| 1. |
- Ahadi, Aylin, et al.
(författare)
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Modeling and simulation of the mechanical response from nanoindentation test of DNA-filled viral capsids
- 2013
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Ingår i: Journal of Biological Physics. - : Springer Science and Business Media LLC. - 0092-0606 .- 1573-0689. ; 39:2, s. 183-199
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Tidskriftsartikel (refereegranskat)abstract
- Viruses can be described as biological objects composed mainly of two parts: a stiff protein shell called a capsid, and a core inside the capsid containing the nucleic acid and liquid. In many double-stranded DNA bacterial viruses (aka phage), the volume ratio between the liquid and the encapsidated DNA is approximately 1:1. Due to the dominant DNA hydration force, water strongly mediates the interaction between the packaged DNA strands. Therefore, water that hydrates the DNA plays an important role in nanoindentation experiments of DNA-filled viral capsids. Nanoindentation measurements allow us to gain further insight into the nature of the hydration and electrostatic interactions between the DNA strands. With this motivation, a continuum-based numerical model for simulating the nanoindentation response of DNA-filled viral capsids is proposed here. The viral capsid is modeled as large- strain isotropic hyper-elastic material, whereas porous elasticity is adopted to capture the mechanical response of the filled viral capsid. The voids inside the viral capsid are assumed to be filled with liquid, which is modeled as a homogenous incompressible fluid. The motion of a fluid flowing through the porous medium upon capsid indentation is modeled using Darcy's law, describing the flow of fluid through a porous medium. The nanoindentation response is simulated using three-dimensional finite element analysis and the simulations are performed using the finite element code Abaqus. Force-indentation curves for empty, partially and completely DNA-filled capsids are directly compared to the experimental data for bacteriophage lambda. Material parameters such as Young's modulus, shear modulus, and bulk modulus are determined by comparing computed force-indentation curves to the data from the atomic force microscopy (AFM) experiments. Predictions are made for pressure distribution inside the capsid, as well as the fluid volume ratio variation during the indentation test.
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| 2. |
- Ahadi, Aylin, et al.
(författare)
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Three-Dimensional Simulation of Nanoindentation Response of Viral Capsids. Shape and Size Effects
- 2009
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 113:11, s. 3370-3378
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Tidskriftsartikel (refereegranskat)abstract
- The nanoindentation response of empty viral capsids is modeled using three-dimensional finite element analysis. Simulation with two different geometries, spherical and icosahedral, is performed using the finite element code Abaqus. The capsids are modeled as nonlinear Hookean elastic, and both small and large deformation analysis is performed. The Young's modulus is determined by calibrating the force-indentation curve to data from atomic force microscopy (AFM) experiments. Force-indentation curves for three different viral capsids are directly compared to experimental data. Predictions are made for two additional viral capsids. The results from the simulation showed a good agreement with AFM data. The paper demonstrates that over the entire range of virus sizes (or Foppl-von Karman numbers) spherical and icosahedral models yield different force responses. In particular, it is shown that capsids with dominantly spherical shape (for low Foppl-von Karman numbers) exhibit nearly linear relationship between force and indentation, which has been experimentally observed on the viral shell studies so far. However, we predict that capsids with significant faceting (for large Foppl-von Karman numbers) and thus more pronounced icosahedral shape will exhibit rather nonlinear deformation behavior.
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| 3. |
- Bauer, D W, et al.
(författare)
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Exploring the balance between DNA pressure and capsid stability in Herpes and phage.
- 2015
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Ingår i: Journal of Virology. - 1098-5514. ; 89:18, s. 9288-9298
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Tidskriftsartikel (refereegranskat)abstract
- We have recently shown in both herpesviruses and phages that packaged viral DNA creates a pressure of tens of atmospheres pushing against the interior capsid wall. For the first time, using differential scanning microcalorimetry, we directly measure the energy powering the release of pressurized DNA from the capsid. Furthermore, using a new calorimetric assay to accurately determine the temperature inducing DNA release, we found a direct influence of internal DNA pressure on the stability of the viral particle. We show that the balance of forces between the DNA pressure and capsid strength, required for DNA retention between rounds of infection, is conserved between evolutionarily diverse bacterial viruses (phage λ and P22), as well as a eukaryotic virus, human Herpes Simplex 1 (HSV-1). Our data also suggest that the portal vertex in these viruses is the weakest point in the overall capsid structure and presents the "Achilles' heel" of virus's stability. Comparison between these viral systems shows that viruses with higher DNA packing density (resulting in higher capsid pressure) have inherently stronger capsid structures preventing spontaneous genome release prior to infection. This force balance is of key importance for viral survival and replication. Investigating the ways to disrupt this balance can lead to development of new mutation resistant anti-virals.
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| 4. |
- Bauer, David W., et al.
(författare)
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Herpes Virus Genome, The Pressure Is On
- 2013
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 135:30, s. 11216-11221
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Tidskriftsartikel (refereegranskat)abstract
- Herpes simplex virus type 1 (HSV-1) packages its micrometers-long double-stranded DNA genome into a nanometer-scale protein shell, termed the capsid. Upon confinement within the capsid, neighboring DNA strands experience repulsive electrostatic and hydration forces as well as bending stress associated with the tight curvature required of packaged DNA. By osmotically suppressing DNA release from HSV-1 capsids, we provide the first experimental evidence of a high internal pressure of tens of atmospheres within a eukaryotic human virus, resulting from the confined genome. Furthermore, the ejection is progressively suppressed by increasing external osmotic pressures, which reveals that internal pressure is capable of powering ejection of the entire genome from the viral capsid. Despite billions of years of evolution separating eukaryotic viruses and bacteriophages, pressure-driven DNA ejection has been conserved. This suggests it is a key mechanism for viral infection and thus presents a new target for antiviral therapies.
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| 5. |
- Bauer, D W, et al.
(författare)
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Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ.
- 2015
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 1089-8638 .- 0022-2836. ; 427:20, s. 3189-3200
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Tidskriftsartikel (refereegranskat)abstract
- Viruses must remain infectious while in harsh extracellular environments. An important aspect of viral particle stability for double-stranded DNA viruses is the energetically unfavorable state of the tightly confined DNA chain within the virus capsid creating pressures of tens of atmospheres. Here, we study the influence of internal genome pressure on the thermal stability of viral particles. Using differential scanning calorimetry to monitor genome loss upon heating, we find that internal pressure destabilizes the virion, resulting in a smaller activation energy barrier to trigger DNA release. These experiments are complemented by plaque assay and electron microscopy measurements to determine the influence of intra-capsid DNA pressure on the rates of viral infectivity loss. At higher temperatures (65-75°C), failure to retain the packaged genome is the dominant mechanism of viral inactivation. Conversely, at lower temperatures (40-55°C), a separate inactivation mechanism dominates, which results in non-infectious particles that still retain their packaged DNA. Most significantly, both mechanisms of infectivity loss are directly influenced by internal DNA pressure, with higher pressure resulting in a more rapid rate of inactivation at all temperatures.
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| 6. |
- Brandariz-Nuñez, Alberto, et al.
(författare)
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Pressure-driven release of viral genome into a host nucleus is a mechanism leading to herpes infection
- 2019
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Ingår i: eLife. - 2050-084X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Many viruses previously have been shown to have pressurized genomes inside their viral protein shell, termed the capsid. This pressure results from the tight confinement of negatively charged viral nucleic acids inside the capsid. However, the relevance of capsid pressure to viral infection has not been demonstrated. In this work, we show that the internal DNA pressure of tens of atmospheres inside a herpesvirus capsid powers ejection of the viral genome into a host cell nucleus. To our knowledge, this provides the first demonstration of a pressure-dependent mechanism of viral genome penetration into a host nucleus, leading to infection of eukaryotic cells.
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| 7. |
- Brandariz-Nuñez, Alberto, et al.
(författare)
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Pressurized DNA state inside herpes capsids-A novel antiviral target
- 2020
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7374. ; 16:7
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Tidskriftsartikel (refereegranskat)abstract
- Drug resistance in viruses represents one of the major challenges of healthcare. As part of an effort to provide a treatment that avoids the possibility of drug resistance, we discovered a novel mechanism of action (MOA) and specific compounds to treat all nine human herpesviruses and animal herpesviruses. The novel MOA targets the pressurized genome state in a viral capsid, "turns off" capsid pressure, and blocks viral genome ejection into a cell nucleus, preventing viral replication. This work serves as a proof-of-concept to demonstrate the feasibility of a new antiviral target-suppressing pressure-driven viral genome ejection-that is likely impervious to developing drug resistance. This pivotal finding presents a platform for discovery of a new class of broad-spectrum treatments for herpesviruses and other viral infections with genome-pressure-dependent replication. A biophysical approach to antiviral treatment such as this is also a vital strategy to prevent the spread of emerging viruses where vaccine development is challenged by high mutation rates or other evasion mechanisms.
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| 8. |
- Castelnovo, M, et al.
(författare)
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Binding effects in multivalent Gibbs-Donnan equilibrium
- 2006
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Ingår i: Europhysics Letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 73:4, s. 635-641
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Tidskriftsartikel (refereegranskat)abstract
- The classical Gibbs-Donnan equilibrium describes excess osmotic pressure associated with confined colloidal charges embedded in an electrolyte solution. In this work, we extend this approach to describe the influence of multivalent ion binding on the equilibrium force acting on a charged rod translocating between two compartments, thereby mimicking ionic effects on force balance during in vitro DNA ejection from bacteriophage. The subtle interplay between Gibbs-Donnan equilibrium and adsorption equilibrium leads to a non-monotonic variation of the ejection force as multivalent salt concentration is increased, in qualitative agreement with experimental observations.
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| 9. |
- Castelnovo, M., et al.
(författare)
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DNA ejection from bacteriophage: Towards a general behavior for osmotic-suppression experiments
- 2007
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Ingår i: European Physical Journal E. Soft Matter. - : Springer Science and Business Media LLC. - 1292-8941 .- 1292-895X. ; 24:1, s. 9-18
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Tidskriftsartikel (refereegranskat)abstract
- We present in this work in vitro measurements of the force ejecting DNA from two distinct bacteriophages (T5 and lambda using the osmotic-suppression technique. Our data are analyzed by revisiting the current theories of DNA packaging in spherical capsids. In particular we show that a simplified analytical model based on bending considerations only is able to account quantitatively for the experimental findings. Physical and biological consequences are discussed.
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| 10. |
- Dou, Tianyi, et al.
(författare)
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Nanoscale Structural Characterization of Individual Viral Particles Using Atomic Force Microscope Infrared (AFM-IR) and Tip-Enhanced Raman Spectroscopy (TERS)
- 2020
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 1520-6882 .- 0003-2700. ; 92:16, s. 11297-11304
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Tidskriftsartikel (refereegranskat)abstract
- Viruses are infections species that infect a large spectrum of living systems. Although displaying a wide variety of shapes and sizes, they are all composed of nucleic acid encapsulated into a protein capsid. After virions enter the host cell, they replicate to produce multiple copies of themselves. They then lyse the host, releasing virions to infect new cells. High proliferation rate of viruses is the underlying cause of their fast transmission among living species. Although many viruses are harmless, some of them are responsible for severe diseases such as AIDS, viral hepatitis and flu. Traditionally, electron microscopy is used to identify and characterize viruses. This approach is time and labor consuming, which is problematic upon pandemic proliferation of previously unknown viruses. Herein, we demonstrate a novel diagnosis approach for label-free identification and structural characterization of individual viruses that is based on a combination of nanoscale Raman and Infrared spectroscopy. Using atomic force microscopy infrared spectroscopy (AFM-IR), we were able to probe structural organization of the virions of herpes simplex type 1 viruses and bacteriophage MS2. We also showed that tip enhanced Raman spectroscopy could be used to reveal protein secondary structure and amino acid composition of the virus surface. Our results show that AFM-IR and TERS provide different but complimentary information about the structure of complex biological specimens. This structural information can be used for fast and reliable identification of viruses. This nanoscale bimodal imaging approach can be also used to investigate the origin of viral polymorphism and study mechanisms of virion assembly.
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| 11. |
- Evilevitch, Alex, et al.
(författare)
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Computer simulation of molecular exchange in colloidal systems
- 2002
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 106:45, s. 11746-11757
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we introduce two computer simulation models to study molecular exchange between aggregates in a colloidal dispersion. The Brownian motion of the colloidal aggregates is simulated as a random walk with a Gaussian distributed step length. In model I, the exchanging molecules are simulated as discrete particles with the exchange process characterized by desorption, molecular diffusion, and adsorption. A molecule desorbed from an aggregate is registered in the simulation and allowed to undergo individual Brownian motion until it adsorbs onto another colloidal aggregate or returns to the same aggregate from which it originated. In this detailed simulation, random size fluctuations are obtained in addition to a net variation in a relaxing, nonequilibrium size distribution. For many processes, net variations are very slow compared to the random fluctuations, making this detailed method very time consuming for studying a relaxing size distribution. For this reason, we also consider, in model II, a more approximate method where only the net flow of molecules between aggregates is considered. Here, the flow of molecules is for each time step calculated assuming steady state conditions and pair wise additivity. The flow between an isolated pair of aggregates can be solved exactly. Although the pair flow is a good approximation at short separations, it becomes significantly reduced at larger separations because of the presence of other aggregates. This screening of the flow at larger separations is accounted for by introducing an exponential damping function. With these models, we have simulated the solubilization of larger oil drops by smaller micelles which has previously been experimentally studied in a nonionic surfactant-water-oil system. Besides comparing with experiments, the simulations provides a test of a previous mean-field cell model analysis of the solubilization process.
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| 12. |
- Evilevitch, Alex
(författare)
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Effects of condensing agent and nuclease on the extent of ejection from phage lambda
- 2006
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 110:44, s. 22261-22265
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Tidskriftsartikel (refereegranskat)abstract
- We have recently demonstrated, that DNA ejection from bacteriophage I can be partially or completely suppressed in vitro by external osmotic pressure. This suggests that DNA ejection from phage is driven by an internal mechanical force consisting of DNA bending and DNA-DNA electrostatic repulsion energies. In the present work we investigate the extent to which DNA ejection is incomplete at zero osmotic external pressure when phage is opened with its receptor in vitro. The DNA fragment remaining in the capsid and the tail that is no longer bent or compressed sand hence for which there is no internal driving force for ejections is shown not to be ejected. We also demonstrate that DNA can be "pulled" out from the capsid by DNase I acting as a DNA binding protein or spermine acting as a DNA condensing agent. In particular, cryo electron microscopy and gel electrophoresis experiments show the following: (i) DNA ejection from bacteriophage I incubated in vitro with its receptor is incomplete at zero external osmotic force, with several persistence lengths of DNA remaining inside the phage capsid, if no nuclease ( DNase I) or DNA condensing agent ( spermine) is present in the host solution; (ii) in the presence of both DNase I and spermine in the host solution, 60% (approximate to 29 kbp) of wild-type lambda DNA (48.5 kbp) remains unejected inside the phage capsid, in the form of an unconstrained toroidal condensate; (iii) with DNase I added, but no spermine, the ejection is complete; (iv) with spermine, but without DNase I added, all the DNA is again ejected, and organized as a toroidal condensate outside.
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| 13. |
- Evilevitch, Alex, et al.
(författare)
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Effects of salt concentrations and bending energy on the extent of ejection of phage genomes
- 2008
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Ingår i: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 94:3, s. 1110-1120
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Tidskriftsartikel (refereegranskat)abstract
- Recent work has shown that pressures inside dsDNA phage capsids can be as high as many tens of atmospheres; it is this pressure that is responsible for initiation of the delivery of phage genomes to host cells. The forces driving ejection of the genome have been shown to decrease monotonically as ejection proceeds, and hence to be strongly dependent on the genome length. Here we investigate the effects of ambient salts on the pressures inside phage-l, for the cases of mono-, di-, and tetravalent cations, and measure how the extent of ejection against a fixed osmotic pressure (mimicking the bacterial cytoplasm) varies with cation concentration. We find, for example, that the ejection fraction is halved in 30 mM Mg21 and is decreased by a factor of 10 upon addition of 1 mM spermine. These effects are calculated from a simple model of genome packaging, using DNA-DNA repulsion energies as determined independently from x-ray diffraction measurements on bulk DNA solutions. By comparing the measured ejection fractions with values implied from the bulk DNA solution data, we predict that the bending energy makes the d- spacings inside the capsid larger than those for bulk DNA at the same osmotic pressure.
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| 14. |
- Evilevitch, Alex, et al.
(författare)
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Effects of Salts on Internal DNA Pressure and Mechanical Properties of Phage Capsids.
- 2011
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 1089-8638 .- 0022-2836. ; 405, s. 18-23
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Tidskriftsartikel (refereegranskat)abstract
- Based on atomic force microscopy nanoindentation measurements of phage λ, we previously proposed a minimal model describing the effect of water hydrating DNA that strengthens viral capsids against external deformation at wild-type DNA packing density. Here, we report proof of this model by testing the prediction that DNA hydration forces can be dramatically decreased by addition of multivalent ions (Mg(2+) and Sp(4+)). These results are explained using a DNA hydration model without adjustable parameters. The model also predicts the stiffness of other DNA-filled capsids, which we confirm using bacteriophage ϕ29 and herpes simplex virus type 1 particles.
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| 15. |
- Evilevitch, Alex
(författare)
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Energetics of the DNA-Filled Head
- 2021
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Ingår i: Reference Module in Life Sciences. ; 4, s. 1-8
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Bokkapitel (refereegranskat)abstract
- Mechanical changes within cells and viruses have been shown to be of great importance for various mechano-signaling processes. In phage and herpesviruses, strong confinement of double-stranded DNA inside the capsid generates tens of atmospheres of pressure. This confinement leads to electrostatic sliding friction between neighboring DNA strands. This affects the mobility of the encapsidated genome which directly impacts the dynamics of viral DNA ejection during infection. When a cell is infected by multiple virions, the dynamics of release of viral genomes into a cell leads to competitive interactions between viral genomes, which in turn influences viral gene expression. This affects cell’s “decision” between lysogeny (dormant state where virus does not replicate) and cell lysis caused by lytic virus replication. This article reviews the energetics, structure and mobility of the intra-capsid genome, influenced by changes in physiological parameters (temperature and ionic conditions) that are important for viral replication. The mechano-regulation of DNA ejection dynamics is also analyzed and placed in the context of viral replication dynamics.
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| 16. |
- Evilevitch, Alex, et al.
(författare)
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Intranuclear HSV-1 DNA ejection induces major mechanical transformations suggesting mechanoprotection of nucleus integrity
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 119:9, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- Maintaining nuclear integrity is essential to cell survival when exposed to mechanical stress. Herpesviruses, like most DNA and some RNA viruses, put strain on the nuclear envelope as hundreds of viral DNA genomes replicate and viral capsids assemble. It remained unknown, however, how nuclear mechanics is affected at the initial stage of herpesvirus infection—immediately after viral genomes are ejected into the nuclear space—and how nucleus integrity is maintained despite an increased strain on the nuclear envelope. With an atomic force microscopy force volume mapping approach on cell-free reconstituted nuclei with docked herpes simplex type 1 (HSV-1) capsids, we explored the mechanical response of the nuclear lamina and the chromatin to intranuclear HSV-1 DNA ejection into an intact nucleus. We discovered that chromatin stiffness, measured as Young’s modulus, is increased by ∼14 times, while nuclear lamina underwent softening. Those transformations could be associated with a mechanism of mechanoprotection of nucleus integrity facilitating HSV-1 viral genome replication. Indeed, stiffening of chromatin, which is tethered to the lamina meshwork, helps to maintain nuclear morphology. At the same time, increased lamina elasticity, reflected by nucleus softening, acts as a “shock absorber,” dissipating the internal mechanical stress on the nuclear membrane (located on top of the lamina wall) and preventing its rupture.
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| 17. |
- Evilevitch, Alex, et al.
(författare)
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Kinetics of oil solubilization in microemulsion droplets. Mechanism of oil transport.
- 2001
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Ingår i: Electroanalysis. - : American Chemical Society (ACS). - 1040-0397. ; 16:23, s. 8755-8762
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the kinetics of the solubilization of oil through a temperature jump into a droplet microemulsion phase in the system water-pentaethylene oxide dodecyl ether-decane at 25 C. The initial state is formed by subjecting the equilibrium system at 25 C to a temperature quench to 22, 20, and 14 C, respectively. At this lower temperature, which at equilibrium corresponds to a two-phase system, oil droplets form and grow in size with increasing time. By varying the time between the quench and the T-jump, the size of the initial oil drops is varied in a systematic and known way in the relaxation study. The relaxation process is monitored by following the turbidity of the system. We find that for all the systems the relaxation back to equlibrium is much faster than the drop growth process observed after the temperature quench. This general observation is explained by realizing that the redissolution of the oil drops is analogous to the oil transfer phase, which in the quench experiment occurs prior to the Ostwald ripening phase. More significant is that we observed a qualitative transition in the relaxation behavior when the initial aggregate distribution is varied. In all cases we have the same initial temperature and overall composition and one population of many small droplets and fewer larger drops. The size of the larger drops only affects the relaxation in a quantitative way. If the small droplets are only slightly smaller than the equilibrium size, equilibration occurs through the diffusion of oil molecules in the bulk phase. When the initial droplets are sufficiently small, a new kinetic route is available where there is an efficient direct oil transfer between the small droplets and large drops. This allows for a fast relaxation of the oil distribution between the two populations of drops.
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| 18. |
- Evilevitch, Alex, et al.
(författare)
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Mechanical Capsid Maturation Facilitates the Resolution of Conflicting Requirements for Herpesvirus Assembly
- 2022
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Ingår i: Journal of Virology. - : American Society for Microbiology. - 0022-538X .- 1098-5514. ; 96:4, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Most viruses undergo a maturation process from a weakly self-assembled, noninfectious particle to a stable, infectious virion. For herpesviruses, this maturation process resolves several conflicting requirements: (i) assembly must be driven by weak, reversible interactions between viral particle subunits to reduce errors and minimize the energy of self-assembly, and (ii) the viral particle must be stable enough to withstand tens of atmospheres of DNA pressure resulting from its strong confinement in the capsid. With herpes simplex virus 1 (HSV-1) as a prototype of human herpesviruses, we demonstrated that this mechanical capsid maturation is mainly facilitated through capsid binding auxiliary protein UL25, orthologs of which are present in all herpesviruses. Through genetic manipulation of UL25 mutants of HSV-1 combined with the interrogation of capsid mechanics with atomic force microscopy nano-indentation, we suggested the mechanism of stepwise binding of distinct UL25 domains correlated with capsid maturation and DNA packaging. These findings demonstrate another paradigm of viruses as elegantly programmed nano-machines where an intimate relationship between mechanical and genetic information is preserved in UL25 architecture. IMPORTANCE The minor capsid protein UL25 plays a critical role in the mechanical maturation of the HSV-1 capsid during virus assembly and is required for stable DNA packaging. We modulated the UL25 capsid interactions by genetically deleting different UL25 regions and quantifying the effect on mechanical capsid stability using an atomic force microscopy (AFM) nanoindentation approach. This approach revealed how UL25 regions reinforced the herpesvirus capsid to stably package and retain pressurized DNA. Our data suggest a mechanism of stepwise binding of two main UL25 domains timed with DNA packaging.
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| 19. |
- Evilevitch, Alex
(författare)
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Molecular Exchange in Colloidal Dispersions
- 2001
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is a study of molecular exchange between the aggregates in a colloidal dispersion. The problem of oil molecular transport at resolubilization of big oil drops by smaller microemulsion droplets is considered as an experimental model system. The resolubilization kinetics was measured through a temperature jump into a droplet microemulsion phase from a two-phase region of microemulsion droplets and separating oil. The relaxation process was monitored by following the turbidity of the system. A quantitative model for the solubilization kinetics was formulated on the basis of experimental observations. The effects of concentrations and sizes of droplets are treated within a framework of a cell model. New computer simulation approach for molecular exchange studies is also introduced. The simulation model describes discreet spherical aggregates moving in a Brownian motion at the same time as small molecules, such as oil or surfactant, are allowed to exchange between the aggregates. The model allows a detailed study of the local exchange between neighbor micelles as well as the collective long-range exchange. The theoretical analysis from both models showed that as a result of high droplet concentration, the molecular exchange between the droplets occurs via diffusive monomer transport only in the vicinity of the droplets’ surface, and not across the entire system as predicted by the infinite dilution limit approximation. A quantitative agreement between the simulation, the cell model, and experiment was obtained in description of the resolubilization process. In addition, structure and transport properties of weakly charged oil-in-water microemulsion droplets, were also studied. Static and dynamic properties such as osmotic pressure, osmotic compressibility, self-diffusion, collective diffusion, and zero shear viscosity were analyzed by experimental and theoretical techniques.
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| 20. |
- Evilevitch, Alex, et al.
(författare)
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Molecular transport in a nonequilibrium droplet microemulsion system.
- 2001
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 17:22, s. 6893-6904
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we consider the problem of oil molecular transport between nonequilibrium microemulsion oil droplets in water. In particular, we have investigated the kinetics of solubilization of big oil drops by smaller microemulsion droplets transforming a bimodal size distribution into an equilibrium microemulsion with a unimodal size distribution. The process involves the diffusion of oil monomers across the aqueous solvent. Solubilization experiments are presented on a well-characterized nonionic microemulsion system, where interfacial area and dispersed volume are conserved and where the excess oil chemical potential is dominated by interfacial curvature energy. An analysis of the experiments shows that the solubilization kinetics depend significantly on the concentrations and sizes of big and small droplets. We formulate a quantitative model for the solubilization kinetics where the effects of size and concentrations are treated within the framework of a cell model. A quantitative agreement between model and experiment is obtained, and the analysis also shows that the majority of oil monomers are captured by small droplets already in the vicinity of the big drop surface when the concentration of small droplets is high.
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| 21. |
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| 22. |
- Evilevitch, Alex, et al.
(författare)
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Physics of viral infectivity : Matching genome length with capsid size
- 2010
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Ingår i: Emerging Topics in Physical Virology. - : IMPERIAL COLLEGE PRESS. - 9781848164642 - 9781848164666 ; , s. 217-253
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Bokkapitel (refereegranskat)abstract
- In this work, we review recent advances in the field of physical virology, presenting both experimental and theoretical studies on the physical properties of viruses. We focus on the double-stranded DNA (dsDNA) bacteriophages as model systems for all of the dsDNA viruses both prokaryotic and eukaryotic. Recent studies demonstrate that the DNA packaged into many dsDNA viral capsids is highly pressurized, which provides a force for the first step of passive injection of viral DNA into either bacterial or eukaryotic cells. Moreover, specific studies on capsid strength show a strong correlation between genome length and capsid size and robustness. The implications of these newly appreciated physical properties of a viral particle with respect to the infection process are discussed.
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| 23. |
- Evilevitch, Alex, et al.
(författare)
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Reconstituted virus-nucleus system reveals mechanics of herpesvirus genome uncoating
- 2022
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Ingår i: QRB Discovery. - : Cambridge University Press (CUP). - 2633-2892. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The viral replication cycle is controlled by information transduced through both molecular and mechanical interactions. Viral infection mechanics remains largely unexplored, however, due to the complexity of cellular mechanical responses over the course of infection as well as a limited ability to isolate and probe these responses. Here, we develop an experimental system consisting of herpes simplex virus type 1 (HSV-1) capsids bound to isolated and reconstituted cell nuclei, which allows direct probing of capsid-nucleus mechanics with atomic force microscopy (AFM). Major mechanical transformations occur in the host nucleus when pressurised viral DNA ejects from HSV-1 capsids docked at the nuclear pore complexes (NPCs) on the nuclear membrane. This leads to structural rearrangement of the host chromosome, affecting its compaction. This in turn regulates viral genome replication and transcription dynamics as well as the decision between a lytic or latent course of infection. AFM probing of our reconstituted capsid-nucleus system provides high-resolution topographical imaging of viral capsid docking at the NPCs as well as force volume mapping of the infected nucleus surface, reflecting mechanical transformations associated with chromatin compaction and stiffness of nuclear lamina (to which chromatin is tethered). This experimental system provides a novel platform for investigation of virus-host interaction mechanics during viral genome penetration into the nucleus.
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| 24. |
- Evilevitch, Alex, et al.
(författare)
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Structure and transport properties of a charged spherical microemulsion system
- 2001
-
Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 17:4, s. 1043-1053
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Tidskriftsartikel (refereegranskat)abstract
- Structure and transport properties of an oil-in-water microemulsion of weakly charged spherical micelles were studied experimentally using viscosity, NMR self-diffusion, and static and dynamic light scattering as well as theoretically by Brownian dynamics and Monte Carlo simulations and the Poisson-Boltzmann equation. The micelles contain decane covered by the nonionic surfactant pentaethylene glycol dodecyl ether (C12E5) and the ionic surfactant sodium dodecyl sulfate. The system has a constant surfactant-to-oil ratio, and the total volume fraction of surfactant and oil, , is varied between 0.01 0.46. The micelles were made weakly charged by replacing a small fraction (0.01, 0.04, and 0.06) of the nonionic surfactant with ionic surfactant, retaining the micellar size. Comparison between self-diffusion and viscosity coefficients measured as a function of concentration showed that the system obeys the generalized Stokes-Einstein relation at lower micellar concentrations. At higher micellar concentrations, a slightly modified equation can be used upon the addition of an extra frictional factor due to stronger interactions. The collective diffusion coefficient shows a maximum as a function of the volume fraction. This result is in good agreement with predictions based on a charged hard-sphere model with hydrodynamic interactions. Other static and dynamic properties such as osmotic pressure, osmotic compressibility, and self-diffusion coefficient were obtained theoretically from simulations based on a charged-sphere model. The static and dynamic properties of the charged hard-sphere model qualitatively describe the behavior of the charged microemulsion micelles. At high volume fractions, > 0.1, the agreement is quantitative, but at < 0.1 the effect of the charge is smaller than what is predicted from the model.
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| 25. |
- Evilevitch, Alex
(författare)
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The mobility of packaged phage genome controls ejection dynamics
- 2018
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Ingår i: eLife. - 2050-084X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The cell decision between lytic and lysogenic infection is strongly influenced by dynamics of DNA injection into a cell from a phage population, as phages compete for limited resources and progeny. However, what controls the timing of viral DNA ejection events was not understood. This in vitro study reveals that DNA ejection dynamics for phages can be synchronized (occurring within seconds) or desynchronized (displaying minutes-long delays in initiation) based on mobility of encapsidated DNA, which in turn is regulated by environmental factors, such as temperature and extra-cellular ionic conditions. This mechano-regulation of ejection dynamics is suggested to influence viral replication where the cell's decision between lytic and latent infection is associated with synchronized or desynchronized delayed ejection events from phage population adsorbed to a cell. Our findings are of significant importance for understanding regulatory mechanisms of latency in phage and Herpesviruses, where encapsidated DNA undergoes a similar mechanical transition.
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