Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins.

RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA granules, but dysregulated assembly can be pathological. Because of their structural heterogeneity, IDRs are best studied by NMR spectroscopy. In this study, we used NMR spectroscopy to investigate the structural propensity and self-association of the IDR of the RBP Musashi-1. We identified two transient α-helical regions (residues ~208-218 and ~270-284 in the IDR, the latter with a polyalanine tract). Strong NMR line broadening in these regions and circular dichroism and micrography data suggest that the two α-helical elements and the hydrophobic residues in between may contribute to the formation of oligomers found in stress granules and implicated in Alzheimer's disease. Bioinformatics analysis suggests that polyalanine stretches in the IDRs of RBPs may have evolved to promote RBP assembly.

Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43's Conformational Transition.

Most biological functions involve protein-protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43's IDR undergoes the neurodegenerative disease related α-helix-to-ß-sheet transition increases in relation to the amount of hnRNP-A2's IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other's functions through their IDRs.

The physical forces mediating self-association and phase-separation in the C-terminal domain of TDP-43.

The TAR DNA-binding protein of 43kDa (TDP-43) has been identified as the main component of amyotrophic lateral sclerosis (ALS) cytoplasmic inclusions. The link between this proteinopathy and TDP-43's intrinsically disordered C-terminal domain is well known, but recently also, this domain has been shown to be involved in the formation of the membraneless organelles that mediate TDP-43's functions. The mechanisms that underpin the liquid-liquid phase separation (LLPS) of these membraneless organelles undergo remain elusive. Crucially though, these factors may be the key to understanding the delicate balance between TDP-43's physiological and pathological functions. In this study, we used nuclear magnetic resonance spectroscopy and optical methods to demonstrate that an α-helical component in the centre (residues 320-340) of the C-terminal domain is related to the protein's self-association and LLPS. Systematically analysing ALS-related TDP-43 mutants (G298S, M337V, and Q331K) in different buffer conditions at different temperatures, we prove that this phase separation is driven by hydrophobic interactions but is inhibited by electrostatic repulsion. Based on these findings, we rationally introduced a mutant, W334G, and demonstrate that this mutant disrupts LLPS without disturbing this α-helical propensity. This tryptophan may serve as a key residue in this protein's LLPS.

MRI Detection of Hepatic N-Acetylcysteine Uptake in Mice.

This proof-of-concept study looked at the feasibility of using a thiol-water proton exchange (i.e., CEST) MRI contrast to detect in vivo hepatic N-acetylcysteine (NAC) uptake. The feasibility of detecting NAC-induced glutathione (GSH) biosynthesis using CEST MRI was also investigated. The detectability of the GSH amide and NAC thiol CEST effect at B0 = 7 T was determined in phantom experiments and simulations. C57BL/6 mice were injected intravenously (IV) with 50 g L-1 NAC in PBS (pH 7) during MRI acquisition. The dynamic magnetisation transfer ratio (MTR) and partial Z-spectral data were generated from the acquisition of measurements of the upfield NAC thiol and downfield GSH amide CEST effects in the liver. The 1H-NMR spectroscopy on aqueous mouse liver extracts, post-NAC-injection, was performed to verify hepatic NAC uptake. The dynamic MTR and partial Z-spectral data revealed a significant attenuation of the mouse liver MR signal when a saturation pulse was applied at -2.7 ppm (i.e., NAC thiol proton resonance) after the IV injection of the NAC solution. The 1H-NMR data revealed the presence of hepatic NAC, which coincided strongly with the increased upfield MTR in the dynamic CEST data, providing strong evidence that hepatic NAC uptake was detected. However, this MTR enhancement was attributed to a combination of NAC thiol CEST and some other upfield MT-generating mechanism(s) to be identified in future studies. The detection of hepatic GSH via its amide CEST MRI contrast was inconclusive based on the current results.

Chemical Exchange Saturation Transfer (CEST) Signal at -1.6 ppm and Its Application for Imaging a C6 Glioma Model.

The chemical exchange saturation transfer (CEST) signal at -1.6 ppm is attributed to the choline methyl on phosphatidylcholines and results from the relayed nuclear Overhauser effect (rNOE), that is, rNOE(-1.6). The formation of rNOE(-1.6) involving the cholesterol hydroxyl is shown in liposome models. We aimed to confirm the correlation between cholesterol content and rNOE(-1.6) in cell cultures, tissues, and animals. C57BL/6 mice (N = 9) bearing the C6 glioma tumor were imaged in a 7 T MRI scanner, and their rNOE(-1.6) images were cross-validated through cholesterol staining with filipin. Cholesterol quantification was obtained using an 18.8-T NMR spectrometer from the lipid extracts of the brain tissues from another group of mice (N = 3). The cholesterol content in the cultured cells was manipulated using methyl-ß-cyclodextrin and a complex of cholesterol and methyl-ß-cyclodextrin. The rNOE(-1.6) of the cell homogenates and their cholesterol levels were measured using a 9.4-T NMR spectrometer. The rNOE(-1.6) signal is hypointense in the C6 tumors of mice, which matches the filipin staining results, suggesting that their tumor region is cholesterol deficient. The tissue extracts also indicate less cholesterol and phosphatidylcholine contents in tumors than in normal brain tissues. The amplitude of rNOE(-1.6) is positively correlated with the cholesterol concentration in the cholesterol-manipulated cell cultures. Our results indicate that the cholesterol dependence of rNOE(-1.6) occurs in cell cultures and solid tumors of C6 glioma. Furthermore, when the concentration of phosphatidylcholine is carefully considered, rNOE(-1.6) can be developed as a cholesterol-weighted imaging technique.

A Gadolinium DO3A Amide m-Phenyl Boronic Acid MRI Probe for Targeted Imaging of Sialated Solid Tumors.

We developed a new probe, Gd-DO3A-Am-PBA, for imaging tumors. Our results showed active targeting of Gd-DO3A-Am-PBA to sialic acid (SA) moieties, with increased cellular labeling in vitro and enhanced tumor accumulation and retention in vivo, compared to the commercial Gadovist. The effectiveness of our newly synthesized probe lies in its adequate retention phase, which is expected to provide a suitable time window for tumor diagnosis and a faster renal clearance, which will reduce toxicity risks when translated to clinics. Hence, this study can be extended to other tumor types that express SA on their surface. Targeting and MR imaging of any type of tumors can also be achieved by conjugating the newly synthesized contrast agent with specific antibodies. This study thus opens new avenues for drug delivery and tumor diagnosis via imaging.

pH Mapping of Skeletal Muscle by Chemical Exchange Saturation Transfer (CEST) Imaging.

Magnetic resonance imaging (MRI) is extensively used in clinical and basic biomedical research. However, MRI detection of pH changes still poses a technical challenge. Chemical exchange saturation transfer (CEST) imaging is a possible solution to this problem. Using saturation transfer, alterations in the exchange rates between the solute and water protons because of small pH changes can be detected with greater sensitivity. In this study, we examined a fatigued skeletal muscle model in electrically stimulated mice. The measured CEST signal ratio was between 1.96 ppm and 2.6 ppm in the z-spectrum, and this was associated with pH values based on the ratio between the creatine (Cr) and the phosphocreatine (PCr). The CEST results demonstrated a significant contrast change at the electrical stimulation site. Moreover, the pH value was observed to decrease from 7.23 to 7.15 within 20 h after electrical stimulation. This pH decrease was verified by 31P magnetic resonance spectroscopy and behavioral tests, which showed a consistent variation over time.

The Nearest-Neighbor Effect on Random-Coil NMR Chemical Shifts Demonstrated Using a Low-Complexity Amino-Acid Sequence.

In NMR experiments, the chemical shift is typically the first parameter measured and is a source of structural information for biomolecules. Indeed, secondary chemical shifts, the difference between the measured chemical shifts and those expected for a randomly oriented sequence of peptides (the "random coil"), are correlated with the secondary structure of proteins; secondary shift analysis is thereby a standard approach in structural biology. For intrinsically disordered or denatured proteins furthermore, secondary chemical shifts reveal the propensity of particular segments to form different secondary structures. However, because the atoms in unfolded proteins all have very similar chemical environments, the chemical shifts measured for a certain atom type vary less than in globular proteins. Since chemical shifts can be measured precisely, the secondary chemical shifts calculated for an unfolded system depend mainly on the particular random coil chemical shift database chosen as a point of reference. Certain databases correct the random coil shift for a given residue based on its neighbors in the amino acid sequence. However, these corrections are typically derived from the analysis of model peptides; there have been relatively few direct and systematic studies of the effect of neighboring residues for specific amino acid sequences in disordered proteins. For the study reported here, we used the intrinsically disordered C-terminal domain of TDP-43, which has a highly repetitive amino-acid sequence, as a model system. We assigned the chemical shifts of this protein at low pH in urea. Our results demonstrate that the identity of the nearest neighbors is decisive in determining the value of the chemical shift for atoms in a random coil arrangement. Based on these observations, we also outline a possible approach to construct a random-coil library of chemical shifts that comprises all possible arrangement of tripeptides from a manageable number of polypeptides.

Synthesis, structure and oxygen-sensing properties of iridium(III)-containing coordination polymers with different cations.

Four iridium(III)-containing coordination polymers 1-4 using Ir(ppy)(2)(H(2)dcbpy)PF(6) (L-H(2), ppy = 2-phenylpyridine, H(2)dcbpy = 4,4'-dicarboxy-2,2'-bipyridine) as the bridging ligand, [ZnL(2)]·3DMF·5H(2)O (1), [CdL(2)(H(2)O)(2)]·3DMF·6H(2)O (2), [CoL(2)(H(2)O)(2)]·2DMF·8H(2)O (3) and [NiL(2)(H(2)O)(2)]·3DMF·6H(2)O (4), have been synthesized and structurally characterized. The emissions from 1-4 are ascribed to a metal-to-ligand charge transfer transition (MLCT). The absolute emission quantum yields for 1-4 in single crystals were measured in air to be 0.274, 0.193, 0.001 and 0.002, respectively. The noteworthy oxygen-sensing properties of 1-4 as well as L-H(2) in a single crystal were also evaluated. The Stern-Volmer quenching constant, K(SV) values, of 1-4 and L-H(2) can be deduced to be 0.834, 2.820, 1.328, 1.111 and 2.476, respectively. The results show promising K(SV) values (e.g.2) that are competitive or even larger than those of many known Ir-complexes. Moreover, the short response time (e.g. compound 2) and recovery times toward oxygen of 1-4 have been measured in their single crystal forms. The reversibility experiments for 1-4 were carried out for seven repeated cycles. As a result, >75% recovery of intensity for 1 and 2 on each cycle demonstrates a high degree of reproducibility during the sensing process. It should be noted that iridium(III)-containing coordination polymers with high emission intensity and notable oxygen sensing properties are obscure, especially in the single crystal form. This, in combination with its fine reversibility, leads to success in single crystal oxygen recognition based on photoluminescence imaging. The detection limit could be 0.50% for gaseous oxygen. Moreover, the temperature effect of compound 2 in a single crystal upon application as an oxygen sensor was expected.