DNA and its counterions: A molecular dynamics study

The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains diffusive in the presence of DNA. Ions sample the complete space available during the simulation time, although individual ions sample only about one-third of the simulation box. Ions preferentially sample electronegative sites around DNA, but direct binding to DNA bases remains a rather rare event, with highest site occupancy values of <13%. The location of direct binding sites depends greatly on the nature of the counterion. While Na+ binding in both grooves is strongly sequence-dependent with the preferred binding site in the minor groove, K+ mainly visits the major groove and binds close to the centre of the oligomer. The electrostatic potential of an average DNA structure therefore cannot account for the ability of a site to bind a given cation; other factors must also play a role. An extensive analysis of the influence of counterions on DNA conformation showed no evidence of minor groove narrowing upon ion binding. A significant difference between the conformations of the double helix in the different simulations can be attributed to extensive (/ transitions in the phosphate backbone during the simulation with Na+. These transitions, with lifetimes over tens of nanoseconds, however, appear to be correlated with ion binding to phosphates. The ion-specific conformational properties of DNA, hitherto largely overlooked, may play an important role in DNA recognition and binding

Differential stability of DNA crossovers in solution mediated by divalent cations

The assembly of DNA duplexes into higher-order structures plays a major role in many vital cellular functions such as recombination, chromatin packaging and gene regulation. However, little is currently known about the molecular structure and stability of direct DNADNA interactions that are required for such functions. In nature, DNA helices minimize electrostatic repulsion between double helices in several ways. Within crystals, B-DNA forms either right-handed crossovers by groovebackbone interaction or left-handed crossovers by groovegroove juxtaposition. We evaluated the stability of such crossovers at various ionic concentrations using large-scale atomistic molecular dynamics simulations. Our results show that right-handed DNA crossovers are thermodynamically stable in solution in the presence of divalent cations. Attractive forces at short-range stabilize such crossover structures with inter-axial separation of helices less than 20 . Right-handed crossovers, however, dissociate swiftly in the presence of monovalent ions only. Surprisingly, left-handed crossovers, assembled by sequence-independent juxtaposition of the helices, appear unstable even at the highest concentration of Mg2+studied here. Our study provides new molecular insights into chiral association of DNA duplexes and highlights the unique role divalent cations play in differential stabilization of crossover structures. These results may serve as a rational basis to understand the role DNA crossovers play in biological processes

Prescribed Performance Control Guided Policy Improvement for Satisfying Signal Temporal Logic Tasks

Signal temporal logic (STL) provides a user-friendly interface for defining complex tasks for robotic systems. Recent efforts aim at designing control laws or using reinforcement learning methods to find policies which guarantee satisfaction of these tasks. While the former suffer from the trade-off between task specification and computational complexity, the latter encounter difficulties in exploration as the tasks become more complex and challenging to satisfy. This paper proposes to combine the benefits of the two approaches and use an efficient prescribed performance control (PPC) base law to guide exploration within the reinforcement learning algorithm. The potential of the method is demonstrated in a simulated environment through two sample navigational tasks.Comment: This is the extended version of the paper accepted to the 2019 American Control Conference (ACC), Philadelphia (to be published

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.

The conformational pathways and the free energy variations for base opening into the major and minor grooves of a B-DNA duplex are studied using umbrella sampling molecular dynamics simulations. We compare both GC and AT base pair opening within a double-stranded d(GAGAGAGAGAGAG). d(CTCTCTCTCTCTC) oligomer, and we are also able to study the impact of opening on the conformational and dynamic properties of DNA and on the surrounding solvent. The results indicate a two-stage opening process with an initial coupling of the movements of the bases within the perturbed base pair. Major and minor groove pathways are energetically comparable in the case of the pyrimidine bases, but the major groove pathway is favored for the larger purine bases. Base opening is coupled to changes in specific backbone dihedrals and certain helical distortions, including untwisting and bending, although all these effects are dependent on the particular base involved. Partial opening also leads to well defined water bridging sites, which may play a role in stabilizing the perturbed base pairs

Rapidly inducible changes in phosphatidylinositol 4,5-bisphosphate levels influence multiple regulatory functions of the lipid in intact living cells

Rapamycin (rapa)-induced heterodimerization of the FRB domain of the mammalian target of rapa and FKBP12 was used to translocate a phosphoinositide 5-phosphatase (5-ptase) enzyme to the plasma membrane (PM) to evoke rapid changes in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) levels. Rapa-induced PM recruitment of a truncated type IV 5-ptase containing only the 5-ptase domain fused to FKBP12 rapidly decreased PM PtdIns(4,5)P2 as monitored by the PLCδ1PH-GFP fusion construct. This decrease was paralleled by rapid termination of the ATP-induced Ca2+ signal and the prompt inactivation of menthol-activated transient receptor potential melastatin 8 (TRPM8) channels. Depletion of PM PtdIns(4,5)P2 was associated with a complete blockade of transferrin uptake and inhibition of epidermal growth factor internalization. None of these changes were observed upon rapa-induced translocation of an mRFP-FKBP12 fusion protein that was used as a control. These data demonstrate that rapid inducible depletion of PM PtdIns(4,5)P2 is a powerful tool to study the multiple regulatory roles of this phospholipid and to study differential sensitivities of various processes to PtdIns(4,5)P2 depletion

Erklärvideos im Physikunterricht

Erklärvideos bilden ein neues informelles Bildungsangebot, welches im großen Maße von Schülerinnen und Schüler angenommen wird. Diese Videos haben bereits Einzug in den Physikunterricht erhalten und sie werden auch in verschiedenen Forschungsprojekten verwendet. Da sie auf die Vermittlung von Handlungen oder abstrakten Inhalten zielen, eignen sie sich z. B zur Unterstützung des Experimentierens oder zur Vertiefung von physikalischen Konzepten. Bisher gibt es keine systematische Untersuchung ihrer fachdidaktischen Qualität und der Wirkung unterrichtlicher Nutzungsformen. Die fachdidaktische Qualität betrifft einerseits die Angemessenheit der Erklärung und andererseits das gewählte Videodesign.Der Beitrag gibt einen Überblick über die diskutierten theoretischen Ansätze und empirischen Befunde zur Wirksamkeit von Erklärvideos. Die Diskussion mündet in Hypothesen und die Begründung eines Untersuchungsdesigns zu ihrer Überprüfung. Der Fokus liegt auf dem Einsatz von Erklärvideos beim Experimentieren. Variiert werden die Erklärqualität, die multimediale Qualität und die Nutzungsform; untersucht wird ihr Einfluss auf das deklarative Handlungs- und Konzeptwissen als abhängige Variablen

Alpha/gamma Transitions in the B-DNA backbone

In the crystal structures of protein complexes with B DNA, a and ¿ DNA backbone torsion angles often exhibit non canonical values. It is not known if these alternative backbone conformations are easily accessible in solution and can contribute to the specific recognition of DNA by proteins. We have analysed the coupled transition of the a and ¿ torsion angles within the central GpC step of a B DNA dodecamer by computer simulations. Five stable or metastable non canonical a/¿ sub states are found. The most favourable pathway from the canonical a/¿ structure to any unusual form involves a counter rotation of a and ¿, via the trans conformation. However, the corresponding free energy indicates that spontaneous flipping of the torsions is improbable in free B DNA. This is supported by an analysis of the available high resolution crystallographic structures showing that unusual a/¿ states are only encountered in B DNA complexed to proteins. An analysis of the structural consequences of a/¿ transitions shows that the non canonical backbone geometry influences essentially the roll and twist values and reduces the equilibrium dispersion of structural parameters. Our results support the hypothesis that unusual a/¿ backbones arise during protein¿DNA complexation, assisting the fine structural adjustments between the two partners and playing a role in the overall complexation free energy

Lenz-Majewski mutations in PTDSS1 affect phosphatidylinositol 4-phosphate metabolism at ER-PM and ER-golgi junctions

Lenz-Majewski syndrome (LMS) is a rare disease characterized by complex craniofacial, dental, cutaneous, and limb abnormalities combined with intellectual disability. Mutations in the PTDSS1 gene coding one of the phosphatidylserine (PS) synthase enzymes, PSS1, were described as causative in LMS patients. Such mutations render PSS1 insensitive to feedback inhibition by PS levels. Here we show that expression of mutant PSS1 enzymes decreased phosphatidylinositol 4-phosphate (PI4P) levels both in the Golgi and the plasma membrane (PM) by activating the Sac1 phosphatase and altered PI4P cycling at the PM. Conversely, inhibitors of PI4KA, the enzyme that makes PI4P in the PM, blocked PS synthesis and reduced PS levels by 50% in normal cells. However, mutant PSS1 enzymes alleviated the PI4P dependence of PS synthesis. Oxysterol-binding protein-related protein 8, which was recently identified as a PI4P-PS exchanger between the ER and PM, showed PI4P-dependent membrane association that was significantly decreased by expression of PSS1 mutant enzymes. Our studies reveal that PS synthesis is tightly coupled to PI4P-dependent PS transport from the ER. Consequently, PSS1 mutations not only affect cellular PS levels and distribution but also lead to a more complex imbalance in lipid homeostasis by disturbing PI4P metabolism