Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole–dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron–electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.
13 January 2021 in ACS Applied Materials & Interfaces
We report a facile and robust room-temperature NO2 sensor fabricated using bi- and multi-layered 2H variant of tungsten di-selenide (2H-WSe2) nanosheets, exhibiting high sensing characteristics. A simple liquid-assisted exfoliation of 2H-WSe2, prepared using ambient pressure chemical vapor deposition, allows smooth integration of these nanosheets on transducers. Three sensor batches are fabricated by modulating the total number of layers (L) obtained from the total number of droplets from a homogeneous 2H-WSe2 dispersion, such as ∼2L, ∼5–6L, and ∼13–17L, respectively. The gas-sensing attributes of 2H-WSe2 nanosheets are investigated thoroughly. Room temperature (RT) experiments show that these devices are specifically tailored for NO2 detection. 2L WSe2 nanosheets deliver the best rapid response compared to ∼5–6L or ∼13–17L. The response of 2L WSe2 at RT is 250, 328, and 361% to 2, 4, and 6 ppm NO2, respectively. The sensor showed nearly the same response toward low NO2 concentration even after 9 months of testing, confirming its remarkable long-term stability. A selectivity study, performed at three working temperatures (RT, 100, and 150 °C), shows high selectivity at 150 and 100 °C. Full selectivity toward NO2 at RT confirms that 2H-WSe2 nanosheet-based sensors are ideal candidates for NO2 gas detection.
19 December 2018 in Angewandte Chemie International Edition
Once coal is excavated it comes into contact with atmospheric oxygen and begins to undergo low temperature oxidation. The mechanism by which the molecular oxygen interacts with the coal macromolecule is suggested to occur in several steps. These steps primarily involve O2 diffusion to the surface where physical adsorption followed by chemical adsorption takes place. The chemical adsorption forms several types of oxides that can subsequently react to form several products, primarily CO2. It has also been suggested that some of these oxidation mechanisms might involve radical reactions. As the previous studies were conducted under conditions where significant structural changes occur it is possible that in the low temperature range (T < 100 °C) the oxidation mechanism is different. Several different rank (lignite–subbituminous–bituminous) coals were isothermally heated at 95 °C in an air atmosphere for a period of up to 6 months and samples were collected at two week intervals. The radical concentration of each sample was measured by Continuous Wave Electron Paramagnetic Resonance (CW-EPR). It is apparent that there are distinct differences between the lower rank (lignite) and the higher rank (subbituminous, bituminous) coals. The lower rank coals exhibited only carbon centered radicals with an adjacent oxygen atom and the higher rank coals exhibited only carbon centered radicals. Interestingly, the lower rank coals exhibited no change in radical concentration due to the long term oxidation treatment while the higher rank coals showed a distinct increase in the radical concentration. These findings shed new light on the complex heterogeneous low temperature oxidation reactions occurring at the coal surface.
1 October 2019 in Current Opinion in Structural Biology
Copper plays a vital role in fundamental cellular functions, and its concentration in the cell must be tightly regulated, as dysfunction of copper homeostasis is linked to severe neurological diseases and cancer. This review provides a compendium of current knowledge regarding the mechanism of copper transfer from the blood system to the Golgi apparatus; this mechanism involves the copper transporter hCtr1, the metallochaperone Atox1, and the ATPases ATP7A/B. We discuss key insights regarding the structural and functional properties of the hCtr1-Atox1-ATP7B cycle, obtained from diverse studies relying on distinct yet complementary biophysical, biochemical, and computational methods. We further address the mechanistic aspects of the cycle that continue to remain elusive. These knowledge gaps must be filled in order to be able to harness our understanding of copper transfer to develop therapeutic approaches with the capacity to modulate copper metabolism.
Thirty-five thousand people die as a result of more than 2.8 million antibiotic-resistant infections in the United States of America per year. Pseudomonas aeruginosa (P. aeruginosa) is classified a serious threat, the second-highest threat category of the U.S. Department of Health and Human Services. Among others, the World Health Organization (WHO) encourages the discovery and development of novel antibiotic classes with new targets and mechanisms of action without cross-resistance to existing classes. To find potential new target sites in pathogenic bacteria, such as P. aeruginosa, it is inevitable to fully understand the molecular mechanism of homeostasis, metabolism, regulation, growth, and resistances thereof. P. aeruginosa maintains a sophisticated copper defense cascade comprising three stages, resembling those of public safety organizations. These stages include copper scavenging, first responder, and second responder. Similar mechanisms are found in numerous pathogens. Here we compare the copper-dependent transcription regulators cueR and copRS of Escherichia coli (E. coli) and P. aeruginosa. Further, phylogenetic analysis and structural modelling of mexPQ-opmE reveal that this efflux pump is unlikely to be involved in the copper export of P. aeruginosa. Altogether, we present current understandings of the copper homeostasis in P. aeruginosa and potential new target sites for antimicrobial agents or a combinatorial drug regimen in the fight against multidrug resistant pathogens.