spectroscopy, circular dichroism (CD), dynamic light scattering, differential scanning calorimetry, and direct observation employing transmission electron microscopy. The data demonstrate that NV-VLPs are highly stable over a pH range of 3-7 and up to 55 degrees C. At pH 8, however, reversible capsid dissociation was correlated with increased solvent exposure of tyrosine residues and subtle changes in secondary structure. Above 60 degrees C NV-VLPs undergo distinct phase transitions arising from secondary-, tertiary-, and quaternary-level protein structural perturbations. By combining the spectroscopic data employing a multidimensional eigenvector phase space approach, an empirical phase diagram for NV-VLP was constructed. This strategy of visualization provides a comprehensive description of the physical stability of NV-VLP over a broad range of pH and temperature. Complementary, differential scanning calorimetric analyses suggest that the two domains of VP1 unfold independently in a pH-dependent manner.
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Affiliation(s)
- Salvador F Ausar
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
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48
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Carreira A, Mateu MG. Structural Tolerance versus Functional Intolerance to Mutation of Hydrophobic Core Residues Surrounding Cavities in a Parvovirus Capsid. J Mol Biol 2006; 360:1081-93. [PMID: 16814321 DOI: 10.1016/j.jmb.2006.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 04/27/2006] [Accepted: 05/04/2006] [Indexed: 11/21/2022]
Abstract
The structural and functional relevance of amino acid residues surrounding cavities within the hydrophobic core of the protein subunits that form the capsid of parvoviruses has been investigated. Several of the evolutionarily conserved, hydrophobic residues that delimit these cavities in the capsid of the minute virus of mice were replaced by other hydrophobic residues that would affect the size and/or shape of the cavity. When four or more methylene-sized groups were introduced, or six or more groups removed, capsid assembly was drastically impaired. In contrast, the introduction or removal of up to three groups had no significant effect on capsid assembly or thermostability. However, many of these mutations affected a capsid conformational transition needed for viral infectivity. Replacement of some polar residues around the largest cavity showed that capsid assembly requires a carboxylate buried within this cavity, but both aspartate and glutamate are structurally accepted. Again, only the aspartate allowed the production of infectious viruses, because of a specific role in encapsidation of the viral genome. These observations provide evidence of a remarkable structural tolerance to mutation of the hydrophobic core of the protein subunits in a viral capsid, and of an involvement of core residues and internal cavities in capsid functions needed for infectivity.
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Affiliation(s)
- Aura Carreira
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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Pattenden LK, Middelberg APJ, Niebert M, Lipin DI. Towards the preparative and large-scale precision manufacture of virus-like particles. Trends Biotechnol 2006; 23:523-9. [PMID: 16084615 DOI: 10.1016/j.tibtech.2005.07.011] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 06/03/2005] [Accepted: 07/21/2005] [Indexed: 11/20/2022]
Abstract
Virus-like particles (VLPs) are of interest in vaccination, gene therapy and drug delivery, but their potential has yet to be fully realized. This is because existing laboratory processes, when scaled, do not easily give a compositionally and architecturally consistent product. Research suggests that new process routes might ultimately be based on chemical processing by self-assembly, involving the precision manufacture of precursor capsomeres followed by in vitro VLP self-assembly and scale-up to required levels. A synergistic interaction of biomolecular design and bioprocess engineering (i.e. biomolecular engineering) is required if these alternative process routes and, thus, the promise of new VLP products, are to be realized.
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Affiliation(s)
- Leonard K Pattenden
- Centre for Biomolecular Engineering, School of Engineering and The Australian Institute for Bioengineering and Nanotechnology, University of Queensland, QLD 4072, Australia
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50
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López-Bueno A, Villarreal LP, Almendral JM. Parvovirus variation for disease: a difference with RNA viruses? Curr Top Microbiol Immunol 2006; 299:349-70. [PMID: 16568906 DOI: 10.1007/3-540-26397-7_13] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Parvoviridae, a family of viruses with single-stranded DNA genomes widely spread from invertebrates to mammal and human hosts, display a remarkable evolutionary capacity uncommon in DNA genomes. Parvovirus populations show high genetic heterogeneity and large population sizes resembling the quasispecies found in RNA viruses. These viruses multiply in proliferating cells, causing acute, persistent or latent infections relying in the immunocompetence and developmental stage of the hosts. Some parvovirus populations in natural settings, such as carnivore autonomous parvoviruses or primate adeno associated virus, show a high degree of genetic heterogeneity. However, other parvoviruses such as the pathogenic B19 human erythrovirus or the porcine parvovirus, show little genetic variation, indicating different virus-host relationships. The Parvoviridae evolutionary potential in mammal infections has been modeled in the experimental system formed by the immunodeficient scid mouse infected by the minute virus of mice (MVM) under distinct immune and adaptive pressures. The sequence of viral genomes (close to 10(5) nucleotides) in emerging MVM pathogenic populations present in the organs of 26 mice showed consensus sequences not representing the complex distribution of viral clones and a high genetic heterogeneity (average mutation frequency 8.3 x 10(-4) substitutions/nt accumulated over 2-3 months). Specific amino acid changes, selected at a rate up to 1% in the capsid and in the NS2 nonstructural protein, endowed these viruses with new tropism and increased fitness. Further molecular analysis supported the notion that, in addition to immune pressures, the affinity of molecular interactions with cellular targets, as the Crml nuclear export receptor or the primary capsid receptor, as well as the adaptation to tissues enriched in proliferating cells, are major selective factors in the rapid parvovirus evolutionary dynamics.
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Affiliation(s)
- A López-Bueno
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
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