Search results for "binding"

Chromatin modifiers and recombination factors promote a telomere fold-back structure, that is lost during replicative senescence.

2020

Telomeres have the ability to adopt a lariat conformation and hence, engage in long and short distance intra-chromosome interactions. Budding yeast telomeres were proposed to fold back into subtelomeric regions, but a robust assay to quantitatively characterize this structure has been lacking. Therefore, it is not well understood how the interactions between telomeres and non-telomeric regions are established and regulated. We employ a telomere chromosome conformation capture (Telo-3C) approach to directly analyze telomere folding and its maintenance in S. cerevisiae. We identify the histone modifiers Sir2, Sin3 and Set2 as critical regulators for telomere folding, which suggests that a dis…

The histone deacetylase Rpd3 regulates the heterochromatin structure of Drosophila telomeres

2011

Telomeres are specialized structures at the end of eukaryotic chromosomes that are required to preserve genome integrity, chromosome stability and nuclear architecture. Telomere maintenance and function are established epigenetically in several eukaryotes. However, the exact chromatin enzymatic modifications regulating telomere homeostasis are poorly understood. In Drosophila melanogaster, telomere length and stability are maintained through the retrotransposition of specialized telomeric sequences and by the specific loading of protecting capping proteins, respectively. Here, we show that the loss of the essential and evolutionarily conserved histone deacetylase Rpd3, the homolog of mammal…

Impairment of Temporal Binding Window in Migraine Patients

Resorcinarene Podand with Amine-Functionalized Side Arms – Synthesis, Structure, and Binding Properties of a Neutral Anion Receptor

2009

The synthesis and structure of a neutral resorcinarene host bearing four amine-functionalized side arms is described. The anion binding properties were investigated in solution by 1H NMR spectroscopic titration and diffusion experiments and in the gas phase by mass spectrometric studies. It was observed that in solution 1:2 (host/guest) complexes were formed between the resorcinarene host and the basic fluoride and acetate anions, whereas in the gas phase 1:1 complexes with other anions (Cl–, HCOO–, NO3–, and BF4–) were detected additionally. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Aromatic Bridged Bis-phenol A Derived Cyclophanes. Synthesis, Molecular Structure and Binding Properties Toward Quats

2003

Three novel polyoxyethylene bridged bis phenol A derived cyclophanes, {\rm 2 -- 4,} with additional aromatic units in the bridge to increase the number of cation–π interactions with guest cations, were synthesized and characterized by means of X-ray crystal structure determinations. The binding properties of these receptors toward tetramethylammonium (TMA), N-methylpyridinium (NMP), acetylcholine (ACh) and N-methylquinolinium (NMQ) salts were evaluated by means of 1H NMR spectroscopy and compared with those of the previously reported receptor 1.

Nickel induces intracellular calcium mobilization and pathophysiological responses in human cultured airway epithelial cells.

2009

Abstract Environmental exposure to nickel is associated to respiratory disorders and potential toxicity in the lung but molecular mechanisms remain incompletely explored. The extracellular Ca 2+ -sensing receptor (CaSR) is widely distributed and may be activated by divalent cations. In this study, we investigated the presence of CaSR in human cultured airway epithelial cells and its activation by nickel. Nickel transiently increased intracellular calcium (−log EC 50  = 4.67 ± 0.06) in A549 and human bronchial epithelial cells as measured by epifluorescence microscopy. Nickel (20 μM)-induced calcium responses were reduced after thapsigargin or ryanodine exposure but not by Ca 2+ -free medium…

New QM/MM implementation of the DFTB3 method in the gromacs package.

2015

The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…

The designer cytokine hyper-interleukin-6 is a potent activator of STAT3-dependent gene transcription in vivo and in vitro.

1999

Interleukin-6 (IL-6) triggers pivotal pathways in vivo. The designer protein hyper-IL-6 (H-IL-6) fuses the soluble IL-6 receptor (sIL-6R) through an intermediate linker with IL-6. The intracellular pathways that are triggered by H-IL-6 are not defined yet. Therefore, we studied the molecular mechanisms leading to H-IL-6-dependent gene activation. H-IL-6 stimulates haptoglobin mRNA expression in HepG2 cells, which is transcriptionally mediated as assessed by run-off experiments. The increase in haptoglobin gene transcription correlates with higher nuclear translocation of tyrosine-phosphorylated STAT3 and its DNA binding. As H-IL-6 stimulates STAT3-dependent gene transcription, we compared t…

Determination of cluster binding energies on metal surfaces by statistics

2000

Abstract Two simple formulae to determine binding energies of two-dimensional clusters on surfaces in thermal equilibrium are derived. One requires measurement of monomer and cluster populations and of the surface temperature. The cluster dissociation rate is derived and related to the atom hopping rate, allowing the theory to be extended to adatom populations that are not in chemical equilibrium. The result gives a recipe for determining dissociation energies that requires measurements of only two rates at a single temperature.

Positron detrapping from defects: A thermodynamic approach

1981

The rate of positron detrapping in thermal equilibrium from lattice defects has been calculated by relating it to the specific trapping rate. The results for vacancies, dislocations and surfaces each show a different temperature dependence for the escape rate. For vacancies a measure of the importance of the detrapping can be obtained from the ratio of the vacancy formation energy to the positron binding energy in the defect. The positronium desorption rate from a surface is also calculated and agreement with experimental results is found.