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The molecular basis of receptor bias in G protein-coupled receptors (GPCRs) caused by mutations that preferentially activate specific intracellular transducers over others remains poorly understood. Two experimentally identified biased variants of β2-adrenergic receptors (β2AR), a prototypical GPCR, are a triple mutant (T68F, Y132A, and Y219A) and a single mutant (Y219A); the former bias the receptor toward the β-arrestin pathway by disfavoring G protein engagement, while the latter induces G protein signaling explicitly due to selection against GPCR kinases (GRKs) that phosphorylate the receptor as a prerequisite of β-arrestin binding. Though rigorous characterizations have revealed functional implications of these mutations, the atomistic origin of the observed transducer selectivity is not clear. In this study, we investigated the allosteric mechanism of receptor bias in β2AR using microseconds of all-atom Gaussian accelerated molecular dynamics (GaMD) simulations. Our observations reveal distinct rearrangements in transmembrane helices, intracellular loop 3, and critical residues R1313.50and Y3267.53in the conserved motifs D(E)RY and NPxxY for the mutant receptors, leading to their specific transducer interactions. Moreover, partial dissociation of G protein from the receptor core is observed in the simulations of the triple mutant in contrast to the single mutant and wild-type receptor. The reorganization of allosteric communications from the extracellular agonist BI-167107 to the intracellular receptor–transducer interfaces drives the conformational rearrangements responsible for receptor bias in the single and triple mutants. The molecular insights into receptor bias of β2AR presented here could improve the understanding of biased signaling in GPCRs, potentially opening new avenues for designing novel therapeutics with fewer side-effects and superior efficacy.

The large conformational flexibility of G protein-coupled receptors (GPCRs) has been a puzzle in structural and pharmacological studies for the past few decades. Apart from structural rearrangements induced by ligands, enzymatic phosphorylations by GPCR kinases (GRKs) at the carboxy-terminal tail (C-tail) of a GPCR also make conformational alterations to the transmembrane helices and facilitates the binding of one of its transducer proteins named β-arrestin. The phosphorylation-induced conformational transition of the receptor that causes specific binding to β-arrestin but prevents the association of other transducers such as G proteins lacks atomistic understanding and is elusive to experimental studies. Using microseconds of all-atom conventional and Gaussian accelerated molecular dynamics (GaMD) simulations, we investigate the allosteric mechanism of phosphorylation induced-conformational changes in β2-adrenergic receptor, a well-characterized GPCR model system. Free energy profiles reveal that the phosphorylated receptor samples a new conformational state in addition to the canonical active state corroborating with recent nuclear magnetic resonance experimental findings. The new state has a smaller intracellular cavity that is likely to accommodate β-arrestin better than G protein. Using contact map and inter-residue interaction energy calculations, we found the phosphorylated C-tail adheres to the cytosolic surface of the transmembrane domain of the receptor. Transfer entropy calculations show that the C-tail residues drive the correlated motions of TM residues, and the allosteric signal is relayed via several residues at the cytosolic surface. Our results also illustrate how the redistribution of inter-residue nonbonding interaction couples with the allosteric communication from the phosphorylated C-tail to the transmembrane. Atomistic insight into phosphorylation-induced β-arrestin specific conformation is therapeutically important to design drugs with higher efficacy and fewer side effects. Our results, therefore, open novel opportunities to fine-tune β-arrestin bias in GPCR signaling.

Porous 2D covalent organic frameworks (COF) that are assembled axially through weak π-stacking interactions can provide reticular charge transport channels while playing host to kinetically stabilized reactive molecular redox states. Here we demonstrate a host–guest supramolecular charge transfer (CT) assembly using photoactive anthraquinone-based COF as an acceptor while incarcerating the electron donor N,N-dimethylaniline (DMA) inside it. Employing femtosecond broadband transient absorption spectroscopy in combination with electron paramagnetic resonance (EPR) studies, we show that the CT occurs rapidly within <110 fs after photoexcitation, subsequently leading to long-lived charge separation with 13% quantum efficiency at room temperature. The photoinduced EPR signature of the long-lived confined DMA cation radical confirms the disparate regions of charge localization while 1H–13C correlation experiments using solid-state NMR spectroscopy enumerate the packing of the amines inside the host–guest COF assembly. Our work demonstrates the potency of charge transport pathways in supramolecular assemblies for efficient charge separation which if optimally tuned should pave the way for COF-based photocatalytic reaction centers.

Solid-state NMR is a powerful tool to measure distances and motional order parameters which are vital tools in characterizing the structure and dynamics of molecules. Magic-angle spinning (MAS), widely employed in solid-state NMR, averages out dipole–dipole couplings that carry such information. Hence, rotor-synchronized radiofrequency (RF) pulses, that interfere with MAS averaging, are commonly employed to measure such couplings. However, most of the methods that achieve this, rotational echo double resonance (REDOR) being a classic example, require RF amplitudes that are greater than or equal to the MAS frequency. While feasible at MAS frequencies <40 kHz, these requirements become prohibitively large for higher MAS frequencies (40–110 kHz), which are now commercially available. Here, we redesign the REDOR experiment so that RF amplitudes as low as 0.5–0.7 times the spinning frequency can be used. This sequence, name deferred rotational echo double resonance (DEDOR), thus extends the utility of this method to the fastest MAS frequencies currently commercially available (111 kHz). The generality of this strategy is shown by extending it to other methods that utilize the same principle as REDOR. They will be useful in obtaining structural parameters for a wide range of molecules using solid-state NMR under fast MAS with the additional advantage of higher spectral resolution under these conditions.

Persistent endodontic infection might be due to retention of microorganisms in dentinal tubules of root canal. C. albicans and E. faecalis are commonly found micro organisms in root canals of previously treated teeth. These micro organisms have shown to be resistant to most of the anti microbial agents used during root canal treatment but were found to be sensitive to Chlorhexidine (CHX).

The depleting Fossil fuels reserves are caused to look into new Renewable energy sources to fulfill Diesel fuel demand in developing countries such as India. Increasing urbanization is lead to the search for new alternative sources like biodiesel. In India demand of diesel fuel in Industry and Transportation sector. To resolve all the above problems, researchers, scientists were produced biodiesel from first, second and third generation biodiesel sources. Among all the sources Algae was the most Oil rich sources. The byproducts in algae to biodiesel conversion process are most valuable than other. In the present work author tried to work in a new approach, i.e. the mixed culture algae particles are emulsified in pure Coconut biodiesel fuel by using TritonX-100 as a surfactant to prepare an emulsified fuel. This fuel sample was applied to DI CI engine to improve performance, emission characteristics. The experimental results were shown that there is the improvement in diesel engine performance; emission characteristics especially break thermal efficiency and NOx emission reduction than diesel fuel due to its clean combustion.

The structural underpinnings for the higher toxicity of the oligomeric intermediates of amyloidogenic peptides, compared to the mature fibrils, remain unknown at present. The transient nature and heterogeneity of the oligomers make it difficult to follow their structure. Here, using vibrational and solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that freely aggregating Aβ40oligomers in physiological solutions have an intramolecular antiparallel configuration that is distinct from the intermolecular parallel β-sheet structure observed in mature fibrils. The intramolecular hydrogen-bonding network flips nearly 90°, and the two β-strands of each monomeric unit move apart, to give rise to the well-known intermolecular in-register parallel β-sheet structure in the mature fibrils. Solid-state nuclear magnetic resonance distance measurements capture the interstrand separation within monomer units during the transition from the oligomer to the fibril form. We further find that the D23–K28 salt-bridge, a major feature of the Aβ40fibrils and a focal point of mutations linked to early onset Alzheimer’s disease, is not detectable in the small oligomers. Molecular dynamics simulations capture the correlation between changes in the D23–K28 distance and the flipping of the monomer secondary structure between antiparallel and parallel β-sheet architectures. Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small Aβ40oligomers to fibrils.

There are three specific regions in the Amyloid beta (Aβ) peptide sequence where variations cause enhanced toxicity in Alzheimer’s disease: the N-terminus, the central salt bridge, and the C-terminus. Here, we investigate if there is a close conformational connection between these three regions, which may suggest a concerted mechanism of toxicity. We measure the effects of Zn2+and curcumin on Aβ40, and compare these with their previously reported effects on Aβ42. Aβ42and Aβ40differ only near the C-terminus, where curcumin interacts, while Zn2+interacts near the N-terminus. Therefore, this comparison should help us differentiate the effect of modulating the C- and the N-termini. We find that curcumin allows fibril-like structures containing the salt bridge to emerge in the mature Aβ40aggregates, but not in Aβ42. In contrast, we find no difference in the effects of Zn+2on Aβ40and Aβ42. In the presence of Zn+2, both of these fail to form proper fibrils, and the salt bridge remains disrupted. These results indicate that modulations of the Aβtermini can determine the fate of a salt bridge far away in the sequence, and this has significant consequences for Aβtoxicity. We also infer that small molecules can alter oligomer-induced toxicity by modulating the aggregation pathway, without substantially changing the final product of aggregation.

The aim of this research is to develop a mathematical model of a compression ignition engine using cylinder-by-cylinder model approach to predict the performances; indicated work, indicated torque, in-cylinder pressures and temperatures and heat release rates. The method used in the study is based on ideal diesel cycle and is modified by the numerical formulations which affect the performance of the engine. The model consists of a set of tuning parameters such as engine geometries, EGR fractions, boost pressures, injection timings, air/fuel ratio, etc. It is developed in Simulink environment to promote modularity. A single-zone combustion model is developed and implemented for the combustion process which accounts for ignition delay, heat release. Derivations from slider-crank mechanism are involved to compute the instantaneous volume, area and stroke at any given crank angle. The results of the simulation model have been validated with experimental results with a close match between them.

Identifying the structures of membrane bound proteins is critical to understanding their function in healthy and diseased states. We introduce a surface enhanced Raman spectroscopy technique which can determine the conformation of membrane-bound proteins, at low micromolar concentrations, and also in the presence of a substantial membrane-free fraction. Unlike conventional surface enhanced Raman spectroscopy, our approach does not require immobilization of molecules, as it uses spontaneous binding of proteins to lipid bilayer-encapsulated Ag nanoparticles. We apply this technique to probe membrane-attached oligomers of Amyloid-β40(Aβ40), whose conformation is keenly sought in the context of Alzheimer’s disease. Isotope-shifts in the Raman spectra help us obtain secondary structure information at the level of individual residues. Our results show the presence of a β-turn, flanked by two β-sheet regions. We use solid-state NMR data to confirm the presence of the β-sheets in these regions. In the membrane-attached oligomer, we find a strongly contrasting and near-orthogonal orientation of the backbone H-bonds compared to what is found in the mature, less-toxic Aβ fibrils. Significantly, this allows a “porin” like β-barrel structure, providing a structural basis for proposed mechanisms of Aβ oligomer toxicity.

Aluminum nitride (AlN) thin films are widely used in sensors, bulk/surface acoustic wave (B/SAW) filters, and optoelectronic devices, etc. It often requires overlapping of two different thin films to obtain functional devices. Normally a part of the AlN film is deposited on a bottom substrate (such as Si, Glass, etc.) while the remaining part spreads over an electrode material (such as Al, Au, Pt, etc.). This often results in cracks at the step edge between the metal electrode and AlN films, leading to short circuiting when the top metallic electrode is deposited. It is thus of significance to study the thin film materials and their deposition parameters in order to successfully fabricate functional thin film AlN sensors without cracking. Various underlying materials were studied. Al2O3is identified as a suitable underlying material below the Au electrode. The AlN deposited at the Au/Al2O3showed no cracks or short circuiting. Thin film AlN piezoelectric force sensors were successfully fabricated on the Al2O3coated Si wafers. The longitudinal charge-to-force coefficient of the thin film force sensors were also characterized.

A promising combustion strategy that combines the advantages of both SI and CI combustion modes is the homogeneous charge compression ignition (HCCI) combustion mode. A volumetric combustion of a lean mixture of charge is the advantage of HCCI combustion, leading to low NOxemissions and soot. In this work, HCCI combustion mode is analyzed to study the effect of swirl motion of intake charge on performance and emissions of the engine using a Three-Zone Extended Coherent Flame Combustion Model (ECFM-3Z, Compression Ignition). The present study revealed that ECFM-3Z of STAR-CD predicts well the in-cylinder pressures, temperatures, cylinder wall heat transfer losses, piston work and emissions such as CO, CO2and NOxof the CI engine in the HCCI mode. The ECFM-3Z model has a predicted variation in turbulent kinetic energy and velocity magnitudes inside the cylinder during combustion, facilitating better understanding of the combustion process. The simulation results show that the there is a reduction in in-cylinder peak pressures and temperatures, as the swirl increases and CO emissions increase because of reduced temperatures, and CO2and NOxemissions decrease because of the reduced in-cylinder temperatures. It is found that there is a trade-off between the emissions and piston work. Higher turbulent energy and velocity magnitude levels are obtained with increase in swirl, indicating efficient combustion without a demanding combustion chamber design.

The structural and dynamical features associated with the phase behavior of water confined in clay nanopores (2D confined water) are studied using positron annihilation spectroscopy, nuclear magnetic resonance, and dielectric relaxation spectroscopy techniques. We report the experimental evidence of a new phase transition (above the bulk freezing point of water) in nanoconfined water, in addition to a low-temperature transition in supercooled water. The study reveals it to be a structural rearrangement of water molecules associated with modification of hydrogen-bonded network. Evidence also suggests the dynamical arrest/immobilization of water layer near the clay platelet surface (bound water molecules) to be associated with this transition. This transition is a manifestation of the role of surface interaction on the phase behavior of confined liquids.

Observations like high Zn2+concentrations in senile plaques found in the brains of Alzheimer's patients and evidences emphasizing the role of Zn2+in amyloid-β(Aβ)-induced toxicity have triggered wide interest in understanding the nature of Zn2+-Aβinteraction. In vivo and in vitro studies have shown that aggregation kinetics, toxicity, and morphology of Aβaggregates are perturbed in the presence of Zn2+. Structural studies have revealed that Zn2+has a binding site in the N-terminal region of monomeric Aβ, but not much is precisely known about the nature of binding of Zn2+with aggregated forms of Aβor its effect on the molecular structure of these aggregates. Here, we explore this aspect of the Zn2+-Aβinteraction using one- and two-dimensional 13C and 15N solid-state NMR. We find that Zn2+causes major structural changes in the N-terminal and the loop region connecting the two β-sheets. It breaks the salt bridge between the side chains of Asp23and Lys28by driving these residues into nonsalt-bridge-forming conformations. However, the cross-βstructure of Aβ42aggregates remains unperturbed though the fibrillar morphology changes distinctly. We conclude that the salt bridge is not important for defining the characteristic molecular architecture of Aβ42but is significant for determining its fibrillar morphology and toxicity.

Summary.:  Experimental and theoretical aspects of the multiple-quantum magic-angle spinning experiment (MQMAS) are discussed in this review. The significance of this experiment, introduced by Frydman and Harwood, is in its ability to provide high-resolution NMR spectra of half-integer quadrupolar nuclei (I ≥ 3/2). This technique has proved to be useful in various systems ranging from inorganic materials to biological samples. This review addresses the development of various pulse schemes aimed at improving the signal-to-noise ratio and anisotropic lineshapes. Representative spectra are shown to underscore the importance and applications of the MQMAS experiment.

The generalized Bloch equations in the rotating frame are solved in Cartesian space by an approach that is different from the earlier Torrey solutions. The solutions are cast into a compact and convenient matrix notation, which paves the way for a direct physical insight and comprehension of the evolution of various magnetization components. The solutions are expressed as a sum of two terms: One describes the decay of the initial state; the other describes the growth of the steady state. The representative trajectories of each component of the above terms plotted separately describe the complete time evolution of each magnetization component. © 1997 John Wiley & Sons, Inc.

Review: 50 refs.

A novel inductive technique for the detection of microcantilever displacement for sensing applications was presented. We highlight the basic structure and evaluate its characteristics with the aid of modeling and simulation. Results generated by numerical simulations using ANSOFT are compared with those obtained from an equivalent circuit model using PSPICE. There are indications that the sensitivity of the inductive cantilever is about one order of magnitude higher as compared to piezoresistive silicon cantilevers of the same dimension under the same cantilever bending.

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ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.