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Inositol poly- and pyrophosphates (InsPs and PP-InsPs) are densely phosphorylated eukaryotic messengers, which are involved in numerous cellular processes. To elucidate their signaling functions at the molecular level, non-hydrolyzable bisphosphonate analogs of inositol pyrophosphates, PCP-InsPs, have been instrumental. Here, an efficient synthetic strategy to obtain these analogs in unprecedented quantities is described – relying on the use of combined phosphate ester-phosphoramidite reagents. The PCP-analogs, alongside their natural counterparts, were applied to investigate their regulatory effect on insulin-degrading enzyme (IDE), using a range of biochemical, biophysical and computational methods. A unique interplay between IDE, its substrates and the PP-InsPs was uncovered, in which the PP-InsPs differentially modulated the activity of the enzyme towards short peptide substrates. Aided by molecular docking and molecular dynamics simulations, a flexible binding mode for the InsPs/PP-InsPs was identified at the anion binding site of IDE. Targeting IDE for therapeutic purposes should thus take regulation by endogenous PP-InsP metabolites into account., An efficient synthesis of non-hydrolyzable inositol pyrophosphate analogs was developed to subsequently investigate the regulation of insulin-degrading enzyme by these hyperphosphorylated signaling molecules.

Regulation of enzymatic 5' decapping of messenger RNA (mRNA), which normally commits transcripts to their destruction, has the capacity to dynamically reshape the transcriptome. For example, protection from 5' decapping promotes accumulation of mRNAs into processing (P) bodies-membraneless, biomolecular condensates. Such compartmentalization of mRNAs temporarily removes them from the translatable pool; these repressed transcripts are stabilized and stored until P-body dissolution permits transcript reentry into the cytosol. Here, we describe regulation of mRNA stability and P-body dynamics by the inositol pyrophosphate signaling molecule 5-InsP7 (5-diphosphoinositol pentakisphosphate). First, we demonstrate 5-InsP7 inhibits decapping by recombinant NUDT3 (Nudix [nucleoside diphosphate linked moiety X]-type hydrolase 3) in vitro. Next, in intact HEK293 and HCT116 cells, we monitored the stability of a cadre of NUDT3 mRNA substrates following CRISPR-Cas9 knockout of PPIP5Ks (diphosphoinositol pentakisphosphate 5-kinases type 1 and 2, i.e., PPIP5K KO), which elevates cellular 5-InsP7 levels by two- to threefold (i.e., within the physiological rheostatic range). The PPIP5K KO cells exhibited elevated levels of NUDT3 mRNA substrates and increased P-body abundance. Pharmacological and genetic attenuation of 5-InsP7 synthesis in the KO background reverted both NUDT3 mRNA substrate levels and P-body counts to those of wild-type cells. Furthermore, liposomal delivery of a metabolically resistant 5-InsP7 analog into wild-type cells elevated levels of NUDT3 mRNA substrates and raised P-body abundance. In the context that cellular 5-InsP7 levels normally fluctuate in response to changes in the bioenergetic environment, regulation of mRNA structure by this inositol pyrophosphate represents an epitranscriptomic control process. The associated impact on P-body dynamics has relevance to regulation of stem cell differentiation, stress responses, and, potentially, amelioration of neurodegenerative diseases and aging.

Homeostasis of cellular fluxes of inorganic phosphate (Pi) supervises its structural roles in bones and teeth, its pervasive regulation of cellular metabolism, and its functionalization of numerous organic compounds. Cellular Pi efflux is heavily reliant on Xenotropic and Polytropic Retrovirus Receptor 1 (XPR1), regulation of which is largely unknown. We demonstrate specificity of XPR1 regulation by a comparatively uncharacterized member of the inositol pyrophosphate (PP-InsP) signaling family: 1,5-bis-diphosphoinositol 2,3,4,6-tetrakisphosphate (InsP(8)). XPR1-mediated Pi efflux was inhibited by reducing cellular InsP(8) synthesis, either genetically (knockout [KO] of diphosphoinositol pentakisphosphate kinases [PPIP5Ks] that synthesize InsP(8)) or pharmacologically [cell treatment with 2.5 µM dietary flavonoid or 10 µM N2-(m-trifluorobenzyl), N6-(p-nitrobenzyl) purine], to inhibit inositol hexakisphosphate kinases upstream of PPIP5Ks. Attenuated Pi efflux from PPIP5K KO cells was quantitatively phenocopied by KO of XPR1 itself. Moreover, Pi efflux from PPIP5K KO cells was rescued by restoration of InsP(8) levels through transfection of wild-type PPIP5K1; transfection of kinase-dead PPIP5K1 was ineffective. Pi efflux was also rescued in a dose-dependent manner by liposomal delivery of a metabolically resistant methylene bisphosphonate (PCP) analog of InsP(8); PCP analogs of other PP-InsP signaling molecules were ineffective. High-affinity binding of InsP(8) to the XPR1 N-terminus (K(d) = 180 nM) was demonstrated by isothermal titration calorimetry. To derive a cellular biology perspective, we studied biomineralization in the Soas-2 osteosarcoma cell line. KO of PPIP5Ks or XPR1 strongly reduced Pi efflux and accelerated differentiation to the mineralization end point. We propose that catalytically compromising PPIP5K mutations might extend an epistatic repertoire for XPR1 dysregulation, with pathological consequences for bone maintenance and ectopic calcification.

Determining the affinity of proteins for uranyl is key to understand the toxicity of this cation and to further develop decorporation strategies. However, usual techniques to achieve that goal often require specific equipment and expertise. Here, we propose a simple, efficient, fluorescence-based method to assess the affinity of proteins and peptides for uranyl, at equilibrium and in buffered solution. We first designed and characterized an original uranyl-binding fluorescent probe. We then built a reference scale for uranyl affinity in solution, relying on signal quenching of our fluorescent probe in presence of high-affinity uranyl-binding peptides. We finally validated our approach by re-evaluating the uranyl-binding affinity of four native proteins. We envision that this tool will facilitate the reliable and reproducible assessment of affinities of peptides and proteins for uranyl.

Nudix hydrolases attract considerable attention for their wide range of specialized activities in all domains of life. One particular group of Nudix phosphohydrolases (DIPPs), through their metabolism of diphosphoinositol polyphosphates (PP-InsPs), regulates the actions of these polyphosphates upon bioenergetic homeostasis. In the current study we describe, at an atomic level, hitherto unknown properties of human DIPP1.We provide X-ray analysis of the catalytic core of DIPP1 in crystals complexed with either natural PP-InsPs, alternative PP-InsP stereoisomers, or non-hydrolysable methylene bisphosphonate analogues (“PCP-InsPs”). The conclusions that we draw from these data are interrogated by studying the impact upon catalytic activity upon mutagenesis of certain key residues. We present a picture of a V-shaped catalytic furrow with overhanging ridges constructed from flexible positively-charged side chains; within this cavity, the labile phosphoanhydride bond is appropriately positioned at the catalytic site by an extensive series of interlocking polar contacts which we analogize as ‘suspension cables’. We demonstrate functionality for a triglycine peptide within a β-strand which represents a non-canonical addition to the standard Nudix catalytic core structure. We describe pre-reaction enzyme/substrate states which we posit to reflect a role for electrostatic steering in substrate capture. Finally, through time-resolved analysis we uncover a chronological sequence of DIPP1/product post-reaction states, one of which may rationalize a role for InsP(6) as an inhibitor of catalytic activity.

Regulation of enzymatic 5′ decapping of messenger RNA (mRNA), which normally commits transcripts to their destruction, has the capacity to dynamically reshape the transcriptome. For example, protection from 5′ decapping promotes accumulation of mRNAs into processing (P) bodies—membraneless, biomolecular condensates. Such compartmentalization of mRNAs temporarily removes them from the translatable pool; these repressed transcripts are stabilized and stored until P-body dissolution permits transcript reentry into the cytosol. Here, we describe regulation of mRNA stability and P-body dynamics by the inositol pyrophosphate signaling molecule 5-InsP(7) (5-diphosphoinositol pentakisphosphate). First, we demonstrate 5-InsP(7) inhibits decapping by recombinant NUDT3 (Nudix [nucleoside diphosphate linked moiety X]-type hydrolase 3) in vitro. Next, in intact HEK293 and HCT116 cells, we monitored the stability of a cadre of NUDT3 mRNA substrates following CRISPR-Cas9 knockout of PPIP5Ks (diphosphoinositol pentakisphosphate 5-kinases type 1 and 2, i.e., PPIP5K KO), which elevates cellular 5-InsP(7) levels by two- to threefold (i.e., within the physiological rheostatic range). The PPIP5K KO cells exhibited elevated levels of NUDT3 mRNA substrates and increased P-body abundance. Pharmacological and genetic attenuation of 5-InsP(7) synthesis in the KO background reverted both NUDT3 mRNA substrate levels and P-body counts to those of wild-type cells. Furthermore, liposomal delivery of a metabolically resistant 5-InsP(7) analog into wild-type cells elevated levels of NUDT3 mRNA substrates and raised P-body abundance. In the context that cellular 5-InsP(7) levels normally fluctuate in response to changes in the bioenergetic environment, regulation of mRNA structure by this inositol pyrophosphate represents an epitranscriptomic control process. The associated impact on P-body dynamics has relevance to regulation of stem cell differentiation, stress responses, and, potentially, amelioration of neurodegenerative diseases and aging.

The inositol pyrophosphates (PP-InsPs) are a ubiquitous group of highly phosphorylated eukaryotic messengers. They have been linked to a panoply of central cellular processes, but a detailed understanding of the discrete signaling events is lacking in most cases. To create a more mechanistic picture of PP-InsP signaling, we sought to annotate the mammalian interactome of the most abundant inositol pyrophosphate 5PP-InsP5. To do so, triplexed affinity reagents were developed, in which a metabolically stable PP-InsP analog was immobilized in three different ways. Application of these triplexed reagents to mammalian lysates identified between 300 and 400 putative interacting proteins. These interactomes revealed connections between 5PP-InsP5 and central cellular regulators, such as lipid phosphatases, protein kinases, and GTPases, and identified protein domains commonly targeted by 5PP-InsP5. Both the triplexed affinity reagents, and the proteomic datasets, constitute powerful resources for the community, to launch future investigations into the multiple signaling modalities of inositol pyrophosphates.

International audience; The spectroscopic properties of two luminescent Re(I) tricarbonyl complexes conjugated with two cell-penetrating peptides were examined. Fluorescence experiments and IR quantification in membrane models and in cells showed unexpectedly strong luminescence enhancement for one of the complexes in a lipid environment.

This study evaluates the penetration of bicosome systems incorporating two different antioxidants into normal skin and skin exposed to ultraviolet-visible radiation (UV-VIS) by Fourier-transform infrared microspectroscopy (FT-IR) using synchrotron radiation. Bicosomes are phospholipid assemblies based on mixtures of discoidal lipid structures protected by spherical lipid vesicles able to incorporate different molecules. In the current work, the antioxidants incorporated in these systems were β-carotene and a Mn complex as a superoxide dismutase (SOD) mimic. Additionally, a rhenium tri-carbonyl derivative was incorporated in the bicosome systems in order to map their penetration following the tag specific carbonyl signal by FT-IR microspectroscopy. The characterization of bicosome systems using the dynamic light scattering technique (DLS) showed a modification in the size of the systems containing β-carotene (Bcβ) or MnII complex (BcMn). After skin permeation, FT-IR results indicated a higher and deeper penetration of the BcMn system than the Bcβ system into the skin. Likely, the different physicochemical properties of both antioxidants could be responsible for this effect. Moreover, the penetration of both bicosome systems in irradiated skin was lower in comparison with the normal skin. This fact could be a consequence of the alteration of water transport in the skin during the irradiation process. In conclusion, these results indicated the effectiveness of bicosome systems as skin carriers, and provide information to protect skin under radiation using antioxidants.

Here we report on the use of a silanol-decorated polyoxotungstate, [SbW9O33(tBuSiOH)3]3\textendash (1), as a molecular support to describe the coordination of a vanadium atom at a single-site on silica surfaces. By reacting [V(Mes)3·thf] (Mes = 2,4,6-trimethylphenyl) with 1 in tetrahydrofuran, the vanadium(III) derivative [SbW9O33(tBuSiO)3V(thf)]3\textendash (2) was obtained. Compound 2 displays the paramagnetic behavior expected for a d2-VIII high spin complex (SQUID measurements) with a triplet electronic ground state (ca. 30 kcal·mol\textendash 1 more stable than the singlet, from DFT calculations). Compound 2 proves to be a reliable model for reduced isolated-vanadium atom dispersed on silica surfaces [(\equivSi\textemdash O)3VIII(OH2)], an intermediate that is often proposed in a Mars\textendash van Krevelen type mechanism for partial oxidation of light alcohols. Oxidation of 2 under air produced the oxo-derivative [SbW9O33(tBuSiO)3VO]3\textendash (3). In compound 2, the d2-electrons are localized in degenerated d(V) orbitals, whereas in the electronically analogous bireduced-[SbW9O33(tBuSiO)3VO]5\textendash, 3·(2e), one electron is localized on d(V) orbital and the second one is delocalized on the polyoxotungstic framework, leading to a unique case of a bireduced heteropolyanion derivative with completely decoupled d1-V(IV) and d1-W(V). Our body of experimental results (EPR, magnetic measurements, spectroelectrochemical studies, Raman spectroscopy) and theoretical studies highlights (i) the role of the apical ligand coordination, i.e., thf (σ-donor) vs oxo (π-donor), in destabilizing or stabilizing the d(V) orbitals relative to the d(W) orbitals, and (ii) a geometrical distortion of the O3VO entity that causes a splitting of the degenerated orbitals and the stabilization of one d(V) orbital in the bireduced compound 3·(2e).

International audience; Bio-imaging techniques alternative to fluorescence microscopy are gaining increasing interest as complementary tools to visualize and analyze biological systems. Among them, X-ray fluorescence microspectroscopy provides information on the local content and distribution of heavy elements (Z $ 14) in cells or biological samples. In this context, similar tools to those developed for fluorescence microscopy are desired, including chemical probes or tags. In this work, we study rhenium complexes as a convenient and sensitive probe for X-ray fluorescence microspectroscopy. We demonstrate their ability to label and sense exogenously incubated or endogenous proteins inside cells. Bio-imaging enables the direct visualization of labeled biomolecules of interest, offering valuable insights into biological processes. Fluorescence microscopy is widely used and offers numerous advantages, including good spatial resolution ($10 2 Â 10 2 nm 2) and availability of numerous probes and tags with high quantum yield and diverse spectroscopic properties. However, uorescence techniques suffer from some drawbacks such as photobleaching. Quantum yields are dependent on the environment, with large variations upon polarity or possible quenching at high concentrations. 1-4 For that reason, absolute quantication using classical uorescence can be tricky. Complementary methods for bio-imaging are now emerging. Microspectroscopies that provide simultaneous information on the local cellular environment can be of particular interest. Recently, vibrational techniques such as infrared microspectros-copies have become more popular, providing spatially resolved chemical information. 5-7 Synchrotron-based X-ray uorescence (SXRF) and absorbance microspectroscopies have also been used for the detection of metal centers in biological samples. 8 Using synchrotron based X-uorescence microspectroscopy (SXRF-MS), the simultaneous collection of data for a large range of elements is carried out, provided their edge energy is lower than the incident energy. Metal-based probes can be imaged using this technique and information on their elemental environment is also immediately available. Moreover, the spatial resolution of this technique is in the 10 nm to 1 mm range, which is relevant for sub-cellular imaging. Finally, XRF is a quantitative technique: 2D-quantication is possible using commercially available standards. Accessibility to new probes for this emerging technique would bolster its use for further investigation of biological mechanisms. Studies have been performed in this direction with the development of particles, quantum dots, polymers containing lanthanide and carbon nanotubes. 9-13 However no graable molecular tag suitable for protein imaging by XRF has been designed so far. Policar's group is strongly interested in the development and use of Re(I) tricarbonyl complexes as multi-modal probes for uorescence microscopy and infrared micro-spectroscopy. 14,15 They display good biocompatibility and stability features, as well as unique spectroscopic properties, and they have been widely used for imaging using a single modality-mainly luminescence 16,17 or as efficient bimodal probes in the mid-IR range and luminescence. 18-27 In the present work, we have investigated the potential of these SCoMPIs (Single Core Multimodal Probes for Imaging) for a new modality, namely X-ray uorescence. The rhenium center displays two intense signals at 8.6 and 10.28 keV, corresponding to its L-bands. Re has a very low natural abundance, 28 which would ease the detection of the SCoMPI-labeled molecule with a high signal-to-noise ratio. Very recently, Massi and Harris have shown that Re complexes can be mapped at the single cell level by XRF. 29 However, X-ray uorescence molecular tags or probes that can be graed onto target biomolecules and that do not modify to a large extent their physico-chemical properties are still needed.

International audience; Hyaluronic acids were labeled with a rhenium-tricarbonyl used as single core multimodal probe for imaging and their penetration into human skin biopsies was studied using IR microscopy and fluorescence imaging (labeled SCoMPI). The penetration was shown to be dependent on the molecular weight of the molecule and limited to the upper layer of the skin.

International audience; Bio-imaging, by enabling the visualization of biomolecules of interest, has proved to be highly informative in the study of biological processes. Although fluorescence microscopy is probably one of the most used techniques, alternative methods of imaging, providing complementary information, are emerging. In this context, metal complexes represent valuable platforms for multimodal imaging, since they may combine interesting spectroscopic features and biologically relevant functionalization on a single molecular core. In particular, d6 low-spin rhenium tri-carbonyl complexes display unique luminescence and vibrational properties, and can be readily functionalized. Here we review their applications and potential as probes or drugs relying on their photophysical properties, before focusing on their use as multimodal probes for the labelling and imaging of peptides and proteins.

A joint experimental and molecular simulation study was performed to investigate the adsorption of tetrachloroethene on two MFI zeolites, ZSM-5 with a Si/Al ratio of 26.5, and silicalite-1, which is the pure silica form of ZSM-5. Adsorption isotherms and isosteric heats of adsorption of tetrachloroethene were measured and compared to molecular simulation results. Experimental curves for both MFI zeolites show a step at loading of 4 molecules·uc−1 that was interpreted in terms of a structural change of the host framework. A thermodynamic analysis based on the osmotic ensemble scheme allowed attributing this step to a symmetry change from ORTHO (orthorhombic form with Pnma symmetry) to PARA (orthorhombic form with P212121 symmetry) of both adsorbents upon micropore filling. The adsorption mechanism was also characterized. The first tetrachloroethene molecules adsorbs in the channel intersections of the MONO (monoclinic form with P21/n11 symmetry) and ORTHO structures of silicalite-1 and ZSM-5, respectively....

A heteroditopic ligand H(2)-L consisting of a dihydroxybenzene (catechol)-unit linked via an amide bond to a pyridyl-unit and its methyl-protected precursor Me(2)-L were synthesized, characterized, and their photophysical properties investigated. The three accessible protonation states of the ligand, H(3)-L(+), H(2)-L, and H-L(-), showed distinct (1)H NMR, absorption and emission spectroscopic characteristics that allow pH-sensing. The spectroscopic signatures obtained act as a guide to understand the signaling mechanism of the luminescent pH and molybdate sensor [Re(bpy)(CO)(3)(H(2)-L)](+). It was found that upon deprotonation of the 2-hydroxy group of H(2)-L, a ligand-based absorption band emerges that overlaps with the Re(dπ)→bpy metal-to-ligand charge transfer (MLCT) band of the sensor, reducing the quantum yield for emission on excitation in the 370 nm region. In addition, deprotonation of the catechol-unit leads to quenching of the emission from the Re(dπ)→bpy (3)MLCT state, consistent with photoinduced electron transfer from the electron-rich, deprotonated catecholate to the Re-based luminophore. Finally, reaction of 2 equiv of [Re(bpy)(CO)(3)(H(2)-L)](+) with molybdate was shown to give the zwitterionic Mo(VI) complex [MoO(2){Re(CO)(3)(bpy)(L)}(2)], as confirmed by electrospray ionization (ESI) mass spectrometry and X-ray crystallography. The crystal structure determination revealed that two fully deprotonated sensor molecules are bound via their oxygen-donors to a cis-dioxo-MoO(2) center.

International audience; A rhenium tris-carbonyl derivative (fac-[Re(CO)(3)Cl(2-(1-dodecyl-1H-1,2,3,triazol-4-yl)-pyridine)]) was incorporated into phospholipid assemblies, called bicosomes, and the penetration of this molecule into skin was monitored using Fourier-transform infrared microspectroscopy (FTIR). To evaluate the capacity of bicosomes to promote the penetration of this derivative, the skin penetration of the Re(CO)(3) derivative dissolved in dimethyl sulfoxide (DMSO), a typical enhancer, was also studied. Dynamic light scattering results (DLS) showed an increase in the size of the bicosomes with the incorporation of the Re(CO)(3) derivative, and the FTIR microspectroscopy showed that the Re(CO)(3) derivative incorporated in bicosomes penetrated deeper into the skin than when dissolved in DMSO. When this molecule was applied on the skin using the bicosomes, 60% of the Re(CO)(3) derivative was retained in the stratum corneum (SC) and 40% reached the epidermis (Epi). Otherwise, the application of this molecule via DMSO resulted in 95% of the Re(CO)(3) derivative being in the SC and only 5% reaching the Epi. Using a Re(CO)(3) derivative with a dodecyl-chain as a model molecule, it was possible to determine the distribution of molecules with similar physicochemical characteristics in the skin using bicosomes. This fact makes these nanostructures promising vehicles for the application of lipophilic molecules inside the skin.

Living systems offer attractive strategies to generate nanoscale structures because of their innate functional properties such as the dynamic assembly of ordered nanometer fibers, the generation of mechanical forces, or the directional transport mediated by molecular motors. The design of hybrid systems, capable of interfacing artificial building blocks with biomolecules, may be a key step toward the rational design of nanoscale devices and materials. Here, we have designed a bottom-up approach to organize cytoskeletal elements in space using the self-assembly properties of magnetic nanoparticles conjugated to signaling proteins involved in microtubule nucleation. We show that magnetic nanoparticles conjugated to signaling proteins involved in microtubule nucleation can control the positioning of microtubule assembly. Under a magnetic field, a self-organized pattern of biofunctionalized nanoparticles is formed and leads to the nucleation of a periodical network of microtubules in Xenopus laevis egg extract. Our method shows how bioactive nanoparticles can generate a biochemically active pattern upon magnetic actuation, which triggers the spatial organization of nonequilibrium biological structures.

Intracellular biochemical reactions are often localized in space and time, inducing gradients of enzymatic activity that may play decisive roles in determining cell's fate and functions. However, the techniques available to examine such enzymatic gradients of activity remain limited. Here, we propose a new method to engineer a spatial gradient of signaling protein concentration within Xenopus egg extracts using superparamagnetic nanoparticles. We show that, upon the application of a magnetic field, a concentration gradient of nanoparticles with a tunable length extension is established within confined egg extracts. We then conjugate the nanoparticles to RanGTP, a small G-protein controlling microtubule assembly. We found that the generation of an artificial gradient of Ran-nanoparticles modifies the spatial positioning of microtubule assemblies. Furthermore, the spatial control of the level of Ran concentration allows us to correlate the local fold increase in Ran-nanoparticle concentration with the spatial positioning of the microtubule-asters. Our assay provides a bottom-up approach to examine the minimum ingredients generating polarization and symmetry breaking within cells. More generally, these results show how magnetic nanoparticles and magnetogenetic tools can be used to control the spatiotemporal dynamics of signaling pathways.