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Pathak AK, Bandyopadhyay T. Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation. J Biomol Struct Dyn 2022; 40:11900-11913. [PMID: 34459706 DOI: 10.1080/07391102.2021.1969283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The capsid-like structure of the virus-based protein nanoparticles (NPs) can serve as bionanomaterials, with applications in biomedicines and nanotechnology. Release of packaged material from these nanocontainers is associated with subtle conformational changes of the NP structure, which in vitro, is readily accomplished by heating. Characterizing the structural changes as a function of temperature may provide fresh insights into nanomaterial/antiviral strategies. Here, we have calculated heat induced changes in the properties of an empty minute virus of mice particle using large-scale ≈ 3.0 × 106 all-atom molecular dynamics simulations. We focus on two heat induced structural changes of the NP, namely, dynamical transition (DT) and breathing transition (BT), both characterized by sudden and sharp change of measured parameters at temperatures, TDT and TBT, respectively. While DT is assessed by mean-square fluctuation of hydrogen atoms of the NP, BT is monitored through internal volume and permeation rate of water molecules through the NP. Both the transitions, resulting primarily from collective atomistic motion, are found to occur at temperatures widely separated from one another (TBT>TDT). The breathing motions, responsible for the translocation events of the packaged materials through the NP to kick off, are further probed by computing atomic resolution stresses from NVE simulations. Distribution of equilibrium atomistic stresses on the NP reveals a largely asymmetric nature and suggests structural breathing may actually represent large dynamic changes in the hotspot regions, far from the NP pores, which is in remarkable resemblance with recently conducted hydrogen-deuterium exchange coupled to mass spectrometry experiment. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
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Herrera MG, Veuthey TV, Dodero VI. Self-organization of gliadin in aqueous media under physiological digestive pHs. Colloids Surf B Biointerfaces 2016; 141:565-575. [PMID: 26897550 DOI: 10.1016/j.colsurfb.2016.02.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 12/22/2022]
Abstract
Here we showed that gliadin, a complex protein system related to celiac disease and other human diseases, is spontaneously self-organized in a very dilute solution at pH 3.0 and 7.0 in water under low ionic strength (10mM NaCl). The spontaneous self-organization at pH 3.0 increases the apparent solubility due to the formation of finite sized aggregates, such as those formed in the micellization of amphiphilic molecules. Switching the pH from 3.0 to 7.0 lead to a phase separation, however part of the nano-particles are stable remaining disperse in water after centrifugation. Also, beside the pH change led to changes in protein composition and concentration, we determined that the secondary structure of both system is the same. Moreover, Tyrs are slightly more buried and Trps are slightly more exposed to water at pH 7.0 than those at pH 3.0. Electron microscopy techniques showed that both gliadin systems are composed of nanostructures and in the case of pH 7.0 amorphous microaggregates were found, too. Only nanostructures at pH 3.0 showed a micromolar binding affinity to Nile red probe, suggesting the presence of accessible hydrophobic patches which are not more accessible at pH 7.0. All our results suggest that gliadin is able to self-organized at pH 3.0 forming protein micelles type nanostructures (ζ=+13, 42 ± 1.55 mV), meanwhile at 7.0 the decrease of superficial charge to ζ of +4, 78 ± 0.48 mV led to the formation of stable colloidal nanoparticles, unable to interact with Nile red probe. Our findings may open new perspectives for the understanding of gliadin ability to avoid proteolysis, to reach and cross the intestinal lumen and to trigger different immunological disorders.
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Affiliation(s)
- María G Herrera
- Departamento de Química-INQUISUR, Universidad Nacional del Su- CONICET, Av. Alem 1253, Bahía Blanca, Argentina
| | - Tania V Veuthey
- Departamento de Química-INQUISUR, Universidad Nacional del Su- CONICET, Av. Alem 1253, Bahía Blanca, Argentina
| | - Verónica I Dodero
- Departamento de Química-INQUISUR, Universidad Nacional del Su- CONICET, Av. Alem 1253, Bahía Blanca, Argentina; Universität Bielefeld, Fakultät für Chemie, Organische Chemie, Universitätsstr. 25, 33615 Bielefeld, Germany.
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3
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Castellanos M, Carrillo PJP, Mateu MG. Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis. NANOSCALE 2015; 7:5654-5664. [PMID: 25744136 DOI: 10.1039/c4nr07046a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.
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Affiliation(s)
- Milagros Castellanos
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid 28049, Spain.
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The adenovirus genome contributes to the structural stability of the virion. Viruses 2014; 6:3563-83. [PMID: 25254384 PMCID: PMC4189039 DOI: 10.3390/v6093563] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/15/2014] [Accepted: 09/17/2014] [Indexed: 11/17/2022] Open
Abstract
Adenovirus (Ad) vectors are currently the most commonly used platform for therapeutic gene delivery in human gene therapy clinical trials. Although these vectors are effective, many researchers seek to further improve the safety and efficacy of Ad-based vectors through detailed characterization of basic Ad biology relevant to its function as a vector system. Most Ad vectors are deleted of key, or all, viral protein coding sequences, which functions to not only prevent virus replication but also increase the cloning capacity of the vector for foreign DNA. However, radical modifications to the genome size significantly decreases virion stability, suggesting that the virus genome plays a role in maintaining the physical stability of the Ad virion. Indeed, a similar relationship between genome size and virion stability has been noted for many viruses. This review discusses the impact of the genome size on Ad virion stability and emphasizes the need to consider this aspect of virus biology in Ad-based vector design.
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Fontana J, Dressick WJ, Phelps J, Johnson JE, Rendell RW, Sampson T, Ratna BR, Soto CM. Virus-templated plasmonic nanoclusters with icosahedral symmetry via directed self-assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3058-63. [PMID: 24733721 PMCID: PMC4283761 DOI: 10.1002/smll.201400470] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 03/19/2014] [Indexed: 05/18/2023]
Abstract
The assembly of plasmonic nanoparticles with precise spatial and orientational order may lead to structures with new electromagnetic properties at optical frequencies. The directed self-assembly method presented controls the interparticle-spacing and symmetry of the resulting nanometer-sized elements in solution. The self-assembly of three-dimensional (3D), icosahedral plasmonic nanosclusters (NCs) with resonances at visible wavelengths is demonstrated experimentally. The ideal NCs consist of twelve gold (Au) nanospheres (NSs) attached to thiol groups at predefined locations on the surface of a genetically engineered cowpea mosaic virus with icosahedral symmetry. In situ dynamic light scattering (DLS) measurements confirm the NSs assembly on the virus. Transmission electron micrographs (TEM) demonstrate the ability of the self-assembly method to control the nanoscopic symmetry of the bound NSs, which reflects the icosahedral symmetry of the virus. Both, TEM and DLS show that the NCs comprise of a distribution of capsids mostly covered (i.e., 6-12 NS/capsid) with NSs. 3D finite-element simulations of aqueous suspensions of NCs reproduce the experimental bulk absorbance measurements and major features of the spectra. Simulations results show that the fully assembled NCs give rise to a 10-fold surface-averaged enhancement of the local electromagnetic field.
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Affiliation(s)
- Jake Fontana
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory4555 Overlook Ave., SW, Code 6900, Washington, DC, 20375, USA
| | - Walter J Dressick
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory4555 Overlook Ave., SW, Code 6900, Washington, DC, 20375, USA
| | - Jamie Phelps
- Department of Molecular Biology, The Scripps Research Institute10550 N. Torrey Pines Road La Jolla, California, 92037, USA
| | - John E Johnson
- Department of Molecular Biology, The Scripps Research Institute10550 N. Torrey Pines Road La Jolla, California, 92037, USA
| | - Ronald W Rendell
- Electronics Science and Technology Division, Naval Research LaboratoryCode 6877 4555 Overlook Ave., SW, Washington, DC, 20375, USA
| | - Travian Sampson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory4555 Overlook Ave., SW, Code 6900, Washington, DC, 20375, USA
| | - Banahalli R Ratna
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory4555 Overlook Ave., SW, Code 6900, Washington, DC, 20375, USA
| | - Carissa M Soto
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory4555 Overlook Ave., SW, Code 6900, Washington, DC, 20375, USA
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A programmable fluorescent viral nanoblock: sensing made easy in a single step. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 1108:155-72. [PMID: 24243248 DOI: 10.1007/978-1-62703-751-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Viral nanoblock provides specific positioning of recognition moieties and dye molecules which can be used as a signal-generating element and enhance detection sensitivity. The methods described herein use a 30 nm viral nanoblock to couple a variety of proteins and peptides for the incorporation of recognition elements along with a large number of dye molecules (200). The bioconjugation techniques were adapted and optimized over the years to fabricate nanoparticles that exhibit high fluorescence output while maintaining the selectivity of the target receptors. These complexes can be used for the detection of pathogens and toxins in a single step since both receptor and reporter are in the same viral nanoblock. Its stability and nanometer size allows for its utilization in well-established sensing platforms like microarrays.
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Characterization of the chandipura virus leader RNA–phosphoprotein interaction using single tryptophan mutants and its detection in viral infected cells. Biochimie 2013; 95:180-94. [DOI: 10.1016/j.biochi.2012.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/11/2012] [Indexed: 11/15/2022]
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Mateu MG. Assembly, stability and dynamics of virus capsids. Arch Biochem Biophys 2012; 531:65-79. [PMID: 23142681 DOI: 10.1016/j.abb.2012.10.015] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/18/2012] [Accepted: 10/28/2012] [Indexed: 12/13/2022]
Abstract
Most viruses use a hollow protein shell, the capsid, to enclose the viral genome. Virus capsids are large, symmetric oligomers made of many copies of one or a few types of protein subunits. Self-assembly of a viral capsid is a complex oligomerization process that proceeds along a pathway regulated by ordered interactions between the participating protein subunits, and that involves a series of (usually transient) assembly intermediates. Assembly of many virus capsids requires the assistance of scaffolding proteins or the viral nucleic acid, which interact with the capsid subunits to promote and direct the process. Once assembled, many capsids undergo a maturation reaction that involves covalent modification and/or conformational rearrangements, which may increase the stability of the particle. The final, mature capsid is a relatively robust protein complex able to protect the viral genome from physicochemical aggressions; however, it is also a metastable, dynamic structure poised to undergo controlled conformational transitions required to perform biologically critical functions during virus entry into cells, intracellular trafficking, and viral genome uncoating. This article provides an updated general overview on structural, biophysical and biochemical aspects of the assembly, stability and dynamics of virus capsids.
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Affiliation(s)
- Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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9
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Kennedy MA, Parks RJ. Adenovirus virion stability and the viral genome: size matters. Mol Ther 2010; 17:1664-6. [PMID: 19789561 DOI: 10.1038/mt.2009.202] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Michael A Kennedy
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada
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10
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Manipulation of the mechanical properties of a virus by protein engineering. Proc Natl Acad Sci U S A 2008; 105:4150-5. [PMID: 18334651 DOI: 10.1073/pnas.0708017105] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In a previous study, we showed that the DNA molecule within a spherical virus (the minute virus of mice) plays an architectural role by anisotropically increasing the mechanical stiffness of the virus. A finite element model predicted that this mechanical reinforcement is a consequence of the interaction between crystallographically visible, short DNA patches and the inner capsid wall. We have now tested this model by using protein engineering. Selected amino acid side chains have been truncated to specifically remove major interactions between the capsid and the visible DNA patches, and the effect of the mutations on the stiffness of virus particles has been measured using atomic force microscopy. The mutations do not affect the stiffness of the empty capsid; however, they significantly reduce the difference in stiffness between the DNA-filled virion and the empty capsid. The results (i) reveal that intermolecular interactions between individual chemical groups contribute to the mechanical properties of a supramolecular assembly and (ii) identify specific protein-DNA interactions as the origin of the anisotropic increase in the rigidity of a virus. This study also demonstrates that it is possible to control the mechanical properties of a protein nanoparticle by the rational application of protein engineering based on a mechanical model.
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11
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Portney NG, Martinez-Morales AA, Ozkan M. Nanoscale memory characterization of virus-templated semiconducting quantum dots. ACS NANO 2008; 2:191-196. [PMID: 19206618 DOI: 10.1021/nn700240z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We have developed a substrate-based bottom-up approach to assemble two different color emitting quantum dots (CdSe/ZnS core/shell QDs) on the surface of a novel virus mutant, CPMV-T184C. Electrical characteristics of individual hybrids were investigated by conductive atomic force microscopy for potential digital memory applications (i.e., RAM). These individual 40 nm CPMV-QD(1,2) hybrids exhibited reversible bistable electrical behavior during repeatable writing-reading-erasing processes at the nanoscale.
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Affiliation(s)
- Nathaniel G Portney
- Department of Bioengineering, University of California, Riverside, California 92521, USA
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12
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Bispo JAC, Santos JLR, Landini GF, Goncalves JM, Bonafe CFS. pH dependence of the dissociation of multimeric hemoglobin probed by high hydrostatic pressure. Biophys Chem 2007; 125:341-9. [PMID: 17046147 DOI: 10.1016/j.bpc.2006.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 09/21/2006] [Accepted: 09/21/2006] [Indexed: 11/19/2022]
Abstract
We investigated the thermodynamic features of the classic alkaline dissociation of multimeric hemoglobin (3.1 MDa) from Glossoscolex paulistus (Annelidea) using high hydrostatic pressure. Light scattering measurements up to microscopic thermodynamic equilibrium indicated a high pH dependency of dissociation and association. Electron microscopy and gel filtration corroborated these findings. The volume change of dissociation decreased in absolute values from -48.0 mL/mol of subunit at pH 6.0 to -19.2 mL/mol at pH 9.0, suggesting a lack of protein interactions under alkaline conditions. Concomitantly, an increase in pH reduced the Gibbs free energy of dissociation from 37.7 to 27.5 kJ/mol of subunit. The stoichiometry of proton release calculated from the pressure-induced dissociation curves was +0.602 mol of H(+)/mol of subunit. These results provide a direct quantification of proton participation in stabilizing the aggregated state of the hemoglobin, and contribute to our understanding of protein-protein interactions and of the surrounding conditions that modulate the process of aggregation.
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Affiliation(s)
- Jose A C Bispo
- Laboratório de Termodinâmica de Proteínas, Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), CP 6109, Campinas, SP, CEP 13083-970, Brazil
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Speir JA, Bothner B, Qu C, Willits DA, Young MJ, Johnson JE. Enhanced local symmetry interactions globally stabilize a mutant virus capsid that maintains infectivity and capsid dynamics. J Virol 2006; 80:3582-91. [PMID: 16537626 PMCID: PMC1440388 DOI: 10.1128/jvi.80.7.3582-3591.2006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Structural transitions in viral capsids play a critical role in the virus life cycle, including assembly, disassembly, and release of the packaged nucleic acid. Cowpea chlorotic mottle virus (CCMV) undergoes a well-studied reversible structural expansion in vitro in which the capsid expands by 10%. The swollen form of the particle can be completely disassembled by increasing the salt concentration to 1 M. Remarkably, a single-residue mutant of the CCMV N-terminal arm, K42R, is not susceptible to dissociation in high salt (salt-stable CCMV [SS-CCMV]) and retains 70% of wild-type infectivity. We present the combined structural and biophysical basis for the chemical stability and viability of the SS-CCMV particles. A 2.7-A resolution crystal structure of the SS-CCMV capsid shows an addition of 660 new intersubunit interactions per particle at the center of the 20 hexameric capsomeres, which are a direct result of the K42R mutation. Protease-based mapping experiments of intact particles demonstrate that both the swollen and closed forms of the wild-type and SS-CCMV particles have highly dynamic N-terminal regions, yet the SS-CCMV particles are more resistant to degradation. Thus, the increase in SS-CCMV particle stability is a result of concentrated tethering of subunits at a local symmetry interface (i.e., quasi-sixfold axes) that does not interfere with the function of other key symmetry interfaces (i.e., fivefold, twofold, quasi-threefold axes). The result is a particle that is still dynamic but insensitive to high salt due to a new series of bonds that are resistant to high ionic strength and preserve the overall particle structure.
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Affiliation(s)
- Jeffrey A Speir
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
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Reguera J, Grueso E, Carreira A, Sánchez-Martínez C, Almendral JM, Mateu MG. Functional Relevance of Amino Acid Residues Involved in Interactions with Ordered Nucleic Acid in a Spherical Virus. J Biol Chem 2005; 280:17969-77. [PMID: 15728575 DOI: 10.1074/jbc.m500867200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the spherical virion of the parvovirus minute virus of mice, several amino acid side chains of the capsid were previously found to be involved in interactions with the viral single-stranded DNA molecule. We have individually truncated by mutation to alanine many (ten) of these side chains and analyzed the effects on capsid assembly, stability and conformation, viral DNA encapsidation, and virion infectivity. Mutation of residues Tyr-270, Asp-273, or Asp-474 led to a drastic reduction in infectivity. Mutant Y270A was defective in capsid assembly; mutant D273A formed stable capsids, but it was essentially unable to encapsidate the viral DNA or to externalize the N terminus of the capsid protein VP2, a connected conformational event. Mutation of residues Asp-58, Trp-60, Asn-183, Thr-267, or Lys-471 led to a moderate reduction in infectivity. None of these mutations had an effect on capsid assembly or stability, or on the DNA encapsidation process. However, those five mutant virions were substantially less stable than the parental virion in thermal inactivation assays. The results with this model spherical virus indicate that several capsid residues that are found to be involved in polar interactions or multiple hydrophobic contacts with the viral DNA molecule contribute to preserving the active conformation of the infectious viral particle. Their effect appears to be mediated by the non-covalent interactions they establish with the viral DNA. In addition, at least one acidic residue at each DNA-binding region is needed for DNA packaging.
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Affiliation(s)
- Juan Reguera
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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15
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Santos JLR, Bispo JAC, Landini GF, Bonafe CFS. Proton dependence of tobacco mosaic virus dissociation by pressure. Biophys Chem 2004; 111:53-61. [PMID: 15450375 DOI: 10.1016/j.bpc.2004.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/15/2004] [Accepted: 04/16/2004] [Indexed: 10/26/2022]
Abstract
Tobacco mosaic virus (TMV) is an intensely studied model of viruses. This paper reports an investigation into the dissociation of TMV by pH and pressure up to 220 MPa. The viral solution (0.25 mg/ml) incubated at 277 K showed a significant decrease in light scattering with increasing pH, suggesting dissociation. This observation was confirmed by HPLC gel filtration and electron microscopy. The calculated volume change of dissociation (DeltaV) decreased (absolute value) from -49.7 ml/mol of subunit at pH 3.8 to -21.7 ml/mol of subunit at pH 9.0. The decrease from pH 9.0 to 3.8 caused a stabilization of 14.1 kJ/mol of TMV subunit. The estimated proton release calculated from pressure-induced dissociation curves was 0.584 mol H(+)/mol of TMV subunit. These results suggest that the degree of virus inactivation by pressure and the immunogenicity of the inactivated structures can be optimized by modulating the surrounding pH.
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Affiliation(s)
- Jose L R Santos
- Laboratório de Termodinâmica de Proteínas, Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, Campinas, SP, CEP 13083-970, Brazil
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16
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Hafenstein SL, Chen M, Fane BA. Genetic and functional analyses of the øX174 DNA binding protein: the effects of substitutions for amino acid residues that spatially organize the two DNA binding domains. Virology 2004; 318:204-13. [PMID: 14972548 DOI: 10.1016/j.virol.2003.09.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2003] [Revised: 09/10/2003] [Accepted: 09/10/2003] [Indexed: 11/22/2022]
Abstract
The øX174 DNA binding protein contains two DNA binding domains, containing a series of DNA binding basic amino acids, separated by a proline-rich linker region. Within each DNA binding domain, there is a conserved glycine residue. Glycine and proline residues were mutated and the effects on virion structure were examined. Substitutions for glycine residues yield particles with similar properties to previously characterized mutants with substitutions for DNA binding residues. Both sets of mutations share a common extragenic second-site suppressor, suggesting that the defects caused by the mutant proteins are mechanistically similar. Hence, glycine residues may optimize DNA-protein contacts. The defects conferred by substitutions for proline residues appear to be fundamentally different. The properties of the mutant particles along with the atomic structure of the virion suggest that the proline residues may act to guide the packaged DNA to the adjacent fivefold related asymmetric unit, thus preventing a chaotic packaging arrangement.
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Affiliation(s)
- Susan L Hafenstein
- Department of Veterinary Sciences and Microbiology, University of Arizona, Tucson, AZ 85721 USA
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Lin T, Cavarelli J, Johnson JE. Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus. Virology 2003; 314:26-33. [PMID: 14517057 DOI: 10.1016/s0042-6822(03)00457-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ordered nucleic acid in an icosahedral virus was first visualized in the X-ray structure of the Picorna-like plant virus, Bean pod mottle virus (BPMV). Virus particles containing the 3500 nucleotide segment of the BPMV bipartite RNA genome (middle component) had nearly 20% of the genome ordered. Here we report the refined structures of the middle component, bottom component (particles containing the 5800 nucleotide segment of the genome), and top component (empty particles of BPMV capsid protein). The bottom component particles contain ordered RNA in the same location as middle component. Although the ordered RNA density in both nucleoprotein particles is the average of the contents of 60 icosahedral asymmetric units, both nucleoprotein components show that the base density for the first two nucleotides is predominantly purine, while the next five appear to be predominantly pyrimidine. The empty capsid demonstrates that RNA dictates the order of the N-terminal 19 residues of the large subunit because these residues are invisible in the top component.
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Affiliation(s)
- Tianwei Lin
- Department of Molecular Biology and Center for Integrative Molecular Biosciences, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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18
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Affiliation(s)
- Tianwei Lin
- Department of Molecular Biology, Center for Integrative Molecular Biosciences, Scripps Research Institute, La Jolla, California 92037, USA
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