scholarly journals A dynamic view of histone tails interaction with clustered abasic sites in a nucleosome core particle

2021 ◽  
Author(s):  
Emmanuelle Bignon ◽  
Natacha Gillet ◽  
Tao Jiang ◽  
Christophe Morell ◽  
Elise Dumont
Keyword(s):  
Dynamical Behavior ◽  
Dna Lesions ◽  
Histone Tails ◽  
Systematic Assessment ◽  
Nucleosome Core ◽  
Abasic Sites ◽  
Mutational Hotspots ◽  
The One ◽  
Dynamics Simulations ◽  
Experimental Findings

AbstractApurinic/apyrimidinic sites are the most common DNA damage under physiological conditions. Yet, their structural and dynamical behavior within nucleosome core particles has just begun to be investigated, and show dramatic differences with the one of abasic sites in B-DNA. Clusters of two or more abasic sites are repaired even less efficiently and hence constitute hotspots of high mutagenicity notably due to enhanced double-strand breaks formation. Based on a X-ray structure of a 146-bp DNA wrapped onto a histone core, we investigate the structural behavior of two bistranded abasic sites positioned at mutational hotspots along microsecond-range molecular dynamics simulations. Our simulations allow us to probe histone tails interactions at clustered abasic sites locations, with a definitive assignment of the key residues in-volved in the NCP-catalyzed formation of DNA–protein cross-linking in line with recent experimental findings, and pave the way towards a systematic assessment of histone tails response to DNA lesions.

scholarly journals Nucleosomal embedding reshapes the dynamics of abasic sites

2020 ◽  
Author(s):  
Emmanuelle Bignon ◽  
Victor Claerbout ◽  
Tao Jiang ◽  
Christophe Morell ◽  
Natacha Gillet ◽  
...  
Keyword(s):  
Conformational Dynamics ◽  
Dna Lesions ◽  
Nucleosome Core ◽  
Abasic Sites ◽  
Nucleosomal Dna ◽  
Cross Links ◽  
Ap Sites ◽  
Base Excision ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTApurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the occurrence of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. This study paves the way towards an in silico mapping of DNA-protein cross-links.

scholarly journals Nucleosomal embedding reshapes the dynamics of abasic sites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Emmanuelle Bignon ◽  
Victor E. P. Claerbout ◽  
Tao Jiang ◽  
Christophe Morell ◽  
Natacha Gillet ◽  
...  
Keyword(s):  
Conformational Dynamics ◽  
Experimental Studies ◽  
Dna Lesions ◽  
Nucleosome Core ◽  
Abasic Sites ◽  
Cross Links ◽  
Ap Sites ◽  
Base Excision ◽  
Dynamics Simulations ◽  
The Impact

Abstract Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links leading to strand breaks, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the frequency of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. Such an in silico mapping of DNA-protein cross-links gives important insights for further experimental studies involving mutagenesis and truncation of histone tails to unravel mechanisms of DPCs formation.

scholarly journals Impact of the nucleosome histone core on the structure and dynamics of DNA containing pyrimidine-pyrimidone (6-4) photoproduct

2020 ◽  
Author(s):  
Eva Matoušková ◽  
Emmanuelle Bignon ◽  
Victor Claerbout ◽  
Tomáš Dršata ◽  
Natacha Gillet ◽  
...  
Keyword(s):  
Conformational Dynamics ◽  
Structural Adaptation ◽  
Histone Tails ◽  
Nucleosome Core ◽  
Dna Lesion ◽  
Repair Protein ◽  
Dynamics Simulations ◽  
Mechanical Restraints ◽  
Histone Core

ABSTRACTThe pyrimidine-pyrimidone (6-4) photoproduct (64-PP) is an important photoinduced DNA lesion, which constitutes a mutational signature for melanoma. The structural impact of 64-PP on DNA complexed with compaction proteins, and notably histones, affects the mechanism of its mutagenicity and repair but remains poorly understood. Here we investigate the conformational dynamics of DNA containing 64-PP lesions within the nucleosome core particle by atomic-resolution molecular dynamics simulations at the multi-microsecond time scale. We demonstrate that the histone core exerts important mechanical restraints that largely decrease global DNA structural fluctuations. However, we also show that local DNA flexibility at the damaged site is enhanced, due to imperfect structural adaptation to restraints imposed by the histone core. In particular, if 64-PP faces the histone core and is therefore not directly accessible by the repair protein, the complementary strand facing the solvent exhibits higher flexibility than the corresponding strand in a naked, undamaged DNA. This may serve as an initial recognition signal for repair. Our simulations also pinpoint the structural role of proximal residues from the truncated histone tails.

General Trend of Negative Transference Number in Li Salt/Ionic Liquid Mixtures

2019 ◽  
Author(s):  
Nicola Molinari ◽  
Jonathan P. Mailoa ◽  
Boris Kozinsky
Keyword(s):  
Ionic Liquid ◽  
Transference Number ◽  
Liquid Mixtures ◽  
Single Linkage ◽  
Self Diffusion ◽  
Wide Range ◽  
Single Linkage Cluster ◽  
Concentrated Solution ◽  
The One ◽  
Dynamics Simulations

We show that strong cation-anion interactions in a wide range of lithium-salt/ionic liquid mixtures result in a negative lithium transference number, using molecular dynamics simulations and rigorous concentrated solution theory. This behavior fundamentally deviates from the one obtained using self-diffusion coefficient analysis and agrees well with experimental electrophoretic NMR measurements, which accounts for ion correlations. We extend these findings to several ionic liquid compositions. We investigate the degree of spatial ionic coordination employing single-linkage cluster analysis, unveiling asymmetrical anion-cation clusters. Additionally, we formulate a way to compute the effective lithium charge that corresponds to and agrees well with electrophoretic measurements and show that lithium effectively carries a negative charge in a remarkably wide range of chemistries and concentrations. The generality of our observation has significant implications for the energy storage community, emphasizing the need to reconsider the potential of these systems as next generation battery electrolytes.<br>

scholarly journals Numerical Study and Experimental Validation of Deformation of FCC CuAl Single Crystal Obtained by Additive Manufacturing

Metals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 582
Author(s):  
Anton Y. Nikonov ◽  
Andrey I. Dmitriev ◽  
Dmitry V. Lychagin ◽  
Lilia L. Lychagina ◽  
Artem A. Bibko ◽  
...  
Keyword(s):  
Single Crystal ◽  
Numerical Study ◽  
Strain Curve ◽  
Aluminum Bronze ◽  
Partial Dislocations ◽  
Slip Planes ◽  
Loaded Material ◽  
Dislocation Movement ◽  
Dynamics Simulations ◽  
Experimental Findings

The importance of taking into account directional solidification of grains formed during 3D printing is determined by a substantial influence of their crystallographic orientation on the mechanical properties of a loaded material. This issue is studied in the present study using molecular dynamics simulations. The compression of an FCC single crystal of aluminum bronze was performed along the <111> axis. A Ni single crystal, which is characterized by higher stacking fault energy (SFE) than aluminum bronze, was also considered. It was found that the first dislocations started to move earlier in the material with lower SFE, in which the slip of two Shockley partials was observed. In the case of the material with higher SFE, the slip of a full dislocation occurred via successive splitting of its segments into partial dislocations. Regardless of the SFE value, the deformation was primarily occurred by means of the formation of dislocation complexes involved stair-rod dislocations and partial dislocations on adjacent slip planes. Hardening and softening segments of the calculated stress–strain curve were shown to correspond to the periods of hindering of dislocations at dislocation pileups and dislocation movement between them. The simulation results well agree with the experimental findings.

scholarly journals Electrically turning periodic structures in cholesteric layer with conical–planar boundary conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Oxana Prishchepa ◽  
Mikhail Krakhalev ◽  
Vladimir Rudyak ◽  
Vitaly Sutormin ◽  
Victor Zyryanov
Keyword(s):  
Boundary Conditions ◽  
Periodic Structures ◽  
Cholesteric Liquid Crystal ◽  
Growth Direction ◽  
Smooth Transition ◽  
Defect Structures ◽  
Optical Cell ◽  
Elastic Continuum ◽  
The One ◽  
Experimental Findings

AbstractElectro-optical cell based on the cholesteric liquid crystal is studied with unique combination of the boundary conditions: conical anchoring on the one substrate and planar anchoring on another one. Periodic structures in cholesteric layer and their transformation under applied electric field are considered by polarizing optical microscopy, the experimental findings are supported by the data of the calculations performed using the extended Frank elastic continuum approach. Such structures are the set of alternating over- and under-twisted defect lines whose azimuthal director angles differ by $$180^\circ$$ 180 ∘ . The $$U^+$$ U + and $$U^-$$ U - -defects of periodicity, which are the smooth transition between the defect lines, are observed at the edge of electrode area. The growth direction of defect lines forming a diffraction grating can be controlled by applying a voltage in the range of $$0\le \, V \le 1.3$$ 0 ≤ V ≤ 1.3  V during the process. Resulting orientation and distance between the lines don’t change under voltage. However, at $$V>1.3$$ V > 1.3  V $$U^+$$ U + -defects move along the defect lines away from the electrode edges, and, finally, the grating lines collapse at the cell’s center. These results open a way for the use of such cholesteric material in applications with periodic defect structures where a periodicity, orientation, and configuration of defects should be adjusted.

scholarly journals Quantum teleportation with imperfect quantum dots

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
F. Basso Basset ◽  
F. Salusti ◽  
L. Schweickert ◽  
M. B. Rota ◽  
D. Tedeschi ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Quantum Teleportation ◽  
Bell State ◽  
Spectral Filtering ◽  
State Measurement ◽  
Communication Architectures ◽  
The One ◽  
Experimental Findings ◽  
Photon Source ◽  
Remarkable Progress

AbstractEfficient all-photonic quantum teleportation requires fast and deterministic sources of highly indistinguishable and entangled photons. Solid-state-based quantum emitters—notably semiconductor quantum dots—are a promising candidate for the role. However, despite the remarkable progress in nanofabrication, proof-of-concept demonstrations of quantum teleportation have highlighted that imperfections of the emitter still place a major roadblock in the way of applications. Here, rather than focusing on source optimization strategies, we deal with imperfections and study different teleportation protocols with the goal of identifying the one with maximal teleportation fidelity. Using a quantum dot with sub-par values of entanglement and photon indistinguishability, we show that the average teleportation fidelity can be raised from below the classical limit to 0.842(14), adopting a polarization-selective Bell state measurement and moderate spectral filtering. Our results, which are backed by a theoretical model that quantitatively explains the experimental findings, loosen the very stringent requirements set on the ideal entangled-photon source and highlight that imperfect quantum dots can still have a say in teleportation-based quantum communication architectures.

Substrate induced freezing, melting and depinning transitions in two-dimensional liquid crystalline systems

2022 ◽  
Author(s):  
Bharti bharti ◽  
Debabrata Deb
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystals ◽  
Molecular Dynamics Simulations ◽  
Liquid Crystalline ◽  
Two Dimensional ◽  
One Dimensional ◽  
The One ◽  
Dynamics Simulations

We use molecular dynamics simulations to investigate the ordering phenomena in two-dimensional (2D) liquid crystals over the one-dimensional periodic substrate (1DPS). We have used Gay-Berne (GB) potential to model the...

ON TWO-DIMENSIONAL DYNAMICAL SYSTEMS ASSOCIATED WITH MEMBRANE KINETICS UNDERLYING CARDIAC ARRHYTHMIAS

2009 ◽  
Vol 19 (05) ◽  
pp. 1709-1732 ◽  
Author(s):  
B. M. BAKER ◽  
M. E. KIDWELL ◽  
R. P. KLINE ◽  
I. POPOVICI
Keyword(s):  
Dynamical Behavior ◽  
Basins Of Attraction ◽  
Two Dimensional ◽  
Stimulus Period ◽  
Smooth Maps ◽  
Periodic Stimulation ◽  
Piecewise Smooth Maps ◽  
Dimensional Version ◽  
Bifurcation Law ◽  
The One

We study the orbits, stability and coexistence of orbits in the two-dimensional dynamical system introduced by Kline and Baker to model cardiac rhythmic response to periodic stimulation — as a function of (a) kinetic parameters (two amplitudes, two rate constants) and (b) stimulus period. The original paper focused mostly on the one-dimensional version of this model (one amplitude, one rate constant), whose orbits, stability properties, and bifurcations were analyzed via the theory of skew-tent (hence unimodal) maps; the principal family of orbits were so-called "n-escalators", with n a positive integer. The two-dimensional analog (motivated by experimental results) has led to the current study of continuous, piecewise smooth maps of a polygonal planar region into itself, whose dynamical behavior includes the coexistence of stable orbits. Our principal results show (1) how the amplitude parameters control which escalators can come into existence, (2) escalator bifurcation behavior as the stimulus period is lowered — leading to a "1/n bifurcation law", and (3) the existence of basins of attraction via the coexistence of three orbits (two of them stable, one unstable) at the first (largest stimulus period) bifurcation. We consider the latter result our most important, as it is conjectured to be connected with arrhythmia.

Sign in / Sign up

Export Citation Format

Share Document