Different modes of interaction by TIAR and HuR with target RNA and DNA

TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanomolar range, with higher overall affinity for U-rich RNA. However, the higher affinity for U–rich sequences is mainly due to faster association with U-rich RNA, which we propose is a reflection of the higher probability of association. Differences between TIAR and HuR are observed in their modes of binding to RNA. TIAR is able to bind deoxy-oligonucleotides with nanomolar affinity, whereas HuR affinity is reduced to a micromolar level. Studies with U-rich DNA reveal that TIAR binding depends less on the 2′-hydroxyl group of RNA than HuR binding. Finally we show that SAXS data, recorded for the first two domains of TIAR in complex with RNA, are more consistent with a flexible, elongated shape and not the compact shape that the first two domains of Hu proteins adopt upon binding to RNA. We thus propose that these triple-RRM proteins, which compete for the same binding sites in cells, interact with their targets in fundamentally different ways

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Transcriptome-wide analysis of protein-RNA interactions predicts the dual splicing effects of TIA proteins, showing that their local enhancing function is associated with diverse distal splicing silencing effects

Orientational Effects and Random Mixing in 1‑Alkanol + Nitrile Mixtures

1-Alkanol + alkanenitrile or + benzonitrile systems have been investigated by means of the molar excess functionsenthalpies (Hm E ), isobaric heat capacities (Cp,m E ), volumes (Vm E ), and entropiesand using the Flory model and the concentration−concentration structure factor (SCC(0)) formalism. From the analysis of the experimental data available in the literature, it is concluded that interactions are mainly of dipolar type. In addition, large Hm E values contrast with rather low Vm E values, indicating the existence of strong structural effects. Hm E measurements have been used to evaluate the enthalpy of the hydroxyl−nitrile interactions (ΔHOH−CN). They are stronger in methanol systems and become weaker when the alcohol size increases. In solutions with a given short chain 1-alkanol (up to 1-butanol), the replacement of ethanenitrile by butanenitrile weakens the mentioned interactions. Application of the Flory model shows that orientational effects exist in methanol or 1- nonanol, or 1-decanol + ethanenitrile mixtures. In the former solution, this is due to the existence of interactions between unlike molecules. For mixtures including 1-nonanol or 1-decanol, the systems at 298.15 K are close to their UCST (upper critical solution temperature), and interactions between like molecules are dominant. Orientational effects also are encountered in methanol or ethanol + butanenitrile mixtures because self-association of the alcohol plays a more important role. Aromaticity effect seems to enhance orientational effects. For the remainder of the systems under consideration, the random mixing hypothesis is attained to a rather large extent. Results from the application of the SCC(0) formalism show that homocoordination is the dominant trend in the investigated solutions, and are consistent with those obtained from the Flory model

Winkler model for predicting the dynamic response of caisson foundations

The paper presents a Winkler-based numerical model for the analysis of the dynamic response of caisson foundations. The model allows the evaluation of the impedance functions and of the foundation input motion (FIM), which can be used in the framework of the substructure approach to compute inertial soil-foundation superstructure interaction analyses. In addition, kinematic stress resultants due to seismic shear waves propagating into the soil can be estimated. The caisson is modelled as a Timoshenko beam and the soil-caisson interaction forces are derived from the analyses of the plane-strain vibration problem of an annular rigid ring embedded into the soil. The problem solution is obtained in the frequency domain exploiting the finite element approach and generic soil stratigraphies can be considered in the applications. The model, which is characterised by a very low computational effort, is validated by performing a parametric investigation, comparing results with those obtained from more rigorous BEM-FEM models of the soil-caissons systems. Finally, some applications to real caisson foundations of offshore wind turbines (OWTs) are shown to demonstrate the model accuracy in capturing the seismic response of the foundations obtained from more rigorous models

The Veterinary Anti-Parasitic Selamectin Is a Novel Inhibitor of the Mycobacterium tuberculosis DprE1 Enzyme

Avermectins are macrocyclic lactones with anthelmintic activity. Recently, they were found to be effective against Mycobacterium tuberculosis, which accounts for one third of the worldwide deaths from antimicrobial resistance. However, their anti-mycobacterial mode of action remains to be elucidated. The activity of selamectin was determined against a panel of M. tuberculosis mutants. Two strains carrying mutations in DprE1, the decaprenylphosphoryl-β-D-ribose oxidase involved in the synthesis of mycobacterial arabinogalactan, were more susceptible to selamectin. Biochemical assays against the Mycobacterium smegmatis DprE1 protein confirmed this finding, and docking studies predicted a binding site in a loop that included Leu275. Sequence alignment revealed variants in this position among mycobacterial species, with the size and hydrophobicity of the residue correlating with their MIC values; M. smegmatis DprE1 variants carrying these point mutations validated the docking predictions. However, the correlation was not confirmed when M. smegmatis mutant strains were constructed and MIC phenotypic assays performed. Likewise, metabolic labeling of selamectin-treated M. smegmatis and M. tuberculosis cells with14C-labeled acetate did not reveal the expected lipid profile associated with DprE1 inhibition. Together, our results confirm the in vitro interactions of selamectin and DprE1 but suggest that selamectin could be a multi-target anti-mycobacterial compound