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  • 1
    Keywords: DYNAMICS ; MELTS
    Abstract: A lattice-based simulation method for polymer diffusion in a viscoelastic medium is presented. This method combines the eight-site bond fluctuation model with an algorithm for the simulation of fractional Brownian motion on the lattice. The method applies to unentangled self-avoiding chains and is probed for anomalous diffusion exponents alpha between 0.7 and 1.0. The simulation results are in very good agreement with the predictions of the generalized Rouse model of a self-avoiding chain polymer in a viscoelastic medium.
    Type of Publication: Journal article published
    PubMed ID: 24972262
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  • 2
    Keywords: MODEL ; GENOME ; DNA ; DYNAMICS ; METHYLATION ; GENE-REGULATION ; CHROMATIN FIBER ; HISTONE H3 ; MATRIX FORMALISM ; CHROMODOMAIN
    Abstract: Heterochromatin protein 1 (HP1) participates in establishing and maintaining heterochromatin via its histone-modification-dependent chromatin interactions. In recent papers HP1 binding to nucleosomal arrays was measured in vitro and interpreted in terms of nearest-neighbour cooperative binding. This mode of chromatin interaction could lead to the spreading of HP1 along the nucleosome chain. Here, we reanalysed previous data by representing the nucleosome chain as a 1D binding lattice and showed how the experimental HP1 binding isotherms can be explained by a simpler model without cooperative interactions between neighboring HP1 dimers. Based on these calculations and spatial models of dinucleosomes and nucleosome chains, we propose that binding stoichiometry depends on the nucleosome repeat length (NRL) rather than protein interactions between HP1 dimers. According to our calculations, more open nucleosome arrays with long DNA linkers are characterized by a larger number of binding sites in comparison to chains with a short NRL. Furthermore, we demonstrate by Monte Carlo simulations that the NRL dependent folding of the nucleosome chain can induce allosteric changes of HP1 binding sites. Thus, HP1 chromatin interactions can be modulated by the change of binding stoichiometry and the type of binding to condensed (methylated) and non-condensed (unmethylated) nucleosome arrays in the absence of direct interactions between HP1 dimers.
    Type of Publication: Journal article published
    PubMed ID: 25563825
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  • 3
    Keywords: transcription ; DYNAMICS ; CHROMATIN ; RNA-POLYMERASE-II ; fluorescence correlation spectroscopy ; CORE ; HUMAN-CELLS ; ACCESSIBILITY ; DOUBLE HELIX ; H2A/H2B DIMER
    Abstract: Nucleosomes have to open to allow access to DNA in transcription, replication, and DNA damage repair. Changes in DNA torsional strain (e.g. during transcription elongation) influence the accessibility of nucleosomal DNA. Here we investigated the effect of DNA supercoiling-induced torsional strain on nucleosome structure and stability by scanning force microscopy (SFM) and fluorescence correlation spectroscopy (FCS). Nucleosomes were reconstituted onto 2.7 kb DNA plasmids with varying superhelical densities. The SFM results show a clear dependence of the amount of DNA wrapped around the nucleosome core on the strength and type of supercoiling. Negative supercoiling led to smaller nucleosome opening angles as compared to relaxed or positively supercoiled DNA. FCS experiments show that nucleosomes reconstituted on negatively superhelical DNA are more resistant to salt-induced destabilization, as seen by reduced H2A-H2B dimer eviction from the nucleosome. Our results show that changes in DNA topology, e.g. during transcription elongation, affect the accessibility of nucleosomal DNA.
    Type of Publication: Journal article published
    PubMed ID: 25563201
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  • 4
    Keywords: SIMULATIONS ; Germany ; MICROSCOPY ; MODEL ; ENZYMES ; DYNAMICS ; SIMULATION ; WATER ; ACID ; MEMBRANE ; fatty acids ; KINETICS ; molecular ; FATTY-ACID ; RE ; PHOSPHOLIPIDS ; SI ; LIPASE ; ENZYME ; DISSIPATIVE PARTICLE DYNAMICS ; ELASTICITY ; ENZYMATIC-ACTIVITY ; HYDROLYSIS ; LIPID-BILAYERS ; phospholipid ; SURFACE-TENSION ; VESICLE
    Abstract: Phospholipases are a class of molecular machines that are involved in the active remodelling processes of biological membranes. These lipases are interfacially activated enzymes and in the specific case of phospholipase A(2) (PLA(2))the enzyme catalyses the hydrolysis of di-acyl phospholipids into products of lysolipids and fatty acids, that dramatically change the physical properties of lipid membrane substrates. Using dissipative particle dynamics simulations on a simple coarse-grained bead-spring model of a fluid lipid bilayer in water, the mechanical and diffusive properties of the bilayer in the pure state and after the action of PLA(2) have been calculated. It is found that, in response to hydrolysis, the lipid membrane. becomes mechanically softened and the various in-plane and trans-bilayer diffusional modes become enhanced. The results compare favourably with available experimental data
    Type of Publication: Journal article published
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  • 5
    Keywords: IN-VIVO ; ATOMIC-FORCE MICROSCOPY ; LIGAND-BINDING ; GENE-REGULATION ; COOPERATIVE BINDING ; TARGET SITES ; TRANSCRIPTION-FACTOR-BINDING ; ONE-DIMENSIONAL LATTICES ; NUCLEOSOME POSITIONS ; LINEAR LATTICE
    Abstract: Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibria measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical-mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.
    Type of Publication: Journal article published
    PubMed ID: 21386588
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  • 6
    Keywords: CELLS ; DYNAMICS ; LIVING CELLS ; MONTE-CARLO ; fluorescence correlation spectroscopy ; SUBDIFFUSION
    Abstract: Anomalous diffusion in crowded fluids, e. g. in the cytoplasm of living cells, is a frequent phenomenon. Despite manifold observations of anomalous diffusion with several experimental techniques, a thorough understanding of the underlying microscopic causes is still lacking. Here, we have quantitatively compared two popular techniques with which anomalous diffusion is typically assessed. Using extensive computer simulations of two prototypical random walks with stationary increments, i.e. fractional Brownian motion and obstructed diffusion, we find that single particle tracking (SPT) yields results for the diffusion anomaly that are equivalent to those obtained by fluorescence correlation spectroscopy (FCS). We also show that positional uncertainties, inherent to SPT experiments, lead to a systematic underestimation of the diffusion anomaly, regardless of the underlying random walk and measurement technique. This effect becomes particularly relevant when the position uncertainty is larger than the average positional displacement between two successive frames
    Type of Publication: Journal article published
    PubMed ID: 21613702
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  • 7
    Keywords: MODEL ; GENE ; MONTE-CARLO ; GENOME ORGANIZATION ; COEFFICIENT ; ANOMALOUS DIFFUSION ; GEOMETRY ; SUBDIFFUSION ; LIVING CELL-NUCLEI ; RANDOM-WALKS
    Abstract: eukaryotic cell nucleus harbours the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the DNA sequence information. However, its physical properties as a reaction medium are poorly understood. Here, we exploit mobility measurements of differently sized inert green fluorescent tracer proteins to characterize the viscoelastic properties of the nuclear interior of a living human cell. We find that it resembles a viscous fluid on small and large scales but appears viscoelastic on intermediate scales that change with protein size. Our results are consistent with simulations of diffusion through polymers and suggest that chromatin forms a random obstacle network rather than a self-similar structure with fixed fractal dimensions. By calculating how long molecules remember their previous position in dependence on their size, we evaluate how the nuclear environment affects search processes of chromatin targets.
    Type of Publication: Journal article published
    PubMed ID: 25563347
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  • 8
    Abstract: Noroviruses are the main cause of viral gastroenteritis with new variants emerging frequently. There are three Norovirus genogroups infecting humans. These genogroups are divided based on the sequence of their major capsid protein, which is able to form virus-like particles (VLPs) when expressed recombinantly. VLPs of the prototypical GI.1 Norwalk virus are known to disassemble into specific capsid protein oligomers upon alkaline treatment. Here, native mass spectrometry and electron microscopy on variants of GI.1 and of GII.17 were performed revealing differences in terms of stability between these groups. Beyond that, these experiments indicate differences even between variants within a genotype. The capsid stability was monitored in different ammonium acetate solutions varying both in ionic strength and pH. The investigated GI.1 isolate West Chester showed comparable disassembly profiles to the previously studied GI.1 Norwalk. However, differences were observed with the West Chester being more sensitive to alkaline pH. In stark contrast to that, capsids of the variant belonging to the currently prevalent genogroup GII were stable in all tested conditions. Both variants formed smaller capsid particles already at neutral pH. Certain amino acid substitutions in the S domain of West Chester relative to Norwalk virus are potentially resulting in formation of these T = 1 capsids.
    Type of Publication: Journal article published
    PubMed ID: 29282349
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  • 9
    Keywords: SIMULATIONS ; CELLS ; PROTEIN ; PROTEINS ; DYNAMICS ; SIMULATION ; CHROMATIN ; YEAST ; PARAMETERS ; CHROMOSOMES
    Abstract: We simulate the extension of spatially confined chromatin fibres modelled as polymer chains and examine the effect of the flexibility of the fibre and its degree of freedom. The developed formalism was used to analyse experimental data of telomere-telomere distances in living yeast cells in the absence of confining factors as identified by the proteins Sir4 and yKu70. Our analysis indicates that intrinsic properties of the chromatin fibre, in particular its elastic properties and flexibility, can influence the juxtaposition of the telomeric ends of chromosomes. However, measurements in intact yeast cells showed that the telomeres of chromosomes 3 and 6 come even closer together than the parameters of constraint imposed on the simulations would predict. This juxtaposition was specific to telomeres on one contiguous chromosome and overrode a tendency for separation that is imposed by anchoring
    Type of Publication: Journal article published
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  • 10
    Keywords: ENZYMES ; ACTIVATION ; MECHANISM ; mechanisms ; ASSOCIATION ; ACIDS ; DEGRADATION ; fatty acids ; INTERFACE ; DENMARK ; SUBSTRATE ; ENZYME ; HYDROLYSIS ; LIPOSOMES ; VIEW ; A2 ; BILAYERS ; DPPC ; PHOSPHOLIPASE A(2) ACTIVITY ; UNILAMELLAR VESICLES
    Abstract: A host of water-soluble enzymes are active at membrane surfaces and in association with membranes. Some of these enzymes are involved in signalling and in modification and remodelling of the membranes. A special class of enzymes, the phospholipases, and in particular secretory phospholipase A(2) (sPLA(2)), are only activated at the interface between water and membrane surfaces, where they lead to a break-down of the lipid molecules into lysolipids and free fatty acids. The activation is critically dependent on the physical properties of the lipid-membrane substrate. A topical review is given of our current understanding of the physical mechanisms responsible for activation of sPLA(2) as derived from a range of different experimental and theoretical investigations
    Type of Publication: Journal article published
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