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Pogan R, Dülfer J, Uetrecht C. Norovirus assembly and stability. Curr Opin Virol 2018; 31:59-65. [DOI: 10.1016/j.coviro.2018.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/05/2018] [Accepted: 05/11/2018] [Indexed: 02/06/2023]
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2
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Lutomski CA, Lyktey NA, Pierson EE, Zhao Z, Zlotnick A, Jarrold MF. Multiple Pathways in Capsid Assembly. J Am Chem Soc 2018; 140:5784-5790. [PMID: 29672035 DOI: 10.1021/jacs.8b01804] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
For a three-dimensional structure to spontaneously self-assemble from many identical components, the steps on the pathway must be kinetically accessible. Many virus capsids are icosahedral and assembled from hundreds of identical proteins, but how they navigate the assembly process is poorly understood. Capsid assembly is thought to involve stepwise addition of subunits to a growing capsid fragment. Coarse-grained models suggest that the reaction occurs on a downhill energy landscape, so intermediates are expected to be fleeting. In this work, charge detection mass spectrometry (CDMS) has been used to track assembly of the hepatitis B virus (HBV) capsid in real time. The icosahedral T = 4 capsid of HBV is assembled from 120 capsid protein dimers. Our results indicate that there are multiple pathways for assembly. Under conditions that favor a modest association energy there is no accumulation of large intermediates, which indicates that available pathways include ones on a downhill energy surface. Under higher salt conditions, where subunit interactions are strengthened, around half of the products of the initial assembly reaction have masses close to the T = 4 capsid and the other half are stalled intermediates which emerge abruptly at around 90 dimers, indicating a bifurcation in the ensemble of assembly paths. When incubated at room temperature, the 90-dimer intermediates accumulate dimers and gradually shift to higher mass and merge with the capsid peak. Though free subunits are present in solution, the stalled intermediates indicate the presence of a local minima on the energy landscape. Some intermediates may result from hole closure, where the growing capsid distorts to close the hole due to the missing capsid proteins or from a species where subsequent additions are particularly labile.
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3
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Abstract
Virus-like particle (VLP) technologies are based on virus-inspired artificial structures and the intrinsic ability of viral proteins to self-assemble at controlled conditions. Therefore, the basic knowledge about the mechanisms of viral particle formation is highly important for designing of industrial applications. As an alternative to genetic and chemical processes, different physical methods are frequently used for VLP construction, including well characterized protein complexes for introduction of foreign molecules in VLP structures.This chapter shortly discusses the mechanisms how the viruses form their perfectly ordered structures as well as the principles and most interesting application examples, how to exploit the structural and assembly/disassembly properties of viral structures for creation of new nanomaterials.
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Affiliation(s)
- Andris Zeltins
- Latvian Biomedical Research and Study Centre, Riga, Latvia.
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4
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Chen J, Chevreuil M, Combet S, Lansac Y, Tresset G. Investigating the thermal dissociation of viral capsid by lattice model. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:474001. [PMID: 29098985 PMCID: PMC7104912 DOI: 10.1088/1361-648x/aa8d88] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/08/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
The dissociation of icosahedral viral capsids was investigated by a homogeneous and a heterogeneous lattice model. In thermal dissociation experiments with cowpea chlorotic mottle virus and probed by small-angle neutron scattering, we observed a slight shrinkage of viral capsids, which can be related to the strengthening of the hydrophobic interaction between subunits at increasing temperature. By considering the temperature dependence of hydrophobic interaction in the homogeneous lattice model, we were able to give a better estimate of the effective charge. In the heterogeneous lattice model, two sets of lattice sites represented different capsid subunits with asymmetric interaction strengths. In that case, the dissociation of capsids was found to shift from a sharp one-step transition to a gradual two-step transition by weakening the hydrophobic interaction between AB and CC subunits. We anticipate that such lattice models will shed further light on the statistical mechanics underlying virus assembly and disassembly.
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Affiliation(s)
- Jingzhi Chen
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Maelenn Chevreuil
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Sophie Combet
- Laboratoire Léon Brillouin (LLB), UMR 12 CEA-CNRS, CEA-Saclay, F-91191 Gif-sur-Yvette Cedex, France
| | - Yves Lansac
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
- GREMAN, CNRS, Université François Rabelais, 73200 Tours, France
| | - Guillaume Tresset
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
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5
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Lutomski CA, Lyktey NA, Zhao Z, Pierson EE, Zlotnick A, Jarrold MF. Hepatitis B Virus Capsid Completion Occurs through Error Correction. J Am Chem Soc 2017; 139:16932-16938. [PMID: 29125756 DOI: 10.1021/jacs.7b09932] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding capsid assembly is important because of its role in virus lifecycles and in applications to drug discovery and nanomaterial development. Many virus capsids are icosahedral, and assembly is thought to occur by the sequential addition of capsid protein subunits to a nucleus, with the final step completing the icosahedron. Almost nothing is known about the final (completion) step because the techniques usually used to study capsid assembly lack the resolution. In this work, charge detection mass spectrometry (CDMS) has been used to track the assembly of the T = 4 hepatitis B virus (HBV) capsid in real time. The initial assembly reaction occurs rapidly, on the time scale expected from low resolution measurements. However, CDMS shows that many of the particles generated in this process are defective and overgrown, containing more than the 120 capsid protein dimers needed to form a perfect T = 4 icosahedron. The defective and overgrown capsids self-correct over time to the mass expected for a perfect T = 4 capsid. Thus, completion is a distinct phase in the assembly reaction. Capsid completion does not necessarily occur by inserting the last building block into an incomplete, but otherwise perfect icosahedron. The initial assembly reaction can be predominently imperfect, and completion involves the slow correction of the accumulated errors.
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Affiliation(s)
- Corinne A Lutomski
- Chemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Nicholas A Lyktey
- Chemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Zhongchao Zhao
- Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Elizabeth E Pierson
- Chemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University , Bloomington, Indiana 47405, United States
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6
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Expression and purification of norovirus virus like particles in Escherichia coli and their immunogenicity in mice. Mol Immunol 2017; 93:278-284. [PMID: 28802994 DOI: 10.1016/j.molimm.2017.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/12/2022]
Abstract
Norovirus (NoV) virus like particles (VLPs) produced in Spodoptera frugiperda (Sf9) cells have been tested in human volunteers as vaccine candidate and were shown to be protective against NoV induced acute gastroenteritis. In this study, prevailing Sydney-2012-like NoV major capsid protein gene with or without N-terminal deletions (N26 and N38, 26 and 38 amino acids deleted from N terminus,respectively) were sub-cloned into prokaryotic expression vector, pCold III and pCold IV. Soluble and insoluble proteins were detected for both vectors after induction and higher levels of protein expression were observed for constructs pCold III-N26 and pCold III-N38. Electron microscopy observation of unpurified and purified lysates indicated in vivo assembly of VLPs with two sizes in accordance with those observed in Sf9 cells. In vitro salivary HBGA-VLP binding assay demonstrated that VLPs assembled in Escherichia coli (E. coli) exhibited the same binding pattern as that of VLPs assembled in Sf9 cells. Immunization of mice with purified VLPs derived from pCold III-N38 demonstrated higher IgG antibody titers and blocking antibody titers when compared with full-length capsid protein assembled VLPs from recombinant baculovirus expression system. In conclusion, NoV VLPs produced in E. coli using pCold expression vector might be used for the development of NoV vaccine.
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7
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Tubiana T, Boulard Y, Bressanelli S. Dynamics and asymmetry in the dimer of the norovirus major capsid protein. PLoS One 2017; 12:e0182056. [PMID: 28750021 PMCID: PMC5531542 DOI: 10.1371/journal.pone.0182056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
Noroviruses are the major cause of non-bacterial acute gastroenteritis in humans and livestock worldwide, despite being physically among the simplest animal viruses. The icosahedral capsid encasing the norovirus RNA genome is made of 90 dimers of a single ca 60-kDa polypeptide chain, VP1, arranged with T = 3 icosahedral symmetry. Here we study the conformational dynamics of this main building block of the norovirus capsid. We use molecular modeling and all-atom molecular dynamics simulations of the VP1 dimer for two genogroups with 50% sequence identity. We focus on the two points of flexibility in VP1 known from the crystal structure of the genogroup I (GI, human) capsid and from subsequent cryo-electron microscopy work on the GII capsid (also human). First, with a homology model of the GIII (bovine) VP1 dimer subjected to simulated annealing then classical molecular dynamics simulations, we show that the N-terminal arm conformation seen in the GI crystal structure is also favored in GIII VP1 but depends on the protonation state of critical residues. Second, simulations of the GI dimer show that the VP1 spike domain will not keep the position found in the GII electron microscopy work. Our main finding is a consistent propensity of the VP1 dimer to assume prominently asymmetric conformations. In order to probe this result, we obtain new SAXS data on GI VP1 dimers. These data are not interpretable as a population of symmetric dimers, but readily modeled by a highly asymmetric dimer. We go on to discuss possible implications of spontaneously asymmetric conformations in the successive steps of norovirus capsid assembly. Our work brings new lights on the surprising conformational range encoded in the norovirus major capsid protein.
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Affiliation(s)
- Thibault Tubiana
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
| | - Yves Boulard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
- * E-mail: (YB); (SB)
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, Gif sur Yvette cedex, France
- * E-mail: (YB); (SB)
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8
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Kondylis P, Zhou J, Harms ZD, Kneller AR, Lee LS, Zlotnick A, Jacobson SC. Nanofluidic Devices with 8 Pores in Series for Real-Time, Resistive-Pulse Analysis of Hepatitis B Virus Capsid Assembly. Anal Chem 2017; 89:4855-4862. [PMID: 28322548 DOI: 10.1021/acs.analchem.6b04491] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To improve the precision of resistive-pulse measurements, we have used a focused ion beam instrument to mill nanofluidic devices with 2, 4, and 8 pores in series and compared their performance. The in-plane design facilitates the fabrication of multiple pores in series which, in turn, permits averaging of the series of pulses generated from each translocation event. The standard deviations (σ) of the pulse amplitude distributions decrease by 2.7-fold when the average amplitudes of eight pulses are compared to the amplitudes of single pulses. Similarly, standard deviations of the pore-to-pore time distributions decrease by 3.2-fold when the averages of the seven measurements from 8-pore devices are contrasted to single measurements from 2-pore devices. With signal averaging, the inherent uncertainty in the measurements decreases; consequently, the resolution (mean/σ) improves by a factor equal to the square root of the number of measurements. We took advantage of the improved size resolution of the 8-pore devices to analyze in real time the assembly of Hepatitis B Virus (HBV) capsids below the pseudocritical concentration. We observe that abundances of assembly intermediates change over time. During the first hour of the reaction, the abundance of smaller intermediates decreased, whereas the abundance of larger intermediates with sizes closer to a T = 4 capsid remained constant.
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Affiliation(s)
- Panagiotis Kondylis
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Jinsheng Zhou
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Zachary D Harms
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Andrew R Kneller
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Lye Siang Lee
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Stephen C Jacobson
- Department of Chemistry and ‡Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
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Law-Hine D, Zeghal M, Bressanelli S, Constantin D, Tresset G. Identification of a major intermediate along the self-assembly pathway of an icosahedral viral capsid by using an analytical model of a spherical patch. SOFT MATTER 2016; 12:6728-36. [PMID: 27444997 DOI: 10.1039/c6sm01060a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Viruses are astonishing edifices in which hundreds of molecular building blocks fit into the final structure with pinpoint accuracy. We established a robust kinetic model accounting for the in vitro self-assembly of a capsid shell derived from an icosahedral plant virus by using time-resolved small-angle X-ray scattering (TR-SAXS) data at high spatiotemporal resolution. By implementing an analytical model of a spherical patch into a global fitting algorithm, we managed to identify a major intermediate species along the self-assembly pathway. With a series of data collected at different protein concentrations, we showed that free dimers self-assembled into a capsid through an intermediate resembling a half-capsid. The typical lifetime of the intermediate was a few seconds and yet the presence of so large an oligomer was not reported before. The progress in instrumental detection along with the development of powerful algorithms for data processing contribute to shedding light on nonequilibrium processes in highly complex systems such as viruses.
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Affiliation(s)
- Didier Law-Hine
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Mehdi Zeghal
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Doru Constantin
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Guillaume Tresset
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
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10
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Lamounier TADC, de Oliveira LM, de Camargo BR, Rodrigues KB, Noronha EF, Ribeiro BM, Nagata T. Production of Brazilian human norovirus VLPs and comparison of purification methods. Braz J Microbiol 2015; 46:1265-8. [PMID: 26691489 PMCID: PMC4704647 DOI: 10.1590/s1517-838246420140925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/12/2015] [Indexed: 11/22/2022] Open
Abstract
Noroviruses (NVs) are responsible for most cases of human nonbacterial
gastroenteritis worldwide. Some parameters for the purification of NV virus-like
particles (VLPs) such as ease of production and yield were studied for future
development of vaccines and diagnostic tools. In this study, VLPs were produced by
the expression of the VP1 and VP2 gene cassette of the Brazilian NV isolate, and two
purification methods were compared: cesium chloride (CsCl) gradient centrifugation
and ion-exchange chromatography (IEC). IEC produced more and purer VLPs of NV
compared to CsCl gradient centrifugation.
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Affiliation(s)
| | | | | | | | | | | | - Tatsuya Nagata
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
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11
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Abstract
The herpes simplex virus 1 (HSV-1) capsid is a massive particle (~200 MDa; 1,250-Å diameter) with T=16 icosahedral symmetry. It initially assembles as a procapsid with ~4,000 protein subunits of 11 different kinds. The procapsid undergoes major changes in structure and composition as it matures, a process driven by proteolysis and expulsion of the internal scaffolding protein. Assembly also relies on an external scaffolding protein, the triplex, an α2β heterotrimer that coordinates neighboring capsomers in the procapsid and becomes a stabilizing clamp in the mature capsid. To investigate the mechanisms that regulate its assembly, we developed a novel isolation procedure for the metastable procapsid and collected a large set of cryo-electron microscopy data. In addition to procapsids, these preparations contain maturation intermediates, which were distinguished by classifying the images and calculating a three-dimensional reconstruction for each class. Appraisal of the procapsid structure led to a new model for assembly; in it, the protomer (assembly unit) consists of one triplex, surrounded by three major capsid protein (MCP) subunits. The model exploits the triplexes’ departure from 3-fold symmetry to explain the highly skewed MCP hexamers, the triplex orientations at each 3-fold site, and the T=16 architecture. These observations also yielded new insights into maturation. This paper addresses the molecular mechanisms that govern the self-assembly of large, structurally complex, macromolecular particles, such as the capsids of double-stranded DNA viruses. Although they may consist of thousands of protein subunits of many different kinds, their assembly is precise, ranking them among the largest entities in the biosphere whose structures are uniquely defined to the atomic level. Assembly proceeds in two stages: formation of a precursor particle (procapsid) and maturation, during which major changes in structure and composition take place. Our analysis of the HSV procapsid by cryo-electron microscopy suggests a hierarchical pathway in which multisubunit “protomers” are the building blocks of the procapsid but their subunits are redistributed into different subcomplexes upon being incorporated into a nascent procapsid and are redistributed again in maturation. Assembly is a highly virus-specific process, making it a potential target for antiviral intervention.
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Law-Hine D, Sahoo AK, Bailleux V, Zeghal M, Prevost S, Maiti PK, Bressanelli S, Constantin D, Tresset G. Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates. J Phys Chem Lett 2015; 6:3471-3476. [PMID: 27120684 DOI: 10.1021/acs.jpclett.5b01478] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments.
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Affiliation(s)
- Didier Law-Hine
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS , 91400 Orsay, France
| | - Anil K Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore, Karnataka 560012, India
| | - Virginie Bailleux
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS , 91400 Orsay, France
| | - Mehdi Zeghal
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS , 91400 Orsay, France
| | - Sylvain Prevost
- European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, F-38043 Grenoble Cedex, France
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore, Karnataka 560012, India
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud , 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Doru Constantin
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS , 91400 Orsay, France
| | - Guillaume Tresset
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS , 91400 Orsay, France
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