Proximity-dependent biotinylation detects associations between SARS coronavirus nonstructural protein 1 and stress granule-associated proteins.

The nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus 2 is a critical viral protein that suppresses host gene expression by blocking the assembly of the ribosome on host mRNAs. To understand the mechanism of inhibition of host gene expression, we sought to identify cellular proteins that interact with nsp1. Using proximity-dependent biotinylation followed by proteomic analyses of biotinylated proteins, here we captured multiple dynamic interactions of nsp1 with host cell proteins. In addition to ribosomal proteins, we identified several pre-mRNA processing proteins that interact with nsp1, including splicing factors and transcription termination proteins, as well as exosome, and stress granule (SG)-associated proteins. We found that the interactions with transcription termination factors are primarily governed by the C-terminal region of nsp1 and are disrupted by the mutation of amino acids K164 and H165 that are essential for its host shutoff function. We further show that nsp1 interacts with Ras GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and colocalizes with G3BP1 in SGs under sodium arsenite-induced stress. Finally, we observe that the presence of nsp1 disrupts the maturation of SGs over a long period. Isolation of SG core at different times shows a gradual loss of G3BP1 in the presence of nsp1.

A probabilistic approach for estimating water permeability in pressure-driven membranes.

A probabilistic approach is proposed to estimate water permeability in a cellulose triacetate (CTA) membrane. Water transport across the membrane is simulated in reverse osmosis mode by means of non-equilibrium molecular dynamics (MD) simulations. Different membrane configurations obtained by an annealing MD simulation are considered and simulation results are analyzed by using a hierarchical Bayesian model to obtain the permeability of the different membranes. The estimated membrane permeability is used to predict full-scale water flux by means of a process-level Monte Carlo simulation. Based on the results, the parameters of the model are observed to converge within 5-ns total simulation time. The results also indicate that the use of unique structural configurations in MD simulations is essential to capture realistic membrane properties at the molecular scale. Furthermore, the predicted full-scale water flux based on the estimated permeability is within the same order of magnitude of bench-scale experimental measurement of 1.72×10(-5) m/s.

Aggregation Kinetics of Higher-Order Fullerene Clusters in Aquatic Systems.

The aggregation kinetics of nC60 and higher-order fullerene (HOF) clusters, i.e., nC70, nC76, and nC84, was systematically studied under a wide range of mono- (NaCl) and divalent (CaCl2) electrolytes and using time-resolved dynamic light scattering. Suwanee River Humic Acid (SRHA) was also used to determine the effect of natural macromolecules on nHOF aggregation. An increase in electrolyte concentration resulted in electrical double-layer compression of the negatively charged fullerene clusters, and the nC60s and nHOFs alike displayed classical Derjaguin-Landau-Verwey-Overbeek (DLVO) type interaction. The critical coagulation concentration (CCC) displayed a strong negative correlation with the carbon number in fullerenes and was estimated as 220, 150, 100, and 70 mM NaCl and 10, 12, 6, and 7.5 mM CaCl2 for nC60, nC70, nC76, and nC84, respectively. The aggregation mechanism (i.e., van der Waals interaction domination) was enumerated via molecular dynamics simulation and modified DLVO model. The presence of SRHA (2.5 mg TOC/L) profoundly influenced the aggregation behavior by stabilizing all fullerene clusters, even at a 100 mM NaCl concentration. The results from this study can be utilized to predict aggregation kinetics of nHOF clusters other than the ones studied here. The scaling factor for van der Waals interaction can also be used to model nHOF cluster interaction.

Adsorption characteristics of diclofenac and sulfamethoxazole to graphene oxide in aqueous solution.

The adsorptive properties of graphene oxide (GO) were characterized, and the binding energies of diclofenac (DCF) and sulfamethoxazole (SMX) on GO adsorption were predicted using molecular modeling. The adsorption behaviors of DCF and SMX were investigated in terms of GO dosage, contact time, and pH. Additionally, the effects of sonication on GO adsorption were examined. GO adsorption involves "oxygen-containing functional groups" (OCFGs) such as COOH, which exhibit negative charges over a wide range of pH values (pH 3-11). DCF (-18.8 kcal mol(-1)) had a more favorable binding energy on the GO surface than SMX (-15.9 kcal mol(-1)). Both DCF and SMX were removed from solution (adsorbed to GO), up to 35% and 12%, respectively, within 6h, and an increase in GO dosage enhanced the removal of DCF. Electrostatic repulsion occurred between dissociated DCF/SMX and the more negatively charged GO at basic pH (>pKa). The sonication of GO significantly improved the removal of DCF (75%) and SMX (30%) due to dispersion of exfoliated GO particles and the reduction of OCFGs on the GO surface. Both DCF and SMX in the adsorption isotherm were explained well by the Freundlich model. The results of this study can be used to maximize the adsorption capacities of micropollutants using GO in water treatment processes.

Preparation of non-aggregating aqueous fullerenes in highly saline solutions with a biocompatible non-ionic polymer.

Size-tunable stable aqueous fullerenes were prepared with different concentrations of biocompatible block-copolymer pluronic (PA) F-127, ranging from 0.001% to 1% (w/v). Size uniformity increased with the increase in PA concentration, yielding optimum 58.8 ± 5.6 and 61.8 ± 5.6 nm nC60s and nC70s, respectively (0.10%w/v PA), as observed using a dynamic light scattering technique. Fullerene aqueous suspensions also manifested enhanced stability in saline solution, Dulbecco's modified Eagle medium (DMEM), and Roswell Park Memorial Institute (RPMI) culture medium. Transmission electron microscopy was performed to elaborate on the morphology and size specificity of fullerene clusters. Physicochemical characterizations of the suspended fullerenes were performed through UV-vis spectroscopy and electrophoretic mobility measurements. PA molecules showed size restriction by encasement, as observed via molecular dynamics simulations. Such solubilization with controllable size and non-aggregating behavior can facilitate application enhancement and mechanistic environmental and toxicological studies of size-specific fullerenes.

Ultrasonic degradation of acetaminophen and naproxen in the presence of single-walled carbon nanotubes.

Ultrasonic (US) and single-walled carbon nanotube (SWNT)-catalyzed ultrasonic (US/SWNT) degradation of a pharmaceutical (PhAC) mixture of acetaminophen (AAP) and naproxen (NPX) used as analgesics was carried out in water. In the absence of SWNTs, maximum degradations of AAP and NPX occurred at a high frequency (1000 kHz) and under acidic conditions (pH 3) and different solution temperatures (25 °C at 28 kHz and 35 °C at 1000 kHz) during US reactions. Rapid degradation of PhACs occurred within 10 min at 28 kHz (44.5% for AAP; 90.3% for NPX) and 1000 kHz (39.2% for AAP; 74.8% for NPX) at a SWNT concentration of 45 mgL(-1) under US/SWNT process, compared with 28 kHz (5.2% for AAP; 10.6% for NPX) and 1000 kHz (29.1% for AAP; 46.2% for NPX) under US process. Degradation was associated with the dispersion of SWNTs; small particles acted as nuclei during US reactions, enhancing the H2O2 production yield. NPX removal was greater than AAP removal under all US-induced reaction and SWNT adsorption conditions, which is governed by the chemical properties of PhACs. Based on the results, the optimal treatment performance was observed at 28 kHz with 45 mgL(-1) SWNTs (US/SWNT) within 10 min.