122 research outputs found
Complexation between oppositely charged polyelectrolytes: beyond the Random Phase Approximation
We consider the phase behavior of polymeric systems by calculating the
structure factors beyond the Random Phase Approximation. The effect of this
correction to the mean-field RPA structure factor is shown to be important in
the case of coulombic systems. Two examples are given: simple electrolytes and
mixtures of incompatible oppositely charged polyelectrolytes. In this last
case, all former studies predicted an enhancement of compatibility for
increasing charge densities; we also describe the complexation transition
between the polyelectrolytes. We determine a phase diagram of the
polyelectrolyte mixture that includes both complexation and incompatibility.Comment: 18 pages, 4 figures. Submitted to EPJ-
Comparing open and closed molecular self-assembly
We study theoretically in the present work the self-assembly of molecules in
an open system, which is fed by monomers and depleted in partial or complete
clusters. Such a scenario is likely to occur for example in the context of
viral self-assembly. We provide a general formula for the mean-field size
distribution which is valid both at equilibrium in a closed system, and in the
stationary state in an open system. This allows us to explore in a simple way
out-of-equilibrium features for self-assembly and compare them to equilibrium
properties. In particular, we identify a region of parameter space for which
the out-of-equilibrium size distribution in the presence of external fluxes is
equal to the equilibrium size distribution in the absence of external fluxes,
up to a constant renormalization factor. The range of validity of this result
and its consequences are discussed.Comment: PACS 81.16.Fg - Supramolecular and biochemical assembly PACS 82.39.-k
- Chemical kinetics in biological systems PACS 05.65.+b - Self-organized
system
Charge Distribution on Annealed Polyelectrolytes
We investigate the equilibrium charge distribution along a single annealed
polyelectrolyte chain under different conditions. The coupling between the
conformation of the chain and the local charge distribution is described for
various solvent qualities and salt concentration. In salt free solution, we
find a slight charge depletion in the central part of the chain: the charges
accumulate at the ends. The effect is less important if salt is added to the
solution since the charge inhomogeneity is localized close to the chain ends
over a distance of order of the Debye length. In the case of poor solvent
conditions we find a different charging of beads and strings in the framework
of the necklace model. This inhomogeneity leads to a charge instability and a
first order transition between spherical globules and elongated chains.Comment: 20 pages, 4 figure
Osmotic pressure: resisting or promoting DNA ejection from phage
Recent in vitro experiments have shown that DNA ejection from bacteriophage
can be partially stopped by surrounding osmotic pressure when ejected DNA is
digested by DNase I on the course of ejection. We argue in this work by
combination of experimental techniques (osmotic suppression without DNaseI
monitored by UV absorbance, pulse-field electrophoresis, and cryo-EM
visualization) and simple scaling modeling that intact genome (i.e. undigested)
ejection in a crowded environment is, on the contrary, enhanced or eventually
complete with the help of a pulling force resulting from DNA condensation
induced by the osmotic stress itself. This demonstrates that in vivo, the
osmotically stressed cell cytoplasm will promote phage DNA ejection rather than
resisting it. The further addition of DNA-binding proteins under crowding
conditions is shown to enhance the extent of ejection. We also found some
optimal crowding conditions for which DNA content remaining in the capsid upon
ejection is maximum, which correlates well with the optimal conditions of
maximum DNA packaging efficiency into viral capsids observed almost 20 years
ago. Biological consequences of this finding are discussed
Entropic control of particle sizes during viral self-assembly
Morphologic diversity is observed across all families of viruses. Yet these supra-molecular assemblies are produced most of the time in a spontaneous way through complex molecular self-assembly scenarios. The modeling of these phenomena remains a challenging problem within the emerging field of Physical Virology. We present in this work a theoretical analysis aiming at highlighting the particular role of configuration entropy in the control of viral particle size distribution. Specializing this model to retroviruses like HIV-1, we predict a new mechanism of entropic control of both RNA uptake into the viral particle, and of the particle's size distribution. Evidence of this peculiar behavior has been recently reported experimentally
Dynamical DNA accessibility induced by chromatin remodeling and protein binding
International audienceChromatin remodeling factors are enzymes being able to alter locally chromatin structure at the nucleosomal level and they actively participate in the regulation of gene expression. Using simple rules for individual nucleosome motion induced by a remodeling factor, we designed simulations of the remodeling of oligomeric chromatin, in order to address quantitatively collective effects in DNA accessibility upon nucleosome mobilization. Our results suggest that accessibility profiles are inhomogeneous thanks to borders effects like protein binding. Remarkably, we show that the accessibility lifetime of DNA sequence is roughly doubled in the vicinity of borders as compared to its value in bulk regions far from the borders. These results are quantitatively interpreted as resulting from the confined diffusion of a large nucleosome depleted region
DNA heats up : Energetics of genome ejection from phage revealed by isothermal titration calorimetry
Most bacteriophages are known to inject their double-stranded DNA into
bacteria upon receptor binding in an essentially spontaneous way. This downhill
thermodynamic process from the intact virion toward the empty viral capsid plus
released DNA is made possible by the energy stored during active packaging of
the genome into the capsid. Only indirect measurements of this energy have been
available until now using either single-molecule or osmotic suppression
techniques. In this paper, we describe for the first time the use of isothermal
titration calorimetry to directly measure the heat released (or equivalently
the enthalpy) during DNA ejection from phage lambda, triggered in solution by a
solubilized receptor. Quantitative analyses of the results lead to the
identification of thermodynamic determinants associated with DNA ejection. The
values obtained were found to be consistent with those previously predicted by
analytical models and numerical simulations. Moreover, the results confirm the
role of DNA hydration in the energetics of genome confinement in viral capsids.Comment: 24 pages including figures and tabl
Challenging packaging limits and infectivity of phage λ
The terminase motors of bacteriophages have been shown to be among the strongest active machines in the biomolecular world, being able to package several tens of kilobase pairs of viral genome into a capsid within minutes. Yet these motors are hindered at the end of the packaging process by the progressive build-up of a force resisting packaging associated with already packaged DNA. In this experimental work, we raise the issue of what sets the upper limit on the length of the genome that can be packaged by the terminase motor of phage λ and still yield infectious virions, and the conditions under which this can be efficiently performed. Using a packaging strategy developed in our laboratory of building phage λ from scratch, together with plaque assay monitoring, we have been able to show that the terminase motor of phage λ is able to produce infectious particles with up to 110% of the wild-type (WT) λ-DNA length. However, the phage production rate, and thus the infectivity, decreased exponentially with increasing DNA length, and was a factor of 103 lower for the 110% λ-DNA phage. Interestingly, our in vitro strategy was still efficient in fully packaging phages with DNA lengths as high as 114% of the WT length, but these viruses were unable to infect bacterial cells efficiently. Further, we demonstrated that the phage production rate is modulated by the presence of multivalent ionic species. The biological consequences of these finding are discussed
RNA Control of HIV-1 Particle Size Polydispersity
HIV-1, an enveloped RNA virus, produces viral particles that are known to be
much more heterogeneous in size than is typical of non-enveloped viruses. We
present here a novel strategy to study HIV-1 Viral Like Particles (VLP)
assembly by measuring the size distribution of these purified VLPs and
subsequent viral cores thanks to Atomic Force Microscopy imaging and
statistical analysis. This strategy allowed us to identify whether the presence
of viral RNA acts as a modulator for VLPs and cores size heterogeneity in a
large population of particles. These results are analyzed in the light of a
recently proposed statistical physics model for the self-assembly process. In
particular, our results reveal that the modulation of size distribution by the
presence of viral RNA is qualitatively reproduced, suggesting therefore an
entropic origin for the modulation of RNA uptake by the nascent VLP
Electrophoresis of positioned nucleosomes
We present in this paper an original approach to compute the electrophoretic
mobility of rigid nucleo-protein complexes like nucleosomes. This model allows
to address theoretically the influence of complex position along DNA, as well
as wrapped length of DNA on the electrophoretic mobility of the complex. The
predictions of the model are in qualitative agreement with experimental results
on mononucleosomes assembled on short DNA fragments (<400bp). Influence of
additional experimental parameters like gel concentration, ionic strength,
effective charges is also discussed in the framework of the model, and is found
to be qualitatively consistent with experiments when available. Based on the
present model, we propose a simple semi-empirical formula describing
positioning of nucleosomes as seen through electrophoresis.Comment: to appear in Biophys. J. 29 page
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