Computing rotational energy transfers of OD−/OH− in collisions with Rb: isotopic effects and inelastic rates at cold ion-trap conditions

[EN]We report close-coupling (CC) quantum dynamics calculations for collisional excitation/de-excitation of the lowest four rotational levels of OD− and of OH− interacting with Rb atoms in a cold ion trap. The calculations are carried out over a range of energies capable of yielding the corresponding rates for state-changing events over a rather broad interval of temperatures which cover those reached in earlier cold trap experiments. They involved sympathetic cooling of the molecular anion through a cloud of laser-cooled Rb atoms, an experiment which is currently being run again through a Heidelberg–Innsbruck collaboration. The significance of isotopic effects is analysed by comparing both systems and the range of temperatures examined in the calculations is extended up to 400 K, starting from a few mK. Both cross sections and rates are found to be markedly larger than in the case of OD−/OH− interacting the He atoms under the same conditions, and the isotopic effects are also seen to be rather significant at the energies examined in the present study. Such findings are discussed in the light of the observed trap losses of molecular anions

The structural features of the ligand-free moaA riboswitch and its ion-dependent folding

Riboswitches are structural elements of mRNA involved in the regulation of gene expression by responding to specific cellular metabolites. To fulfil their regulatory function, riboswitches prefold into an active state, the so-called binding competent form, that guarantees metabolite binding and allows a consecutive refolding of the RNA. Here, we describe the folding pathway to the binding competent form as well as the ligand free structure of the moaA riboswitch of E. coli. This RNA proposedly responds to the molybdenum cofactor (Moco), a highly oxygen-sensitive metabolite, essential in the carbon and sulfur cycles of eukaryotes. K+- and Mg2+-dependent footprinting assays and spectroscopic investigations show a high degree of structure formation of this RNA already at very low ion-concentrations. Mg2+ facilitates additionally a general compaction of the riboswitch towards its proposed active structure. We show that this fold agrees with the earlier suggested secondary structure which included also a long-range tetraloop/tetraloop-receptor like interaction. Metal ion cleavage assays revealed specific Mg2+-binding pockets within the moaA riboswitch. These Mg2+ binding pockets are good indicators for the potential Moco binding site, since in riboswitches, Mg2+ was shown to be necessary to bind phosphate-carrying metabolites. The importance of the phosphate and of other functional groups of Moco is highlighted by binding assays with tetrahydrobiopterin, the reduced and oxygen-sensitive core moiety of Moco. We demonstrate that the general molecular shape of pterin by its own is insufficient for the recognition by the riboswitch

Conditions for the stable adsorption of lipid monolayers to solid surfaces

Lipid monolayers are ubiquitous in biological systems and have multiple roles in biotechnological applications, such as lipid coatings that enhance colloidal stability or prevent surface fouling. Despite the great technological importance of surface-adsorbed lipid monolayers, the connection between their formation and the chemical characteristics of the underlying surfaces has remained poorly understood. Here, we elucidate the conditions required for stable lipid monolayers nonspecifically adsorbed on solid surfaces in aqueous solutions and water/alcohol mixtures. We use a framework that combines the general thermodynamic principles of monolayer adsorption with fully atomistic molecular dynamics simulations. We find that, very universally, the chief descriptor of adsorption free energy is the wetting contact angle of the solvent on the surface. It turns out that monolayers can form and remain thermodynamically stable only on substrates with contact angles above the adsorption contact angle, θads⁠. Our analysis establishes that θads falls into a narrow range of around 60∘–70∘ in aqueous media and is only weakly dependent on the surface chemistry. Moreover, to a good approximation, θads is roughly determined by the ratio between the surface tensions of hydrocarbons and the solvent. Adding small amounts of alcohol to the aqueous medium lowers θads and thereby facilitates monolayer formation on hydrophilic solid surfaces. At the same time, alcohol addition weakens the adsorption strength on hydrophobic surfaces and results in a slowdown of the adsorption kinetics, which can be useful for the preparation of defect-free monolayers

Stick, Flick, Click: DNA-guided Fluorescent Labeling of Long RNA for Single-molecule FRET

Exploring the spatiotemporal dynamics of biomolecules on a single-molecule level requires innovative ways to make them spectroscopically visible. Fluorescence resonance energy transfer (FRET) uses a pair of organic dyes as reporters to measure distances along a predefined biomolecular reaction coordinate. For this nanoscopic ruler to work, the fluorescent labels need to be coupled onto the molecule of interest in a bioorthogonal and site-selective manner. Tagging large non-coding RNAs with single-nucleotide precision is an open challenge. Here we summarize current strategies in labeling riboswitches and ribozymes for fluorescence spectroscopy and FRET in particular. A special focus lies on our recently developed, DNA-guided approach that inserts two fluorophores through a stepwise process of templated functionality transfer and click chemistry

Force Response of Polypeptide Chains from Water-Explicit MD Simulations

Using molecular dynamics simulations in explicit water, the force–extension relations for the five homopeptides polyglycine, polyalanine, polyasparagine, poly(glutamic acid), and polylysine are investigated. From simulations in the low-force regime the Kuhn length is determined, from simulations in the high-force regime the equilibrium contour length and the linear and nonlinear stretching moduli, which agree well with quantum-chemical density-functional theory calculations, are determined. All these parameters vary considerably between the different polypeptides. The augmented inhomogeneous partially freely rotating chain (iPFRC) model, which accounts for side-chain interactions and restricted dihedral rotation, is demonstrated to describe the simulated force–extension relations very well. We present a quantitative comparison between published experimental single-molecule force–extension curves for different polypeptides with simulation and model predictions. The thermodynamic stretching properties of polypeptides are investigated by decomposition of the stretching free energy into energetic and entropic contributions

Disseminating health evidence summaries to increase evidence use in health care

OBJECTIVE: To verify whether an intervention based on disseminating health evidence summaries by e-mail to health professionals increases access to health evidence databases, and whether health professionals intend to apply the evidence received by e-mail in their clinical practice. METHODS: This quantitative study started with a survey to collect demographic data and patterns of access to health evidence databases. It was followed by a longitudinal intervention, over 48 weeks, that disseminated 143 health evidence summaries to 339 health professionals with higher education degree who work in the Brazilian Unified Health System. In the longitudinal intervention phase, health professionals voluntarily assessed the received health evidence summaries using the information assessment method. Finally, the study concluded with a survey to identify changes in accessing health evidence databases. RESULTS: Of the 339 Brazilian health professionals participating in this research, 90 (26.5%) answered the initial and final surveys. After 48 weeks, there was an increase in the use of health evidence databases; 186 (54.9%) participants submitted 7,942 assessments of health evidence summaries, which were relevant for patient care in 5,409 (68%) assessments. CONCLUSIONS: The dissemination of health evidence summaries by e-mail to health professionals in Brazil increases the reported use of evidence in clinical practice

Pharmacology and clinical drug candidates in redox medicine

SIGNIFICANCE Oxidative stress is suggested to be a disease mechanism common to a wide range of disorders affecting human health. However, so far, the pharmacotherapeutic exploitation of this, for example, based on chemical scavenging of pro-oxidant molecules, has been unsuccessful. Recent Advances: An alternative emerging approach is to target the enzymatic sources of disease-relevant oxidative stress. Several such enzymes and isoforms have been identified and linked to different pathologies. For some targets, the respective pharmacology is quite advanced, that is, up to late-stage clinical development or even on the market; for others, drugs are already in clinical use, although not for indications based on oxidative stress, and repurposing seems to be a viable option. CRITICAL ISSUES For all other targets, reliable preclinical validation and drug ability are key factors for any translation into the clinic. In this study, specific pharmacological agents with optimal pharmacokinetic profiles are still lacking. Moreover, these enzymes also serve largely unknown physiological functions and their inhibition may lead to unwanted side effects. FUTURE DIRECTIONS The current promising data based on new targets, drugs, and drug repurposing are mainly a result of academic efforts. With the availability of optimized compounds and coordinated efforts from academia and industry scientists, unambiguous validation and translation into proof-of-principle studies seem achievable in the very near future, possibly leading towards a new era of redox medicine