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Raviv U, Asor R, Shemesh A, Ginsburg A, Ben-Nun T, Schilt Y, Levartovsky Y, Ringel I. Insight into structural biophysics from solution X-ray scattering. J Struct Biol 2023; 215:108029. [PMID: 37741561 DOI: 10.1016/j.jsb.2023.108029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
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Affiliation(s)
- Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yaelle Schilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
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2
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Kler S, Zalk R, Upcher A, Kopatz I. Packaging of DNA origami in viral capsids: towards synthetic viruses. NANOSCALE 2022; 14:11535-11542. [PMID: 35861608 DOI: 10.1039/d2nr01316a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report a new type of nanoparticle, consisting of a nucleic acid core (>7500 nt) folded into a 35 nm DNA origami sphere, encapsulated by a capsid composed of all three SV40 virus capsid proteins. Compared to the prototype reported previously, whose capsid consists of VP1 only, the new nanoparticle closely adopts the unique intracellular pathway of the native SV40, suggesting that the proteins of the synthetic capsid retain their native viral functionality. Some of the challenges in the design of such near-future composite drugs destined for gene delivery are discussed.
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Affiliation(s)
| | - Ran Zalk
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
| | - Alexander Upcher
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
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HIRA Supports Hepatitis B Virus Minichromosome Establishment and Transcriptional Activity in Infected Hepatocytes. Cell Mol Gastroenterol Hepatol 2022; 14:527-551. [PMID: 35643233 PMCID: PMC9304598 DOI: 10.1016/j.jcmgh.2022.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022]
Abstract
BACKGROUND & AIMS Upon hepatitis B virus (HBV) infection, partially double-stranded viral DNA converts into a covalently closed circular chromatinized episomal structure (cccDNA). This form represents the long-lived genomic reservoir responsible for viral persistence in the infected liver. Although the involvement of host cell DNA damage response in cccDNA formation has been established, this work investigated the yet-to-be-identified histone dynamics on cccDNA during early phases of infection in human hepatocytes. METHODS Detailed studies of host chromatin-associated factors were performed in cell culture models of natural infection (ie, Na+-taurocholate cotransporting polypeptide (NTCP)-overexpressing HepG2 cells, HepG2hNTCP) and primary human hepatocytes infected with HBV, by cccDNA-specific chromatin immunoprecipitation and loss-of-function experiments during early kinetics of viral minichromosome establishment and onset of viral transcription. RESULTS Our results show that cccDNA formation requires the deposition of the histone variant H3.3 via the histone regulator A (HIRA)-dependent pathway. This occurs simultaneously with repair of the cccDNA precursor and independently from de novo viral protein expression. Moreover, H3.3 in its S31 phosphorylated form appears to be the preferential H3 variant found on transcriptionally active cccDNA in infected cultured cells and human livers. HIRA depletion after cccDNA pool establishment showed that HIRA recruitment is required for viral transcription and RNA production. CONCLUSIONS Altogether, we show a crucial role for HIRA in the interplay between HBV genome and host cellular machinery to ensure the formation and active transcription of the viral minichromosome in infected hepatocytes.
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Role of the DNA-Binding Protein pA104R in ASFV Genome Packaging and as a Novel Target for Vaccine and Drug Development. Vaccines (Basel) 2020; 8:vaccines8040585. [PMID: 33023005 PMCID: PMC7712801 DOI: 10.3390/vaccines8040585] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
The recent incursions of African swine fever (ASF), a severe, highly contagious, transboundary viral disease that affects members of the Suidae family, in Europe and China have had a catastrophic impact on trade and pig production, with serious implications for global food security. Despite efforts made over past decades, there is no vaccine or treatment available for preventing and controlling the ASF virus (ASFV) infection, and there is an urgent need to develop novel strategies. Genome condensation and packaging are essential processes in the life cycle of viruses. The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. pA104R is a highly conserved HU/IHF-like DNA-packaging protein identified in the ASFV nucleoid that appears to be profoundly involved in the spatial organization and packaging of the ASFV genome. Here, we briefly review the components of the ASFV packaging machinery, the structure, function, and phylogeny of pA104R, and its potential as a target for vaccine and drug development.
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Waltmann C, Asor R, Raviv U, Olvera de la Cruz M. Assembly and Stability of Simian Virus 40 Polymorphs. ACS NANO 2020; 14:4430-4443. [PMID: 32208635 PMCID: PMC7232851 DOI: 10.1021/acsnano.9b10004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of N = 12 pentamers (T = 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here "C-terminal ligands", which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the T = 1 feature the ability to dynamically rearrange and are thus termed "pseudo-closed". The N = 13 shell can even spontaneously "self-correct" by losing a pentamer and become a T = 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing via the pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.
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Affiliation(s)
- Curt Waltmann
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscale Science and Technology, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscale Science and Technology, The Hebrew University of Jerusalem, Edmond J Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Asor R, Schlicksup CJ, Zhao Z, Zlotnick A, Raviv U. Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly. J Am Chem Soc 2020; 142:7868-7882. [PMID: 32233479 PMCID: PMC7242811 DOI: 10.1021/jacs.0c01092] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There are ∼1030 possible intermediates on the assembly path from hepatitis B capsid protein dimers to the 120-dimer capsid. If every intermediate was tested, assembly would often get stuck in an entropic trap and essentially every capsid would follow a unique assembly path. Yet, capsids assemble rapidly with minimal trapped intermediates, a realization of the Levinthal paradox. To understand the fundamental mechanisms of capsid assembly, it is critical to resolve the early stages of the reaction. We have used time-resolved small angle X-ray scattering, which is sensitive to solute size and shape and has millisecond temporal resolution. Scattering curves were fit to a thermodynamically curated library of assembly intermediates, using the principle of maximum entropy. Maximum entropy also provides a physical rationale for the selection of species. We found that the capsid assembly pathway was exquisitely sensitive to initial assembly conditions. With the mildest conditions tested, the reaction appeared to be two-state from dimer to 120-dimer capsid with some dimers-of-dimers and trimers-of-dimers. In slightly more aggressive conditions, we observed transient accumulation of a decamer-of-dimers and the appearance of 90-dimer capsids. In conditions where there is measurable kinetic trapping, we found that highly diverse early intermediates accumulated within a fraction of a second and propagated into long-lived kinetically trapped states (≥90-mer). In all cases, intermediates between 35 and 90 subunits did not accumulate. These results are consistent with the presence of low barrier paths that connect early and late intermediates and direct the ultimate assembly path to late intermediates where assembly can be paused.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Christopher John Schlicksup
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Zhongchao Zhao
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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Asor R, Khaykelson D, Ben-Nun-Shaul O, Levi-Kalisman Y, Oppenheim A, Raviv U. pH stability and disassembly mechanism of wild-type simian virus 40. SOFT MATTER 2020; 16:2803-2814. [PMID: 32104873 PMCID: PMC7189960 DOI: 10.1039/c9sm02436k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Viruses are remarkable self-assembled nanobiomaterial-based machines, exposed to a wide range of pH values. Extreme pH values can induce dramatic structural changes, critical for the function of the virus nanoparticles, including assembly and genome uncoating. Tuning cargo-capsid interactions is essential for designing virus-based delivery systems. Here we show how pH controls the structure and activity of wild-type simian virus 40 (wtSV40) and the interplay between its cargo and capsid. Using cryo-TEM and solution X-ray scattering, we found that wtSV40 was stable between pH 5.5 and 9, and only slightly swelled with increasing pH. At pH 3, the particles aggregated, while capsid protein pentamers continued to coat the virus cargo but lost their positional correlations. Infectivity was only partly lost after the particles were returned to pH 7. At pH 10 or higher, the particles were unstable, lost their infectivity, and disassembled. Using time-resolved experiments we discovered that disassembly began by swelling of the particles, poking a hole in the capsid through which the genetic cargo escaped, followed by a slight shrinking of the capsids and complete disassembly. These findings provide insight into the fundamental intermolecular forces, essential for SV40 function, and for designing virus-based nanobiomaterials, including delivery systems and antiviral drugs.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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Ben-Nun-Shaul O, Srivastava R, Elgavish S, Gandhi S, Nevo Y, Benyamini H, Eden A, Oppenheim A. Empty SV40 capsids increase survival of septic rats by eliciting numerous host signaling networks that participate in a number of systemic functions. Oncotarget 2020; 11:574-588. [PMID: 32110278 PMCID: PMC7021236 DOI: 10.18632/oncotarget.27448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/26/2019] [Indexed: 11/25/2022] Open
Abstract
Sepsis is an excessive, dysregulated immune response to infection that activates inflammatory and coagulation cascades, which may lead to tissue injury, multiple organ dysfunction syndrome and death. Millions of individuals die annually of sepsis. To date, the only treatment available is antibiotics, drainage of the infection source when possible, and organ support in intensive care units. Numerous previous attempts to develop therapeutic treatments, directed at discreet targets of the sepsis cascade, could not cope with the complex pathophysiology of sepsis and failed. Here we describe a novel treatment, based on empty capsids of SV40 (nanocapsids - NCs). Studies in a severe rat sepsis model showed that pre-treatment by NCs led to a dramatic increase in survival, from zero to 75%. Transcript analyses (RNAseq) demonstrated that the NC treatment is a paradigm shift. The NCs affect multiple facets of biological functions. The affected genes are modified with time, adjusting to the recovery processes. The NCs effect on normal control rats was negligible. The study shows that the NCs are capable of coping with diseases with intricate pathophysiology. Further studies are needed to determine whether when applied after sepsis onset, the NCs still improve outcome.
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Affiliation(s)
| | | | - Sharona Elgavish
- Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Shashi Gandhi
- The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Yuval Nevo
- Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Hadar Benyamini
- Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Arieh Eden
- Department of Anesthesiology, Critical Care and Pain Medicine, Lady Davis Carmel Medical Center, Haifa, Israel
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9
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Kopatz I, Zalk R, Levi-Kalisman Y, Zlotkin-Rivkin E, Frank GA, Kler S. Packaging of DNA origami in viral capsids. NANOSCALE 2019; 11:10160-10166. [PMID: 30994643 DOI: 10.1039/c8nr10113b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here we show the encapsulation of 35 nm diameter, nearly-spherical, DNA origami by self-assembly of SV40-like (simian virus 40) particles. The self-assembly of this new type of nanoparticles is highly reproducible and efficient. The structure of these particles was determined by cryo-EM. The capsid forms a regular SV40 lattice of T = 7d icosahedral symmetry and the structural features of encapsulated DNA origami are fully visible. These particles are a promising biomaterial for use in various medical applications.
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10
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Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Fink L, Tekoah R, Levartovsky Y, Khaykelson D, Dharan R, Fellig A, Raviv U. D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. J Appl Crystallogr 2019; 52:219-242. [PMID: 31057345 PMCID: PMC6495662 DOI: 10.1107/s1600576718018046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/20/2018] [Indexed: 11/10/2022] Open
Abstract
This paper presents the computer program D+ (https://scholars.huji.ac.il/uriraviv/book/d-0), where the reciprocal-grid (RG) algorithm is implemented. D+ efficiently computes, at high-resolution, the X-ray scattering curves from complex structures that are isotropically distributed in random orientations in solution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures (containing over 100 protein subunits), a hybrid method can be used to avoid numerical artifacts. In the hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. This article describes how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a Protein Data Bank file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. A Python wrapper (https://scholars.huji.ac.il/uriraviv/book/python-api) is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, a large number of tests are presented. The results of D+ are compared with those of other programs when possible, and the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number is demonstrated. D+ and its source code are freely available for academic users and developers (https://bitbucket.org/uriraviv/public-dplus/src/master/).
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Affiliation(s)
- Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401 Jerusalem, Israel
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Lea Fink
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Roee Tekoah
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Daniel Khaykelson
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Amos Fellig
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
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11
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Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Fink L, Tekoah R, Levartovsky Y, Khaykelson D, Dharan R, Fellig A, Raviv U. D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. J Appl Crystallogr 2019; 52:219-242. [PMID: 31057345 DOI: 10.26434/chemrxiv.7012622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/20/2018] [Indexed: 05/23/2023] Open
Abstract
This paper presents the computer program D+ (https://scholars.huji.ac.il/uriraviv/book/d-0), where the reciprocal-grid (RG) algorithm is implemented. D+ efficiently computes, at high-resolution, the X-ray scattering curves from complex structures that are isotropically distributed in random orientations in solution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures (containing over 100 protein subunits), a hybrid method can be used to avoid numerical artifacts. In the hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. This article describes how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a Protein Data Bank file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. A Python wrapper (https://scholars.huji.ac.il/uriraviv/book/python-api) is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, a large number of tests are presented. The results of D+ are compared with those of other programs when possible, and the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number is demonstrated. D+ and its source code are freely available for academic users and developers (https://bitbucket.org/uriraviv/public-dplus/src/master/).
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Affiliation(s)
- Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401 Jerusalem, Israel
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Lea Fink
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Roee Tekoah
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Daniel Khaykelson
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Amos Fellig
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
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12
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Asor R, Khaykelson D, Ben-nun-Shaul O, Oppenheim A, Raviv U. Effect of Calcium Ions and Disulfide Bonds on Swelling of Virus Particles. ACS OMEGA 2019; 4:58-64. [PMID: 30729220 PMCID: PMC6356861 DOI: 10.1021/acsomega.8b02753] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/13/2018] [Indexed: 05/08/2023]
Abstract
Multivalent ions affect the structure and organization of virus nanoparticles. Wild-type simian virus 40 (wt SV40) is a nonenveloped virus belonging to the polyomavirus family, whose external diameter is 48.4 nm. Calcium ions and disulfide bonds are involved in the stabilization of its capsid and are playing a role in its assembly and disassembly pathways. Using solution small-angle X-ray scattering (SAXS), we found that the volume of wt SV40 swelled by about 17% when both of its calcium ions were chelated by ethylene glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid and its disulfide bonds were reduced by dithiothreitol. By applying osmotic stress, the swelling could be reversed. DNA-containing virus-like particles behaved in a similar way. The results provide insight into the structural role of calcium ions and disulfide bonds in holding the capsid proteins in compact conformation.
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Affiliation(s)
- Roi Asor
- Institute
of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 9190401, Israel
| | - Daniel Khaykelson
- Institute
of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 9190401, Israel
| | - Orly Ben-nun-Shaul
- Department
of Haematology, The Hebrew University-Hadassah
Medical School, Ein Karem, Jerusalem 91120, Israel
| | - Ariella Oppenheim
- Department
of Haematology, The Hebrew University-Hadassah
Medical School, Ein Karem, Jerusalem 91120, Israel
| | - Uri Raviv
- Institute
of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat
Ram, Jerusalem 9190401, Israel
- E-mail: . Phone: +972-2-6586030. Fax: +972-2-566-0425
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13
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Chechetkin VR, Lobzin VV. Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences. J Biomol Struct Dyn 2018; 37:2322-2338. [PMID: 30044190 DOI: 10.1080/07391102.2018.1479660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The assembly and maturation of viruses with icosahedral capsids must be coordinated with icosahedral symmetry. The icosahedral symmetry imposes also the restrictions on the cooperative specific interactions between genomic RNA/DNA and coat proteins that should be reflected in quasi-regular segmentation of viral genomic sequences. Combining discrete direct and double Fourier transforms, we studied the quasi-regular large-scale segmentation in genomic sequences of different ssRNA, ssDNA, and dsDNA viruses. The particular representatives included satellite tobacco mosaic virus (STMV) and the strains of satellite tobacco necrosis virus (STNV), STNV-C, STNV-1, STNV-2, Escherichia phages MS2, ϕX174, α3, and HK97, and Simian virus 40. In all their genomes, we found the significant quasi-regular segmentation of genomic sequences related to the virion assembly and the genome packaging within icosahedral capsid. We also found good correspondence between our results and available cryo-electron microscopy data on capsid structures and genome packaging in these viruses. Fourier analysis of genomic sequences provides the additional insight into mechanisms of hierarchical genome packaging and may be used for verification of the concepts of 3-fold or 5-fold intermediates in virion assembly. The results of sequence analysis should be taken into account at the choice of models and data interpretation. They also may be helpful for the development of antiviral drugs.
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Affiliation(s)
- V R Chechetkin
- a Engelhardt Institute of Molecular Biology of Russian Academy of Sciences , Moscow , Russia.,b Theoretical Department of Division for Perspective Investigations , Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI) , Moscow , Troitsk District , Russia
| | - V V Lobzin
- c School of Physics , University of Sydney , Sydney , NSW , Australia
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14
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Asor R, Ben-Nun-Shaul O, Oppenheim A, Raviv U. Crystallization, Reentrant Melting, and Resolubilization of Virus Nanoparticles. ACS NANO 2017; 11:9814-9824. [PMID: 28956913 PMCID: PMC6545118 DOI: 10.1021/acsnano.7b03131] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Crystallization is a fundamental and ubiquitous process that is well understood in the case of atoms or small molecules, but its outcome is still hard to predict in the case of nanoparticles or macromolecular complexes. Controlling the organization of virus nanoparticles into a variety of 3D supramolecular architectures is often done by multivalent ions and is of great interest for biomedical applications such as drug or gene delivery and biosensing, as well as for bionanomaterials and catalysis. In this paper, we show that slow dialysis, over several hours, of wild-type Simian Virus 40 (wt SV40) nanoparticle solution against salt solutions containing MgCl2, with or without added NaCl, results in wt SV40 nanoparticles arranged in a body cubic center crystal structure with Im3m space group, as a thermodynamic product, in coexistence with soluble wt SV40 nanoparticles. The nanoparticle crystals formed above a critical MgCl2 concentrations. Reentrant melting and resolubilization of the virus nanoparticles took place when the MgCl2 concentrations passed a second threshold. Using synchrotron solution X-ray scattering we determined the structures and the mass fraction of the soluble and crystal phases as a function of MgCl2 and NaCl concentrations. A thermodynamic model, which balances the chemical potentials of the Mg2+ ions in each of the possible states, explains our observations. The model reveals the mechanism of both the crystallization and the reentrant melting and resolubilization and shows that counterion entropy is the main driving force for both processes.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Orly Ben-Nun-Shaul
- Department of Haematology, Hebrew University Faculty of Medicine and Hadassah Medical Organization , Ein Karem, Jerusalem, 91120, Israel
| | - Ariella Oppenheim
- Department of Haematology, Hebrew University Faculty of Medicine and Hadassah Medical Organization , Ein Karem, Jerusalem, 91120, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
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15
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Marion S, San Martín C, Šiber A. Role of Condensing Particles in Polymer Confinement: A Model for Virus-Packed "Minichromosomes". Biophys J 2017; 113:1643-1653. [PMID: 29045859 PMCID: PMC5647577 DOI: 10.1016/j.bpj.2017.08.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/18/2017] [Accepted: 08/14/2017] [Indexed: 12/22/2022] Open
Abstract
Confined mixtures of a polymer and nonspecifically binding particles (condensers) are studied as models for viruses containing double-stranded DNA (polymer) and condensing proteins (particles). We explore a model in which all interactions between the packed content (polymer and particles) and its confinement are purely repulsive, with only a short-range attraction between the condensers and polymer to simulate binding. In the range of physical parameters applicable to viruses, the model predicts reduction of pressure in the system effected by the condensers, despite the reduction in free volume. Condensers are found to be interspersed throughout the spherical confinement and only partially wrapped in the polymer, which acts as an effective medium for the condenser interactions. Crowding of the viral interior influences the DNA and protein organization, producing a picture inconsistent with a chromatin-like, beads-on-a-string structure. The model predicts an organization of the confined interior compatible with experimental data on unperturbed adenoviruses and polyomaviruses, at the same time providing insight into the role of condensing proteins in the viral infectious cycles of related viral families.
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Affiliation(s)
- Sanjin Marion
- Center of Excellence for Advanced Materials and Sensing Devices, Institute of Physics, Zagreb, Croatia; Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - Carmen San Martín
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Antonio Šiber
- Center of Excellence for Advanced Materials and Sensing Devices, Institute of Physics, Zagreb, Croatia.
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16
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Schreiner S, Nassal M. A Role for the Host DNA Damage Response in Hepatitis B Virus cccDNA Formation-and Beyond? Viruses 2017; 9:v9050125. [PMID: 28531167 PMCID: PMC5454437 DOI: 10.3390/v9050125] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/12/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection puts more than 250 million people at a greatly increased risk to develop end-stage liver disease. Like all hepadnaviruses, HBV replicates via protein-primed reverse transcription of a pregenomic (pg) RNA, yielding an unusually structured, viral polymerase-linked relaxed-circular (RC) DNA as genome in infectious particles. Upon infection, RC-DNA is converted into nuclear covalently closed circular (ccc) DNA. Associating with cellular proteins into an episomal minichromosome, cccDNA acts as template for new viral RNAs, ensuring formation of progeny virions. Hence, cccDNA represents the viral persistence reservoir that is not directly targeted by current anti-HBV therapeutics. Eliminating cccDNA will thus be at the heart of a cure for chronic hepatitis B. The low production of HBV cccDNA in most experimental models and the associated problems in reliable cccDNA quantitation have long hampered a deeper understanding of cccDNA molecular biology. Recent advancements including cccDNA-dependent cell culture systems have begun to identify select host DNA repair enzymes that HBV usurps for RC-DNA to cccDNA conversion. While this list is bound to grow, it may represent just one facet of a broader interaction with the cellular DNA damage response (DDR), a network of pathways that sense and repair aberrant DNA structures and in the process profoundly affect the cell cycle, up to inducing cell death if repair fails. Given the divergent interactions between other viruses and the DDR it will be intriguing to see how HBV copes with this multipronged host system.
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Affiliation(s)
- Sabrina Schreiner
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, D-85764 Munich, Germany.
| | - Michael Nassal
- Dept. of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany.
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17
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Wu W, Newcomb WW, Cheng N, Aksyuk A, Winkler DC, Steven AC. Internal Proteins of the Procapsid and Mature Capsids of Herpes Simplex Virus 1 Mapped by Bubblegram Imaging. J Virol 2016; 90:5176-86. [PMID: 26984725 PMCID: PMC4859710 DOI: 10.1128/jvi.03224-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/09/2016] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED The herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. First, a procapsid is formed through coassembly of the surface shell with an inner scaffolding shell; then the procapsid matures via a major structural transformation, triggered by limited proteolysis of the scaffolding proteins. Three mature capsids are found in the nuclei of infected cells. A capsids are empty, B capsids retain a shrunken scaffolding shell, and C capsids-which develop into infectious virions-are filled with DNA and ostensibly have expelled the scaffolding shell. The possible presence of other internal proteins in C capsids has been moot as, in cryo-electron microscopy (cryo-EM), they would be camouflaged by the surrounding DNA. We have used bubblegram imaging to map internal proteins in all four capsids, aided by the discovery that the scaffolding protein is exceptionally prone to radiation-induced bubbling. We confirmed that this protein forms thick-walled inner shells in the procapsid and the B capsid. C capsids generate two classes of bubbles: one occupies positions beneath the vertices of the icosahedral surface shell, and the other is distributed throughout its interior. A likely candidate is the viral protease. A subpopulation of C capsids bubbles particularly profusely and may represent particles in which expulsion of scaffold and DNA packaging are incomplete. Based on the procapsid structure, we propose that the axial channels of hexameric capsomers afford the pathway via which the scaffolding protein is expelled. IMPORTANCE In addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are difficult to locate within the virion. A novel adaptation of cryo-EM based on detecting gas bubbles generated by radiation damage was used to localize internal proteins of HSV-1, yielding insights into how capsid maturation is regulated. The scaffolding protein, which forms inner shells in the procapsid and B capsid, is exceptionally bubbling-prone. In the mature DNA-filled C capsid, a previously undetected protein was found to underlie the icosahedral vertices: this is tentatively assigned as a storage form of the viral protease. We also observed a capsid species that appears to contain substantial amounts of scaffolding protein as well as DNA, suggesting that DNA packaging and expulsion of the scaffolding protein are coupled processes.
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Affiliation(s)
- Weimin Wu
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - William W Newcomb
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anastasia Aksyuk
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dennis C Winkler
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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18
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New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy. Structure 2016; 24:528-536. [PMID: 26996963 PMCID: PMC4826271 DOI: 10.1016/j.str.2016.02.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/22/2016] [Accepted: 02/17/2016] [Indexed: 11/22/2022]
Abstract
BK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins.
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19
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Teich EG, van Anders G, Klotsa D, Dshemuchadse J, Glotzer SC. Clusters of polyhedra in spherical confinement. Proc Natl Acad Sci U S A 2016; 113:E669-78. [PMID: 26811458 PMCID: PMC4760782 DOI: 10.1073/pnas.1524875113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dense particle packing in a confining volume remains a rich, largely unexplored problem, despite applications in blood clotting, plasmonics, industrial packaging and transport, colloidal molecule design, and information storage. Here, we report densest found clusters of the Platonic solids in spherical confinement, for up to [Formula: see text] constituent polyhedral particles. We examine the interplay between anisotropic particle shape and isotropic 3D confinement. Densest clusters exhibit a wide variety of symmetry point groups and form in up to three layers at higher N. For many N values, icosahedra and dodecahedra form clusters that resemble sphere clusters. These common structures are layers of optimal spherical codes in most cases, a surprising fact given the significant faceting of the icosahedron and dodecahedron. We also investigate cluster density as a function of N for each particle shape. We find that, in contrast to what happens in bulk, polyhedra often pack less densely than spheres. We also find especially dense clusters at so-called magic numbers of constituent particles. Our results showcase the structural diversity and experimental utility of families of solutions to the packing in confinement problem.
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Affiliation(s)
- Erin G Teich
- Applied Physics Program, University of Michigan, Ann Arbor, MI 48109
| | - Greg van Anders
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Daphne Klotsa
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Julia Dshemuchadse
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Sharon C Glotzer
- Applied Physics Program, University of Michigan, Ann Arbor, MI 48109; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109; Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
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20
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Schilt Y, Berman T, Wei X, Barenholz Y, Raviv U. Using solution X-ray scattering to determine the high-resolution structure and morphology of PEGylated liposomal doxorubicin nanodrugs. Biochim Biophys Acta Gen Subj 2016; 1860:108-19. [DOI: 10.1016/j.bbagen.2015.09.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/02/2015] [Accepted: 09/15/2015] [Indexed: 11/28/2022]
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21
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Ben-Nun T, Asor R, Ginsburg A, Raviv U. Solution X-ray Scattering Form-Factors with Arbitrary Electron Density Profiles and Polydispersity Distributions. Isr J Chem 2015. [DOI: 10.1002/ijch.201500037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tal Ben-Nun
- The Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
- Department of Computer Science; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Roi Asor
- The Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Avi Ginsburg
- The Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
- The Institute for Drug Research; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Uri Raviv
- The Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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22
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Turjeman K, Bavli Y, Kizelsztein P, Schilt Y, Allon N, Katzir TB, Sasson E, Raviv U, Ovadia H, Barenholz Y. Nano-Drugs Based on Nano Sterically Stabilized Liposomes for the Treatment of Inflammatory Neurodegenerative Diseases. PLoS One 2015; 10:e0130442. [PMID: 26147975 PMCID: PMC4492950 DOI: 10.1371/journal.pone.0130442] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/20/2015] [Indexed: 12/28/2022] Open
Abstract
The present study shows the advantages of liposome-based nano-drugs as a novel strategy of delivering active pharmaceutical ingredients for treatment of neurodegenerative diseases that involve neuroinflammation. We used the most common animal model for multiple sclerosis (MS), mice experimental autoimmune encephalomyelitis (EAE). The main challenges to overcome are the drugs’ unfavorable pharmacokinetics and biodistribution, which result in inadequate therapeutic efficacy and in drug toxicity (due to high and repeated dosage). We designed two different liposomal nano-drugs, i.e., nano sterically stabilized liposomes (NSSL), remote loaded with: (a) a “water-soluble” amphipathic weak acid glucocorticosteroid prodrug, methylprednisolone hemisuccinate (MPS) or (b) the amphipathic weak base nitroxide, Tempamine (TMN). For the NSSL-MPS we also compared the effect of passive targeting alone and of active targeting based on short peptide fragments of ApoE or of β-amyloid. Our results clearly show that for NSSL-MPS, active targeting is not superior to passive targeting. For the NSSL-MPS and the NSSL-TMN it was demonstrated that these nano-drugs ameliorate the clinical signs and the pathology of EAE. We have further investigated the MPS nano-drug’s therapeutic efficacy and its mechanism of action in both the acute and the adoptive transfer EAE models, as well as optimizing the perfomance of the TMN nano-drug. The highly efficacious anti-inflammatory therapeutic feature of these two nano-drugs meets the criteria of disease-modifying drugs and supports further development and evaluation of these nano-drugs as potential therapeutic agents for diseases with an inflammatory component.
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Affiliation(s)
- Keren Turjeman
- Laboratory of Membrane and Liposome Research, Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
| | - Yaelle Bavli
- Laboratory of Membrane and Liposome Research, Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Pablo Kizelsztein
- Laboratory of Membrane and Liposome Research, Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yaelle Schilt
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Nahum Allon
- Laboratory of Membrane and Liposome Research, Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | | - Efrat Sasson
- BioImage MRI Research & Consulting, Tel Aviv, Israel
| | - Uri Raviv
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Haim Ovadia
- Department of Neurology, Agnes Ginges Center for Human Neurogenetics, Hadassah University Hospital, Jerusalem, Israel
| | - Yechezkel Barenholz
- Laboratory of Membrane and Liposome Research, Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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23
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de Carvalho SJ, Metzler R, Cherstvy AG. Inverted critical adsorption of polyelectrolytes in confinement. SOFT MATTER 2015; 11:4430-4443. [PMID: 25940939 DOI: 10.1039/c5sm00635j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of surface coating applications, various complex formation phenomena, as well as in the context of cellular and viral biophysics. It has been a long-standing challenge in theoretical polymer physics; for realistic systems the quantitative understanding is however often achievable only by computer simulations. In this study, we present the findings of such extensive Monte-Carlo in silico experiments for polymer-surface adsorption in confined domains. We study the inverted critical adsorption of finite-length polyelectrolytes in three fundamental geometries: planar slit, cylindrical pore, and spherical cavity. The scaling relations extracted from simulations for the critical surface charge density σc-defining the adsorption-desorption transition-are in excellent agreement with our analytical calculations based on the ground-state analysis of the Edwards equation. In particular, we confirm the magnitude and scaling of σc for the concave interfaces versus the Debye screening length 1/κ and the extent of confinement a for these three interfaces for small κa values. For large κa the critical adsorption condition approaches the known planar limit. The transition between the two regimes takes place when the radius of surface curvature or half of the slit thickness a is of the order of 1/κ. We also rationalize how σc(κ) dependence gets modified for semi-flexible versus flexible chains under external confinement. We examine the implications of the chain length for critical adsorption-the effect often hard to tackle theoretically-putting an emphasis on polymers inside attractive spherical cavities. The applications of our findings to some biological systems are discussed, for instance the adsorption of nucleic acids onto the inner surfaces of cylindrical and spherical viral capsids.
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Affiliation(s)
- Sidney J de Carvalho
- Institute of Biosciences, Letters and Exact Sciences, Sao Paulo State University, 15054-000 Sao Jose do Rio Preto, Brazil.
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24
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Pérez-Berná AJ, Marion S, Chichón FJ, Fernández JJ, Winkler DC, Carrascosa JL, Steven AC, Šiber A, San Martín C. Distribution of DNA-condensing protein complexes in the adenovirus core. Nucleic Acids Res 2015; 43:4274-83. [PMID: 25820430 PMCID: PMC4417152 DOI: 10.1093/nar/gkv187] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 12/12/2014] [Accepted: 02/22/2015] [Indexed: 01/22/2023] Open
Abstract
Genome packing in adenovirus has long evaded precise description, since the viral dsDNA molecule condensed by proteins (core) lacks icosahedral order characteristic of the virus protein coating (capsid). We show that useful insights regarding the organization of the core can be inferred from the analysis of spatial distributions of the DNA and condensing protein units (adenosomes). These were obtained from the inspection of cryo-electron tomography reconstructions of individual human adenovirus particles. Our analysis shows that the core lacks symmetry and strict order, yet the adenosome distribution is not entirely random. The features of the distribution can be explained by modeling the condensing proteins and the part of the genome in each adenosome as very soft spheres, interacting repulsively with each other and with the capsid, producing a minimum outward pressure of ∼0.06 atm. Although the condensing proteins are connected by DNA in disrupted virion cores, in our models a backbone of DNA linking the adenosomes is not required to explain the experimental results in the confined state. In conclusion, the interior of an adenovirus infectious particle is a strongly confined and dense phase of soft particles (adenosomes) without a strictly defined DNA backbone.
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Affiliation(s)
- Ana J Pérez-Berná
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain NanoBiomedicine Initiative, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Sanjin Marion
- Institute of Physics, Bijenička cesta 46, HR-10000 Zagreb, Croatia
| | - F Javier Chichón
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain NanoBiomedicine Initiative, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - José J Fernández
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Dennis C Winkler
- Laboratory of Structural Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - José L Carrascosa
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain NanoBiomedicine Initiative, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Alasdair C Steven
- Laboratory of Structural Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Antonio Šiber
- Institute of Physics, Bijenička cesta 46, HR-10000 Zagreb, Croatia Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Carmen San Martín
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain NanoBiomedicine Initiative, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
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25
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Revisiting the genome packaging in viruses with lessons from the "Giants". Virology 2014; 466-467:15-26. [PMID: 24998349 DOI: 10.1016/j.virol.2014.06.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 11/23/2022]
Abstract
Genome encapsidation is an essential step in the life cycle of viruses. Viruses either use some of the most powerful ATP-dependent motors to compel the genetic material into the preformed capsid or make use of the positively charged proteins to bind and condense the negatively charged genome in an energy-independent manner. While the former is a hallmark of large DNA viruses, the latter is commonly seen in small DNA and RNA viruses. Discoveries of many complex giant viruses such as mimivirus, megavirus, pandoravirus, etc., belonging to the nucleo-cytoplasmic large DNA virus (NCLDV) superfamily have changed the perception of genome packaging in viruses. From what little we have understood so far, it seems that the genome packaging mechanism in NCLDVs has nothing in common with other well-characterized viral packaging systems such as the portal-terminase system or the energy-independent system. Recent findings suggest that in giant viruses, the genome segregation and packaging processes are more intricately coupled than those of other viral systems. Interestingly, giant viral packaging systems also seem to possess features that are analogous to bacterial and archaeal chromosome segregation. Although there is a lot of diversity in terms of host range, type of genome, and genome size among viruses, they all seem to use three major types of independent innovations to accomplish genome encapsidation. Here, we have made an attempt to comprehensively review all the known viral genome packaging systems, including the one that is operative in giant viruses, by proposing a simple and expanded classification system that divides the viral packaging systems into three large groups (types I-III) on the basis of the mechanism employed and the relatedness of the major packaging proteins. Known variants within each group have been further classified into subgroups to reflect their unique adaptations.
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26
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Kler S, Wang JCY, Dhason M, Oppenheim A, Zlotnick A. Scaffold properties are a key determinant of the size and shape of self-assembled virus-derived particles. ACS Chem Biol 2013; 8:2753-61. [PMID: 24093474 DOI: 10.1021/cb4005518] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Controlling the geometry of self-assembly will enable a greater diversity of nanoparticles than now available. Viral capsid proteins, one starting point for investigating self-assembly, have evolved to form regular particles. The polyomavirus SV40 assembles from pentameric subunits and can encapsidate anionic cargos. On short ssRNA (≤814 nt), SV40 pentamers form 22 nm diameter capsids. On RNA too long to fit a T = 1 particle, pentamers forms strings of 22 nm particles and heterogeneous particles of 29-40 nm diameter. However, on dsDNA SV40 forms 50 nm particles composed of 72 pentamers. A 7.2-Å resolution cryo-EM image reconstruction of 22 nm particles shows that they are built of 12 pentamers arranged with T = 1 icosahedral symmetry. At 3-fold vertices, pentamers each contribute to a three-helix triangle. This geometry of interaction is not seen in crystal structures of T = 7 viruses and provides a structural basis for the smaller capsids. We propose that the heterogeneous particles are actually mosaics formed by combining different geometries of interaction from T = 1 capsids and virions. Assembly can be trapped in novel conformations because SV40 interpentamer contacts are relatively strong. The implication is that by virtue of their large catalog of interactions, SV40 pentamers have the ability to self-assemble on and conform to a broad range of shapes.
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Affiliation(s)
- Stanislav Kler
- Department
of Hematology, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Joseph Che-Yen Wang
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Mary Dhason
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Ariella Oppenheim
- Department
of Hematology, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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27
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Teunissen EA, de Raad M, Mastrobattista E. Production and biomedical applications of virus-like particles derived from polyomaviruses. J Control Release 2013; 172:305-321. [PMID: 23999392 DOI: 10.1016/j.jconrel.2013.08.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/18/2013] [Accepted: 08/20/2013] [Indexed: 10/26/2022]
Abstract
Virus-like particles (VLPs), aggregates of capsid proteins devoid of viral genetic material, show great promise in the fields of vaccine development and gene therapy. These particles spontaneously self-assemble after heterologous expression of viral structural proteins. This review will focus on the use of virus-like particles derived from polyomavirus capsid proteins. Since their first recombinant production 27 years ago these particles have been investigated for a myriad of biomedical applications. These virus-like particles are safe, easy to produce, can be loaded with a broad range of diverse cargoes and can be tailored for specific delivery or epitope presentation. We will highlight the structural characteristics of polyomavirus-derived VLPs and give an overview of their applications in diagnostics, vaccine development and gene delivery.
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Affiliation(s)
- Erik A Teunissen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
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