CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling

Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model.     

Tissue-Specific stem cell differentiation in an in vitro airway model

The respiratory tract is the primary site of exposure to airborne compounds, with the bronchial epithelium providing one of the first lines of defence. A growing need exists for an accurate in vitro model of the bronchial epithelium. Here, normal human bronchial epithelial (NHBE) cells cultured at an air/liquid interface create a fully differentiated, in-vivo-like model of the human bronchial epithelium. Developmental characterisation includes (i) trans-epithelial electrical resistance, (ii) morphology and (iii) bronchial cell specific stains/markers. It is concluded that the basal/progenitor cells create a pseudo-stratified, mucociliary NHBE model containing basal, serous, Clara, goblet and ciliated cells, reflective of the normal human bronchial epithelium (days 24-33 ALI culture).     

I(-)·(CH3I)2 photoexcitation: the influence of dipole bound states on detachment and fragmentation

We present the results of a photoelectron imaging study of the I(-)·(CH(3)I)(2) cluster anion over excitation wavelengths 355-260 nm. The resulting spectra and photoelectron angular distributions (PADs) suggest extensive electron-molecule interaction following photoexcitation. Fragmentation channels are observed subsequent to excitation between 355 and 330 nm. The origin of these features, which begin 200 meV and peak 70 meV below the X band direct detachment threshold, is described in terms of a predissociative dipole bound state. The nature of the fragments detected and the energetics of the channel opening argue strongly in favor of an asymmetric, head to tail cluster anion geometry posited by Dessent et al. [Acc. Chem. Res. 31, 527 (1998)]. Above the direct detachment threshold, PADs display evidence of phenomena akin to electron-molecule scattering. The fragment anions disappear above the X band threshold but reappear some distance below the second (A) direct detachment band. At these energies there is also rapid variation of the X band PAD, an observation attributed to autodetachment via spin-orbit relaxation of the iodine core of the cluster.     

Circadian variations in biologically closed electrochemical circuits in Aloe vera and Mimosa pudica

The circadian clock regulates a wide range of electrophysiological and developmental processes in plants. This paper presents, for the first time, the direct influence of a circadian clock on biologically closed electrochemical circuits in vivo. Here we show circadian variation of the plant responses to electrical stimulation. The biologically closed electrochemical circuits in the leaves of Aloe vera and Mimosa pudica, which regulate their physiology, were analyzed using the charge stimulation method. The electrostimulation was provided with different timing and different voltages. Resistance between Ag/AgCl electrodes in the leaf of Aloe vera was higher during the day than at night. Discharge of the capacitor in Aloe vera at night was faster than during the day. Discharge of the capacitor in a pulvinus of Mimosa pudica was faster during the day. The biologically closed electrical circuits with voltage gated ion channels in Mimosa pudica are also activated the next day, even in the darkness. These results show that the circadian clock can be maintained endogenously and has electrochemical oscillators, which can activate ion channels in biologically closed electrochemical circuits. We present the equivalent electrical circuits in both plants and their circadian variation to explain the experimental data.     

Determination of operating characteristic, retesting, and testing amount probabilities associated with testing for the presence of Salmonella in foods

The relatively small perceived probability associated with retesting a food for the presence of Salmonella at low levels is often considered as one of the reasons that a confirmatory or check-analysis tends to disagree in practice with the results of an original test. Given a retesting process where a retest is only performed to confirm an original positive Salmonella test, the probability that both the original and retest will test positive for Salmonella has been traditionally determined by some as the product of the probabilities of a positive Salmonella test for the original and retest samples. When examining the probabilities associated with the retesting process, we found that our results disagreed with those based on intuitions apparently held by others concerning how these probabilities should be calculated. For Salmonella testing, operating characteristic values were computed to demonstrate the protections afforded by the Salmonella sampling plans presented in the U.S. Food and Drug Administration's Bacteriological Analytical Manual and to obtain the probability of a positive Salmonella test. The geometric distribution was examined for possible utility in determining the probabilities associated with testing amounts, i.e., the number of Salmonella tests needed to obtain a positive test.     

Hydrophobicity within the three-dimensional Mercedes-Benz model: potential of mean force

We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.     

A microwave-assisted sequential extraction of water and dilute acid soluble arsenic species from marine plant and animal tissues

This paper describes the use of dilute nitric acid for the extraction and quantification of arsenic species. A number of extractants (e.g. water, 1.5 M orthophosphoric acid, methanol-water and dilute nitric acid) were tested for the extraction of arsenic from marine biological samples, such as plants that have proved difficult to quantitatively extract. Dilute 2% (v/v) nitric acid was found to give the highest recoveries of arsenic overall and was chosen for further optimisation. The optimal extraction conditions for arsenic were 2% (v/v) HNO₃, 6 min⁻¹, 90 °C. Arsenic species were found to be stable under the optimised conditions with the exception of the arsenoriboses which degraded to a product eluting at the same retention time as glycerol arsenoribose. Good agreement was found between the 2% (v/v) HNO₃ extraction and the methanol-water extraction for the certified reference material DORM-2 (AB 17.1 and 16.2 μg g⁻¹, respectively, and TETRA 0.27 and 0.25 μg g⁻¹, respectively), which were in close agreement with the certified concentrations of AB 16.4 ± 1.1 μg g⁻¹ and TETRA 0.248 ± 0.054 μg g⁻¹.To preserve the integrity of arsenic species, a sequential extraction technique was developed where the previously methanol-water extracted pellet was further extracted with 2% (v/v) HNO₃ under the optimised conditions. Increases in arsenic recoveries between 13% and 36% were found and speciation of this faction revealed that only inorganic and simple methylated species were extracted.     

Preparation of Bottlebrush Polymers via a One‐Pot Ring‐Opening Polymerization (ROP) and Ring‐Opening Metathesis Polymerization (ROMP) Grafting‐Through Strategy

Bottlebrush polymers are synthesized using a tandem ring‐opening polymerization (ROP) and ring‐opening metathesis polymerization (ROMP) strategy. For the first time, ROP and ROMP are conducted sequentially in the same pot to yield well‐defined bottlebrush polymers with molecular weights in excess of 10⁶ Da. The first step of this process involves the synthesis of a polylactide macromonomer (MM) via ROP of d ,l ‐lactide initiated by an alcohol‐functionalized norbornene. ROMP grafting‐through is then carried out in the same pot to produce the bottlebrush polymer. The applicability of this methodology is evaluated for different MM molecular weights and bottlebrush backbone degrees of polymerization. Size‐exclusion chromatographic and ¹H NMR spectroscopic analyses confirm excellent control over both polymerization steps. In addition, bottlebrush polymers are imaged using atomic force microscopy and stain‐free transmission electron microscopy on graphene oxide.

     

Uncovering the Stoichiometry of Pyrococcus furiosus RNase P,a Multi‐Subunit Catalytic Ribonucleoprotein Complex,by Surface‐Induced Dissociation and Ion Mobility Mass Spectrometry

We demonstrate that surface‐induced dissociation (SID) coupled with ion mobility mass spectrometry (IM‐MS) is a powerful tool for determining the stoichiometry of a multi‐subunit ribonucleoprotein (RNP) complex assembled in a solution containing Mg²⁺. We investigated Pyrococcus furiosus (Pfu) RNase P, an archaeal RNP that catalyzes tRNA 5′ maturation. Previous step‐wise, Mg²⁺‐dependent reconstitutions of Pfu RNase P with its catalytic RNA subunit and two interacting protein cofactor pairs (RPP21⋅RPP29 and POP5⋅RPP30) revealed functional RNP intermediates en route to the RNase P enzyme, but provided no information on subunit stoichiometry. Our native MS studies with the proteins showed RPP21⋅RPP29 and (POP5⋅RPP30)₂ complexes, but indicated a 1:1 composition for all subunits when either one or both protein complexes bind the cognate RNA. These results highlight the utility of SID and IM‐MS in resolving conformational heterogeneity and yielding insights on RNP assembly.     

Environmental Research for Art Conservation and Assessment of Indoor Conditions Surrounding Cultural Objects

This paper describes the results and conclusions of research directed towards the development and evaluation of a chemical sensor which would provide information on the quality of indoor environments surrounding cultural objects. In our case these objects were paintings housed in major European galleries and the main objective is their preservation through an improved understanding of their microenvironment. The concept was to prepare and expose test tempera paintings which would behave as dosimeters and integrate the environmental response at these locations. Artificial ageing of similar samples was performed to provide a means of calibrating the test paintings. Samples from the test paintings were compared with artificially aged samples and this enabled the sites to be ranked in terms of their suitability for exposure of cultural objects. Additionally, novel methodology involving piezoelectric sensors was designed for monitoring the relative humidity and temperature of the microenvironment of paintings. Dielectric techniques were also used for measuring the effect of relative humidity fluctuations on artists' materials and novel non-invasive dielectric techniques in the microwave region were used for the determination of their moisture content. This revised version was published online in August 2006 with corrections to the Cover Date.