Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

Hen egg-white lysozyme has long been the paradigm for enzymatic glycosyl hydrolysis with retention of configuration, with a protonated carboxylic acid and a deprotonated carboxylate participating in general acid-base catalysis. In marked contrast, the retaining chitin degrading enzymes from glycosyl hydrolase families 18 and 20 all have a single glutamic acid as the catalytic acid but lack a nucleophile on the enzyme. Both families have a catalytic (βα)8-barrel domain in common. X-ray structures of three different chitinolytic enzymes complexed with substrates or inhibitors identify a retaining mechanism involving a protein acid and the carbonyl oxygen atom of the substrate’s C2 N-acetyl group as the nucleophile. These studies unambiguously demonstrate the distortion of the sugar ring toward a sofa conformation, long postulated as being close to that of the transition state in glycosyl hydrolysis.

The formation of CO2_2 through consumption of gas-phase CO on vacuum-UV irradiated water ice

[Abridged] Observations of protoplanetary disks suggest that they are depleted in gas-phase CO. It has been posed that gas-phase CO is chemically consumed and converted into less volatile species through gas-grain processes. Observations of interstellar ices reveal a CO$_2$ component within H$_2$O ice suggesting co-formation. The aim of this work is to experimentally verify the interaction of gas-phase CO with solid-state OH radicals above the sublimation temperature of CO. Amorphous solid water (ASW) is deposited at 15 K and followed by vacuum-UV (VUV) irradiation to dissociate H$_2$O and create OH radicals. Gas-phase CO is simultaneously admitted and only adsorbs with a short residence time on the ASW. Products in the solid state are studied with infrared spectroscopy and once released into the gas phase with mass spectrometry. Results show that gas-phase CO is converted into CO$_2$, with an efficiency of 7-27%, when interacting with VUV irradiated ASW. Between 40 and 90 K, CO$_2$ production is constant, above 90 K, O$_2$ production takes over. In the temperature range of 40-60 K, the CO$_2$ remains in the solid state, while at temperatures $\geq$ 70 K the formed CO$_2$ is released into the gas phase. We conclude that gas-phase CO reacts with solid-state OH radicals above its sublimation temperature. This gas-phase CO and solid-state OH radical interaction could explain the observed CO$_2$ embedded in water-rich ices. It may also contribute to the observed lack of gas-phase CO in planet-forming disks, as previously suggested. Our experiments indicate a lower water ice dissociation efficiency than originally adopted in model descriptions of planet-forming disks and molecular clouds. Incorporation of the reduced water ice dissociation and increased binding energy of CO on a water ice surfaces in these models would allow investigation of this gas-grain interaction to its full extend.Comment: Accepted for publication in Astronomy & Astrophysic

The formation of peptide-like molecules on interstellar dust grains

Molecules with an amide functional group resemble peptide bonds, the molecular bridges that connect amino acids, and may thus be relevant in processes that lead to the formation of life. In this study, the solid state formation of some of the smallest amides is investigated in the laboratory. To this end, CH$_{4}$:HNCO ice mixtures at 20 K are irradiated with far-UV photons, where the radiation is used as a tool to produce the radicals required for the formation of the amides. Products are identified and investigated with infrared spectroscopy and temperature programmed desorption mass spectrometry. The laboratory data show that NH$_{2}$CHO, CH$_{3}$NCO, NH$_{2}$C(O)NH$_{2}$, CH$_{3}$C(O)NH$_{2}$ and CH$_{3}$NH$_{2}$ can simultaneously be formed. The NH$_{2}$CO radical is found to be key in the formation of larger amides. In parallel, ALMA observations towards the low-mass protostar IRAS 16293-2422B are analysed in search of CH$_{3}$NHCHO (N-methylformamide) and CH$_{3}$C(O)NH$_{2}$ (acetamide). CH$_{3}$C(O)NH$_{2}$ is tentatively detected towards IRAS 16293-2422B at an abundance comparable with those found towards high-mass sources. The combined laboratory and observational data indicates that NH$_{2}$CHO and CH$_{3}$C(O)NH$_{2}$ are chemically linked and form in the ice mantles of interstellar dust grains. A solid-state reaction network for the formation of these amides is proposed.Comment: Accepted for publication in MNRA

Brief Communication: CATALYST - a multi-regional stakeholder think tank for fostering capacity development in disaster risk reduction and climate change adaptation

Abstract. This brief communication presents the work and objectives of the CATALYST project on "Capacity Development for Hazard Risk Reduction and Adaptation" funded by the European Commission (October 2011–September 2013). CATALYST set up a multi-regional think tank covering four regions (Central America and the Caribbean, East and West Africa, the European Mediterranean, and South and Southeast Asia), intending to strengthen capacity development for stakeholders involved in disaster risk reduction (DRR) and climate change adaptation, in the context of natural hazards. This communication concludes with a selection of recommendations for capacity development in DRR and climate change adaptation from the perspective of governance issues

Smoothness metrics for reaching performance after stroke:Part 1: which one to choose?

BACKGROUND: Smoothness is commonly used for measuring movement quality of the upper paretic limb during reaching tasks after stroke. Many different smoothness metrics have been used in stroke research, but a ‘valid’ metric has not been identified. A systematic review and subsequent rigorous analysis of smoothness metrics used in stroke research, in terms of their mathematical definitions and response to simulated perturbations, is needed to conclude whether they are valid for measuring smoothness. Our objective was to provide a recommendation for metrics that reflect smoothness after stroke based on: (1) a systematic review of smoothness metrics for reaching used in stroke research, (2) the mathematical description of the metrics, and (3) the response of metrics to simulated changes associated with smoothness deficits in the reaching profile. METHODS: The systematic review was performed by screening electronic databases using combined keyword groups Stroke, Reaching and Smoothness. Subsequently, each metric identified was assessed with mathematical criteria regarding smoothness: (a) being dimensionless, (b) being reproducible, (c) being based on rate of change of position, and (d) not being a linear transform of other smoothness metrics. The resulting metrics were tested for their response to simulated changes in reaching using models of velocity profiles with varying reaching distances and durations, harmonic disturbances, noise, and sub-movements. Two reaching tasks were simulated; reach-to-point and reach-to-grasp. The metrics that responded as expected in all simulation analyses were considered to be valid. RESULTS: The systematic review identified 32 different smoothness metrics, 17 of which were excluded based on mathematical criteria, and 13 more as they did not respond as expected in all simulation analyses. Eventually, we found that, for reach-to-point and reach-to-grasp movements, only Spectral Arc Length (SPARC) was found to be a valid metric. CONCLUSIONS: Based on this systematic review and simulation analyses, we recommend the use of SPARC as a valid smoothness metric in both reach-to-point and reach-to-grasp tasks of the upper limb after stroke. However, further research is needed to understand the time course of smoothness measured with SPARC for the upper limb early post stroke, preferably in longitudinal studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12984-021-00949-6

The TW Hya Rosetta Stone Project. I. Radial and Vertical Distributions of DCN and DCO⁺

Molecular D/H ratios are frequently used to probe the chemical past of solar system volatiles. Yet it is unclear which parts of the solar nebula hosted an active deuterium fractionation chemistry. To address this question, we present 0farcs2–0farcs4 Atacama Large Millimeter/submillimeter Array (ALMA) observations of DCO⁺ and DCN 2–1, 3–2, and 4–3 toward the nearby protoplanetary disk around TW Hya, taken as part of the TW Hya Rosetta Stone project, augmented with archival data. DCO⁺ is characterized by an excitation temperature of ~40 K across the 70 au radius pebble disk, indicative of emission from a warm, elevated molecular layer. Tentatively, DCN is present at even higher temperatures. Both DCO⁺ and DCN present substantial emission cavities in the inner disk, while in the outer disk the DCO⁺ and DCN morphologies diverge: most DCN emission originates from a narrow ring peaking around 30 au, with some additional diffuse DCN emission present at larger radii, while DCO⁺ is present in a broad structured ring that extends past the pebble disk. Based on a set of simple parametric disk abundance models, these emission patterns can be explained by a near-constant DCN abundance exterior to the cavity, and an increasing DCO⁺ abundance with radius. In conclusion, the ALMA observations reveal an active deuterium fractionation chemistry in multiple disk regions around TW Hya, but not in the cold planetesimal-forming midplane and in the inner disk. More observations are needed to explore whether deuterium fractionation is actually absent in these latter regions, and if its absence is a common feature or something peculiar to the old TW Hya disk