Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map

Vertebrate segmentation has been proved to be under a strict temporal control governed by a biological clock, known as the segmentation clock. The present experimental evidence suggests that the segmentation clock initiates and maintains its periodic cycle by the periodic activation or inhibition of the Notch signaling pathway as well as the periodic autoregulation of the cyclic genes themselves. In this paper, we investigate the structural and evolutionary properties of the Notch pathway proteins involved in the mice segmentation clock and computationally identify the interaction map within the Notch signaling pathway. The results of our analysis strongly indicate that most of the pathway proteins are intrinsically disordered and that the mechanism of their interaction likely involves helical molecular recognition elements, short loosely structured segments within disordered regions which are directly involved in protein-protein interactions. Predicted interactions are in agreement with gene knock-out studies available in the literature.     

Synthesis and structural characterization of lanthanide(III) nitrate complexes of a tetraiminodiphenol macrocycle in the solid state and in solution

The lanthanide(III) complexes [Ln(LH2)(NO3)3] 1-11(La-Er), 15(Y) and [Ln(LH2)(NO3)2(H2O)](NO3) 12-14 (Tm-Lu) of the tetraiminodiphenolate macrocycle L2- have been prepared by the transmetallation reaction between [Pb(LH2)(NO3)2] and Ln(NO3)3.nH2O. In these compounds, the uncoordinated imino nitrogens are protonated and are hydrogen bonded to the phenolate oxygens. The X-ray crystal structures of the La (1), Ho (10) and Lu (14) compounds have been determined. Compounds 1 and 10, in which all the three nitrates are bound in bidentate fashion, are isostructural with distorted bicapped square antiprism geometry for the metal centre. In [Lu(LH2)(NO3)2(H2O)](NO3) 14, of the two metal bound nitrates one is bidentate and the other is unidentate, while the metal centre obtains a distorted square antiprism coordination environment. Proton NMR spectra of the paramagnetic lanthanide complexes have been studied in detail. Contributions of contact and pseudo-contact shifts to the lanthanide induced isotropic shifts (LIS) of the macrocycle protons have been separated and good agreement has been obtained between the calculated LIS values and the experimentally observed values. Analysis of the NMR data has led us to conclude that all the complexes in dimethyl sulfoxide solution attain similar configurations. The absorption and emission spectral characteristic of several compounds have been investigated. The complexes of samarium (5) and europium (6) on photoexcitation at 400 nm exhibit well-resolved luminescence spectra at 77 K both in the solid state and a methanol-ethanol (1 : 4) glassy matrix. For the terbium (8) and dysprosium (9) complexes, however, the observed luminescence peaks are less resolved and weak in intensity.     

A Quinoxaline−Naphthaldehyde Conjugate for Colorimetric Determination of Copper Ion

This work facilitates detection of bivalent copper ion by a simple Schiff base probe QNH based on a quinoxaline−naphthaldehyde framework. The detailed study in absorption spectroscopy and theoretical aspects and crystal study of the probe and probe−copper complex has been discussed. The detection limit of the probe in the presence of Cu²⁺ is 0.45 µM in HEPES−buffer/acetonitrile (3/7, v/v) medium for absorption study. The reversibility of the probe−copper complex has been investigated by EDTA. The selective visual detection of copper has been established also in gel form.     

Activation and Conversion of Molecular Nitrogen to the Precursor of Ammonia on Silicon Substituted Cyclo[18]Carbon: a DFT Design

Recent synthesis of sp-hybridized cyclo[18]carbon allotrope has attracted immense curiosity. Since then, a generous amount of theoretical studies concerning aromaticity, adsorption, and spectra of the molecule have been performed. However, very few stuides have been carried out concerning its reactivities and catalytic behaviour. In this article, a DFT-based inquisition has been reported regarding the reactivity of Si substituted cyclo[18]carbon molecule towards molecular N₂. Results show that the Si substituted derivative is effective in producing adducts with molecular nitrogen. Charge calculations and IRC trapping methods indicate that only the Si center of C₁₇Si and its (HOMO-1) level participate in N₂ addition. The N-adduct so formed, is then found to spontaneously react with molecular H₂. The addition of two H₂ molecules to the activated nitrogen molecule to give respective amine derivatives have also been studied. The successful generation of the precursor of NH₃ by C₁₇Si lays a clear emphasis on its potentiality.     

Mechanism of B-H Redistribution during Reduction of Polyborazylene by Hydrazine

Density functional theory has been used to elucidate the mechanistic underpinnings of the regeneration of ammonia-borane (H₃B−NH₃, AB ) from polyborazylene (B_xN_xH_x, PBz ) in the presence of hydrazine (H₂N−NH₂, Hz ). Herein, borazine (B₃N₃H₆, Bz ) is used as the simplest relevant model of PBz for the regeneration process. Digestion of Bz using Hz was found to occur by a string of Lewis acid base adduct (between B atoms of Bz and Hz molecule) formation and Hz assisted proton transfer processes. Later, B−H bonds of HB(NHNH₂)₂, the Bz digested product, are redistributed to form hydrazine-borane (H₃B−NH₂NH₂, HzB ) and B(NHNH₂)₃. Redistribution of B−H bonds occurs through hydroboration and concerted proton-hydride transfer. Another B−H redistributed product, B(NHNH₂)₃, produces HzB as a result of proton and hydride transfer from cis-diazene ( Dz ), the oxidized product of Hz in presence of O₂.     

A Small-Molecule Fluorescence Probe for Nuclear ATP

Fluorescence monitoring of ATP in different organelles is now feasible with a few biosensors developed, which, however, show low sensitivity, limited biocompatibility, and accessibility. Small-molecule ATP probes that alleviate those limitations thus have received much attention recently, leading to a few ATP probes that target several organelles except for the nucleus. We disclose the first small-molecule probe that selectively detects nuclear ATP through reversible binding, with 25-fold fluorescence enhancement at pH 7.4 and excellent selectivity against various biologically relevant species. Using the probe, we observed 2.1–3.3-fold and 3.9–7.8-fold higher nuclear ATP levels in cancerous cell lines and tumor tissues compared with normal cell lines and tissues, respectively, which are explained by the higher nuclear ATP level in the mitosis phase. The probe has great potential for studying nuclear ATP-associated biology.     

Dinuclear PdII complexes bearing mixed NHC/Py/PPh3 donor set ligands: Catalytic applications and electrochemical investigations

Bimetallic palladium(II) complexes containing classical NHC donor ligands are becoming increasingly popular owing to their various catalytic applications. However, examples of the aforementioned complexes with mixed NHC/PPh₃ ligands are still rare. Bimetallic palladium(II) complexes possessing these mixed ligands are described starting from a C2-symmetric bis-imidazolium salt containing 4,4′-substituted central biphenyl ring. All the palladium(II) complexes have been tested as precatalysts in α-arylation of oxindole and Suzuki–Miyaura coupling reactions. The complex composed of mixed NHC/PPh₃ donor ligands shows superior catalytic activity compared with the corresponding PEPPSI type complexes when applied in α-arylation of oxindole. The dinuclear complexes display better activity compared with the mononuclear complexes. The preliminary electrochemical measurements show the facile oxidation of Pd^II in the presence of combined NHC/PPh₃ ligands compared with a combination of NHC/Py ligands.     

Harnessing Deep Neural Networks to Analyze Multi-Channel Anion Sensing Characteristics of a Ru(II)-Pyrazolyl-Bis(Benzimidazole) Complex

In this work, the anion-responsive conduct of a Ru(II)-bipyridine complex incorporating pyrazolyl-bis (benzimidazole) ligand is thoroughly investigated in acetonitrile and water via absorption and emission spectroscopy as well as by square-wave voltammetry (SWV). Substantial alteration of the photo-redox behavior of the complex is observed in the presence of the selected anions. The free form of the complex exhibits emission indicating the “on-state”, while inclusion of anions leads to quenching of emission and represents the “off-state”. The restoration of the initial state of the complex is feasible in the presence of acid and the process is reversible and can be recycled. In essence, the complex functions as anion- and acid-responsive molecular switches. Additionally, we applied herein neural network based deep learning methodologies, viz. Artificial Neural Networks (ANNs) and Adaptive Neuro-Fuzzy Inference System (ANFIS)} for thorough analysis and fully understand the multi-channel anion sensing behavior of the complex.