Paramagnetic spherical nanoparticles by the self-assembly of persistent trityl radicals

Spherical nanoparticles and fibres observable by cryo-electron microscopy are spontaneously formed by the Finland trityl radical at concentrations above 15 mM. These species represent a new class of paramagnetic, metal-free, nanoscale supramolecular materials. Self-association was observed under a variety of experimental conditions, including aqueous solution at room temperature, low temperature frozen glasses and the gas phase. Oligomers formed by at least 5 Finland radicals were detected by ion-mobility mass spectrometry. Magnetic susceptibility data as well as low temperature EPR spectra show coupling between electronic spins in the self-assembled species. Quantum chemical calculations show stacking along the C3 symmetry axis. Nanoparticle formation requires additional lateral packing that can be provided by bydrogen bonding involving the triangular array of carboxylic acid groups leading to the assembly of geodesic spheres

Direct evidence of the presence of cross-linked Aβ dimers in the brains of Alzheimer's disease patients

Brain-derived amyloid-β (Aβ) dimers are associated with Alzheimer´s disease (AD). However, their covalent nature remains controversial. This feature is relevant, as a covalent cross-link would make brain-derived dimers (brain dimers) more synaptotoxic than Aβ monomers and would make them suitable candidates for biomarker development. To resolve this controversy, we here present a three-step approach. First, we validated a type of synthetic cross-linked Aβ (CL Aβ) dimers, obtained by means of the photo-induced cross-linking of unmodified proteins (PICUP) reaction, as well-defined mimics of putative brain CL Aβ dimers. Second, we used these PICUP CL Aβ dimers as standards to improve the isolation of brain Aβ dimers and to develop state-of-the-art mass spectrometry (MS) strategies to allow their characterization. Third, we applied these MS methods to the analysis of brain Aβ dimer samples allowing the detection of the CL [Aβ(6-16)]2 peptide comprising a dityrosine cross-link. This result demonstrates the presence of CL Aβ dimers in the brains of patients with AD and opens up avenues for establishing new therapeutic targets and developing novel biomarkers for this disease

Self-assembled trityl radical capsules implications for dynamic nuclear polarization

A new class of guest-induced, bi-radical self-assembled organic capsules is reported. They are formed by the inclusion of a tetramethylammonium (TMA) cation between two monomers of the stable trityl radical OX63. OX63 is extensively used in dissolution dynamic nuclear polarization (DNP) where it leads to NMR sensitivity enhancements of several orders of magnitude. The supramolecular properties of OX63 have a strong impact on its DNP properties. An especially relevant case is the polarization of choline-containing metabolites, where complex formation between choline and OX63 results in faster relaxation

Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase

Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confers IMMS great potential for the study of proteins in slow (μs-ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP)-a model of a large dynamic enzyme in the μs-ms range-by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas-phase collapsed form of POP was also detected. Therefore, our findings support the potential of IMMS for the study of multiple co-existing conformations of large proteins in slow dynamic equilibrium in solution, but also stress the need for careful data analysis to avoid artefacts

Multi-phosphorylation of the intrinsically disordered unique domain of c-Src studied by in-cell and real-time NMR

Intrinsically disordered regions (IDRs) are preferred sites for post-translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase-phosphatase networks. Here we used real-time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the 'unique domain' of c-Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin-dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP-dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK-dependent sites, thus suggesting indirect effects of kinase-phosphatase networks. This study provides a proof-of-concept of the use of real-time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains

The human mitochondrial transcription factor A is a versatile G-quadruplex binding protein

The ability of the guanine-rich strand of the human mitochondrial DNA (mtDNA) to form G-quadruplex structures (G4s) has been recently highlighted, suggesting potential functions in mtDNA replication initiation and mtDNA stability. G4 structures in mtDNA raise the question of their recognition by factors associated with the mitochondrial nucleoid. The mitochondrial transcription factor A (TFAM), a highmobility group (HMG)-box protein, is the major binding protein of human mtDNA and plays a critical role in its expression and maintenance. HMG-box proteins are pleiotropic sensors of DNA structural alterations. Thus, we investigated and uncovered a surprising ability of TFAM to bind to DNA or RNA G4 with great versatility, showing an affinity similar than to double-stranded DNA. The recognition of G4s by endogenous TFAM was detected in mitochondrial extracts by pull-down experiments using a G4-DNA from the mtDNA conserved sequence block II (CSBII). Biochemical characterization shows that TFAM binding to G4 depends on both the G-quartets core and flanking single-stranded overhangs. Additionally, it shows a structure-specific binding mode that differs from B-DNA, including G4- dependent TFAM multimerization. These TFAM-G4 interactions suggest functional recognition of G4s in the mitochondria

An oxygen-sensitive toxin-antitoxin system

The Hha and TomB proteins from Escherichia coli form an oxygen-dependent toxin-antitoxin (TA) system. Here we show that YmoB, the Yersinia orthologue of TomB, and its single cysteine variant [C117S]YmoB can replace TomB as antitoxins in E. coli. In contrast to other TA systems, [C117S]YmoB transiently interacts with Hha (rather than forming a stable complex) and enhances the spontaneous oxidation of the Hha conserved cysteine residue to a -SOxH- containing species (sulfenic, sulfinic or sulfonic acid), which destabilizes the toxin. The nuclear magnetic resonance structure of [C117S]YmoB and the homology model of TomB show that the two proteins form a four-helix bundle with a conserved buried cysteine connected to the exterior by a channel with a diameter comparable to that of an oxygen molecule. The Hha interaction site is located on the opposite side of the helix bundle

Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase

Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confers IMMS great potential for the study of proteins in slow (μs-ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP)-a model of a large dynamic enzyme in the μs-ms range-by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas-phase collapsed form of POP was also detected. Therefore, our findings support the potential of IMMS for the study of multiple co-existing conformations of large proteins in slow dynamic equilibrium in solution, but also stress the need for careful data analysis to avoid artefacts

Paramagnetic spherical nanoparticles by the self-assembly of persistent trityl radicals

Spherical nanoparticles and fibres observable by cryo-electron microscopy are spontaneously formed by the Finland trityl radical at concentrations above 15 mM. These species represent a new class of paramagnetic, metal-free, nanoscale supramolecular materials. Self-association was observed under a variety of experimental conditions, including aqueous solution at room temperature, low temperature frozen glasses and the gas phase. Oligomers formed by at least 5 Finland radicals were detected by ion-mobility mass spectrometry. Magnetic susceptibility data as well as low temperature EPR spectra show coupling between electronic spins in the self-assembled species. Quantum chemical calculations show stacking along the C3 symmetry axis. Nanoparticle formation requires additional lateral packing that can be provided by bydrogen bonding involving the triangular array of carboxylic acid groups leading to the assembly of geodesic spheres

Direct evidence of the presence of cross-linked Aβ dimers in the brains of Alzheimer's disease patients

Brain-derived amyloid-β (Aβ) dimers are associated with Alzheimer´s disease (AD). However, their covalent nature remains controversial. This feature is relevant, as a covalent cross-link would make brain-derived dimers (brain dimers) more synaptotoxic than Aβ monomers and would make them suitable candidates for biomarker development. To resolve this controversy, we here present a three-step approach. First, we validated a type of synthetic cross-linked Aβ (CL Aβ) dimers, obtained by means of the photo-induced cross-linking of unmodified proteins (PICUP) reaction, as well-defined mimics of putative brain CL Aβ dimers. Second, we used these PICUP CL Aβ dimers as standards to improve the isolation of brain Aβ dimers and to develop state-of-the-art mass spectrometry (MS) strategies to allow their characterization. Third, we applied these MS methods to the analysis of brain Aβ dimer samples allowing the detection of the CL [Aβ(6-16)]2 peptide comprising a dityrosine cross-link. This result demonstrates the presence of CL Aβ dimers in the brains of patients with AD and opens up avenues for establishing new therapeutic targets and developing novel biomarkers for this disease