Biomedical subjects

H Schiessel

Publications and source records attributed to H Schiessel.

12 recordsLinked to original sources

PubMed2006

Tail-induced attraction between nucleosome core particles.

We study a possible electrostatic mechanism underlying the compaction of DNA inside the nuclei of eucaryotes: the tail-bridging effect between nucleosomes, the fundamental DNA packaging units of the chromatin complex. As a simple model of the nucleosome we introduce the eight-tail colloid, a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We show that our complexes attract each other via the formation of chain bridges and contrast this to the effect of attraction via charge patches. We demonstrate that the attraction between eight-tail colloids can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation is controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.

Animals↗

PubMed2006

Rayleigh instability of charged aggregates: Role of the dimensionality, ionic strength, and dielectric contrast.

We extended a previous analysis of the classical Rayleigh instability of spherical charged droplets in the presence of neutralizing monovalent counterions [M. Deserno, Eur. Phys. J. E 6, 163 (2001)], by generalizing the problem for suspensions of aggregates with D-dimensional symmetry, corresponding for D = 2 to infinite (rodlike) cylindrical charged bundles and for D = 3 to spherical charged droplets. In addition, we include the effects of added monovalent salt and of dielectric contrast between the charged aggregate and the surrounding solvent. The electrostatic energy taking the microion screening into account is estimated using uniform profiles within the framework of the cell model. We verify the robustness of these results by also considering Debye-Hückel-type microion profiles that are obtained by the minimization of a linearized Poisson-Boltzmann free-energy functional. In the case when the microions can enter inside the charged aggregates, we confirm the occurrence of a discontinuous phase change between aggregates of finite size and an infinite aggregate, which takes place at a collapse temperature that depends on their volume fraction phi and on the salt content. Decrease of phi shifts the phase-change temperature toward higher values, while salt addition has an opposite effect. We obtain analytical expressions for the phase-separation line in the asymptotic limit of infinite dilution (phi-->0), showing that the collapse temperature depends logarithmically on phi . As an application for D = 3 we discuss the stability of the pearl-necklace structures of flexible polyelectrolytes in poor solvents. The case D = 2 is applied to the problem of finite bundle sizes of stiff polyelectrolytes that attract each other-via, e.g., multivalent counterions-leading to an effective surface tension.

Journal Article↗

PubMed2006

Comment on "Chromatin fiber functional organization: some plausible models" by A. Lesne and J.-M. Victor.

In this comment on the contribution of A. Lesne and J.-M. Victor I provide some additional ideas on the hypothesis that higher-order chromatin structures stamp their marks on their small subunits.

Chromatin↗

PubMed2006

The nucleosome: a transparent, slippery, sticky and yet stable DNA-protein complex.

Roughly three quarters of eucaryotic DNA are tightly wrapped onto protein cylinders organized in so-called nucleosomes. Despite this fact, the wrapped DNA cannot be inert since DNA is at the heart of many crucial life processes. We focus here on physical mechanisms that might allow nucleosomes to perform a great deal of such processes, specifically 1) on unwrapping fluctuations that give DNA-binding proteins access to the wrapped DNA portions without disrupting the nucleosome as a whole, 2) on corkscrew sliding along DNA and some implications and on 3) tail-bridging-induced attraction between nucleosomes as a means of controlling higher-order folding.

Base Sequence↗

PubMed2005

Statics and dynamics of polymer-wrapped colloids.

We study the complex between a colloidal particle and a semiflexible polymer chain that "wraps" around it. Via molecular dynamics simulation we investigate statistical and dynamical properties of this system. First we establish the dependence of wrapped chain length on absorption energy and chain persistence length and obtain the distribution of wrapped-sphere positions. Then we study the length and position distributions of thermally excited loop defects. Finally we consider the repositioning dynamics of the colloid, focusing on the case where the chain stays wrapped onto the complex. Specifically we determine the mean square displacement of the central monomer of the wrapped chain and the resulting diffusion coefficient of the chain as a function of its persistence length, absorption energy, chain length, and size of the sphere. We argue that both statics and dynamics of these complexes can be mainly understood by energetic arguments, whereas entropic contributions from the chain configurations play only a minor role.

Journal Article↗

PubMed2004

DNA spools under tension.

DNA spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core, are ubiquitous in nature. We develop a general theory describing the nonequilibrium behavior of DNA spools under linear tension. Two puzzling and seemingly unrelated recent experimental findings, the sudden quantized unwrapping of nucleosomes and that of DNA toroidal condensates under tension, are theoretically explained and shown to be of the same origin. The study provides new insights into nucleosome and chromatin fiber stability and dynamics.

DNA↗

PubMed2003

Where the linearized Poisson-Boltzmann cell model fails: the planar case as a prototype study.

The linearized Poisson-Boltzmann (PB) approximation is investigated for the classical problem of two infinite, uniformly charged planes in electrochemical equilibrium with an infinite monovalent salt reservoir. At the nonlinear level, we obtain an explicit expression of the associated electrostatic contribution to the semi-grand-canonical potential. The linearized osmotic-pressure difference between the interplane region and the salt reservoir becomes negative in the low-temperature, large-separation, or high-surface charge limits, in disagreement with the exact (at mean-field level) nonlinear PB solution. We show that these artifacts--although thermodynamically consistent with quadratic expansions of the nonlinear functional--can be traced back to the nonfulfillment of the underlying assumptions of the linearization. Explicit comparison between the analytical expressions of the exact nonlinear solution and the corresponding linearized equations allows us to show that the linearized results are asymptotically exact in the weak-coupling and counterionic ideal-gas limits, but always fail otherwise, predicting negative osmotic-pressure differences. By taking appropriate limits of the full nonlinear PB solution, we provide asymptotic expressions for the semi-grand-canonical potential and the osmotic-pressure difference that involve only elementary functions, which cover the complementary region where the linearized theory breaks down.

Journal Article↗

PubMed2003

Chromatin dynamics: nucleosomes go mobile through twist defects.

We study the spontaneous "sliding" of histone spools (nucleosomes) along DNA as a result of thermally activated single base pair twist defects. To this end we map the system onto a suitably extended Frenkel-Kontorova model. Combining results from several recent experiments we are able to estimate the nucleosome mobility without adjustable parameters. Our model shows also how the local mobility is intimately linked to the underlying base pair sequence.

Chromatin↗

PubMed2003

Nucleosome repositioning via loop formation.

Active (catalyzed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eukaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by earlier works. The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model-being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed, and compared to existing experimental findings.

Binding Sites↗

PubMed2002

Defect-induced perturbations of atomic monolayers on solid surfaces.

We study long-range morphological changes in atomic monolayers on solid substrates induced by different types of defects; e.g., by monoatomic steps in the surface, or by the tip of an atomic force microscope (AFM), placed at some distance above the substrate. Representing the monolayer in terms of a suitably extended Frenkel-Kontorova-type model, we calculate the defect-induced density profiles for several possible geometries. In case of an AFM tip, we also determine the extra force exerted on the tip due to the tip-induced dehomogenization of the monolayer.

Journal Article↗

PubMed2001

Polymer reptation and nucleosome repositioning.

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem arises in the case of globular aggregates of proteins (histones) that are wound by DNA in the chromosomes of plants and animals; these beads (nucleosomes) are multiply wrapped and yet are able to reposition themselves over long distances, while remaining bound by the DNA chain.

Animals↗

PubMed2001

DNA folding: structural and mechanical properties of the two-angle model for chromatin.

We present a theoretical analysis of the structural and mechanical properties of the 30-nm chromatin fiber. Our study is based on the two-angle model introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A. Horowitz, and N. Whitaker. 1993. Proc. Natl. Acad. Sci. USA. 90:9021-9025) that describes the chromatin fiber geometry in terms of the entry-exit angle of the nucleosomal DNA and the rotational setting of the neighboring nucleosomes with respect to each other. We analytically explore the different structures that arise from this building principle, and demonstrate that the geometry with the highest density is close to the one found in native chromatin fibers under physiological conditions. On the basis of this model we calculate mechanical properties of the fiber under stretching. We obtain expressions for the stress-strain characteristics that show good agreement with the results of recent stretching experiments (Cui, Y., and C. Bustamante. 2000. Proc. Natl. Acad. Sci. USA. 97:127-132) and computer simulations (Katritch, V., C. Bustamante, and W. K. Olson. 2000. J. Mol. Biol. 295:29-40), and which provide simple physical insights into correlations between the structural and elastic properties of chromatin.

Chromatin↗