Detection and characterization of nonspecific,sparsely populated binding modes in the early stages of complexation

A method is proposed to study protein–ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first‐encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide–protein complex. The peptide adopts several low‐population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. © 2015 Wiley Periodicals, Inc.     

Sensitivity Analysis of Contact Type Vibration Measuring Sensors

With the Internet of Things (IoT) era dawning in, we are surrounded by a plethora of sensors. The present paper focuses on MEMS-based vibration measuring accelerometers, which are ubiquitously present in smartphones, tablets, smartwatches/bands, etc. These contact type vibration sensors have the unique advantage of being very small, low cost, low power, less weighing, and easily accommodatable in electronics. However, the accuracy of these sensors needs to be quantified with respect to more accurate sensors. With this objective, the paper presents a comparison of the relative sensitivity of a MEMS-based accelerometer (MPU 6050), a Geophone, and a sensor from Xiaomi Y2 smartphone with respect to a more standard Piezoelectric ICP based accelerometer, when all sensors are tested on a shaker table. Data are measured with harmonic excitation over a frequency range of 2–184 Hz. The relative sensitivity of MPU 6050 was 90% accurate in the frequency range 18–116 Hz for RMS measurements. Other sensors such as the one used in the Xiaomi Y2 smartphone and the Geophone were less accurate. The relative sensitivity measured in this work can be used to obtain sensitivity and hence more accurate data from these low-cost accelerometers.     

Synthesis and evaluation of deep cavity imidazolyl calix[n]arenes

A series of deep cavity diphenyl imidazolyl calix[n]arenes (4, 6, 8) have been obtained from readily available starting materials through a five step synthetic methodology involving appropriate alkylation of lower rim of preformed calixarene, formylation of the upper rim and subsequent condensation with aryl diketones in the presence of ammonium acetate and glacial acetic acid. Optimized reaction conditions for obtaining the titled derivatives in their cone configuration and their characterization by spectroscopic methods (IR, UV, NMR and FAB mass) have been delineated. The synthesized imidazolyl calixarenes have preliminarily been examined for selective recognition of monovalent metal ions (Li⁺, Na⁺, K⁺, Cs⁺, Ag⁺).     

Silica nanocapsules of fluorescent conjugated polymers and superparamagnetic nanocrystals for dual-mode cellular imaging

We describe here a facile and benign synthetic strategy to integrate the fluorescent behavior of conjugated polymers and superparamagnetic properties of iron oxide nanocrystals into silica nanocapsules, forming a new type of bifunctional magnetic fluorescent silica nanocapsule (BMFSN). The resultant BMFSNs are uniform, colloidally stable in aqueous medium, and exhibit the desired dual functionality of fluorescence and superparamagnetism in a single entity. Four conjugated polymers with different emissions were used to demonstrate the versatility of employing this class of fluorescent materials for the preparation of BMFSNs. The applicability of BMFSNs in cellular imaging was studied by incubating them with human liver cancer cells, the result of which demonstrated that the cells could be visualized by dual-mode fluorescence and magnetic resonance imaging. Furthermore, the superparamagnetic behavior of the BMFSNs was exploited for in vitro magnetic-guided delivery of the nanocapsules into the cancer cells, thereby highlighting their potential for targeting biomedical applications.     

Photochemistry of 5-aminoquinoline in protic and aprotic solvents

Photophysical properties of 5-aminoquinoline (5AQ) have been investigated in various non-polar and polar (protic and aprotic) solvents using steady state and time resolved fluorescence. In aprotic solvents, the spectral maxima depend on the polarity. However, in protic solvents both the fluorescence intensity as well decay time show decrease depending on the hydrogen bonding ability of the solvent. The results suggest that photochemistry 5AQ is quite sensitive towards the polarity as well as protic character of the solvent.     

Dynamics of Ligand Binding to a Rigid Glycosidase**

The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.     

Direct conversion of natural gas to higher hydrocarbons:A review

Direct conversion of methane to higher hydrocarbons is an effective process to solve the problem of natural gas utilization. Although remarkable progress has been achieved on the dehydro-aromatization of methane (DAM), low conversion caused by severe thermodynamic limitations,coke formation, and catalysis deactivation remain important drawbacks to the direct conversion process. Molybdenum catalysts supported on HZSM-5 type zeolite support are among the most promising catalysts. This review focuses on the aspects of direct methane conversion, in terms of catalysts containing metal and support, reaction conditions, and conversion in different types of reactors. The reaction mechanism for this catalytic process is also discussed.     

Flux line lattice symmetries in the borocarbide superconductor LuNi2B2C

We compare the results of small angle neutron scattering on the flux line lattice (FLL) obtained in the borocarbide superconductor LuNi₂B₂C with the applied field along the c- and a-axes. For H‖c the temperature dependence of the FLL structural phase transition from square to hexagonal symmetry was investigated. Above 10 K the transition onset field. H ₂(T), rises sharply, bending away from H _c2(T) in contradiction to theoretical predictions of the two merging. For H‖a a first order FLL reorientation transition is observed at H _tr=3–3.5 kOe. Below H _tr the FLL nearest neighbor direction is parallel to the b-axis, and above H _tr to the c-axis. This transition cannot be explained using nonlocal corrections to the London model.     

Atomic transport and chemical stability of nitrogen in ultrathin HfSiON gate dielectrics

HfSiO and HfSiON films with thicknesses compatible with the requirements for gate dielectrics alternatives to SiO₂ in ultra-large scale integration silicon-based CMOSFET devices were deposited on an ultrathin HfSiO¹⁵N interfacial layer on Si(001). These structures were submitted to thermal processing routines typical of post-deposition annealing and dopant activation steps in fabrication technology, namely at 450 or 1000 °C, respectively, and in atmospheres of N₂ and/or O₂. N transport and loss were determined by nuclear reaction analysis, including sub-nanometric depth resolution profiling with narrow nuclear reaction resonances. The chemical states of N were accessed by angle-resolved X-ray photoelectron spectroscopy. After annealing at 450 °C, N is seen to be mobile, whereas the chemical environment of N is not changed at this temperature. Annealing at 1000 °C renders N mobile and its most abundant chemical state in near-surface regions is unstable. Annealing in O₂ atmosphere promotes incorporation of O from the gas phase into the films, partly in exchange for N and O atoms and partly by net incorporation of oxygen in the films. The profiles of the newly incorporated O atoms are also determined with sub-nanometric depth resolution by narrow nuclear reaction resonance profiling. PACS 68.60.-p; 68.55.-a; 73.61.Ng; 73.40.Qv