One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics.

The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin. As the interaction process is dynamic, the acquired NMR data only reflect the time average of the different steps. We have used molecular dynamics (MD) simulations to get a deeper insight into the detailed interaction scenario at the microsecond scale. This NMR/MD approach enabled us to establish that the tris-dipicolinate complex interacts specifically with arginines and lysines, while the crystallophore explores the protein surface through weak interactions with carboxylates. These observations shed new light on the dynamic interaction properties of these complexes, which will ultimately enable us to propose a crystallization mechanism.

The absence of surface D-alanylation, localized on lipoteichoic acid, impacts the Clostridioides difficile way of life and antibiotic resistance.

Introduction: The dlt operon encodes proteins responsible for the esterification of positively charged D-alanine on the wall teichoic acids and lipoteichoic acids of Gram-positive bacteria. This structural modification of the bacterial anionic surface in several species has been described to alter the physicochemical properties of the cell-wall. In addition, it has been linked to reduced sensibilities to cationic antimicrobial peptides and antibiotics. Methods: We studied the D-alanylation of Clostridioides difficile polysaccharides with a complete deletion of the dltDABCoperon in the 630 strain. To look for D-alanylation location, surface polysaccharides were purified and analyzed by NMR. Properties of the dltDABCmutant and the parental strains, were determined for bacterial surface's hydrophobicity, motility, adhesion, antibiotic resistance. Results: We first confirmed the role of the dltDABCoperon in D-alanylation. Then, we established the exclusive esterification of D-alanine on C. difficile lipoteichoic acid. Our data also suggest that D-alanylation modifies the cell-wall's properties, affecting the bacterial surface's hydrophobicity, motility, adhesion to biotic and abiotic surfaces,and biofilm formation. In addition, our mutant exhibitedincreased sensibilities to antibiotics linked to the membrane, especially bacitracin. A specific inhibitor DLT-1 of DltA reduces the D-alanylation rate in C. difficile but the inhibition was not sufficient to decrease the antibiotic resistance against bacitracin and vancomycin. Conclusion: Our results suggest the D-alanylation of C. difficile as an interesting target to tackle C. difficile infections.

Polysaccharide II Surface Anchoring, the Achilles' Heel of Clostridioides difficile.

Cell wall glycopolymers (CWPGs) in Gram-positive bacteria have been reported to be involved in several bacterial processes. These polymers, pillars for proteins and S-layer, are essential for the bacterial surface setup, could be essential for growth, and, in pathogens, participate most often in virulence. CWGPs are covalently anchored to peptidoglycan by proteins that belong to the LytR-CpsA-PSr (LCP) family. This anchoring, important for growth, was reported as essential for some bacteria such as Bacillus subtilis, but the reason why CWGP anchoring is essential remains unknown. We studied LcpA and LcpB of Clostridioides difficile and showed that they have a redundant activity. To delete both lcp genes, we set up the first conditional-lethal mutant method in C. difficile and showed that polysaccharide II (PSII) anchoring at the bacterial surface is essential for C. difficile survival. In the conditional-lethal mutant, C. difficile morphology was impaired, suggesting that peptidoglycan synthesis was affected. Because Lcp proteins are transferring CWPGs from the C55-undecaprenyl phosphate (also needed in the peptidoglycan synthesis process), we assumed that there was competition between PSII and peptidoglycan synthesis pathways. We confirmed that UDP-MurNAc-pentapeptide precursor was accumulated, showing that peptidoglycan synthesis was blocked. Our results provide an explanation for the essentiality of PSII anchoring in C. difficile and suggest that the essentiality of the anchoring of CWPGs in other bacteria can also be explained by the blocking of peptidoglycan synthesis. To conclude, our results suggest that Lcps are potential new targets to combat C. difficile infection. IMPORTANCE Cell wall glycopolymers (CWGPs) in Gram-positive bacteria have been reported to be involved in several bacterial processes. CWGP anchoring to peptidoglycan is important for growth and virulence. We set up the first conditional-lethal mutant method in Clostridioides difficile to study LcpA and LcpB involved in the anchoring of CWPGs to peptidoglycan. This study offers new tools to reveal the role of essential genes in C. difficile. LcpA and LcpB activity was shown to be essential, suggesting that they are potential new targets to combat C. difficile infection. In this study, we also showed that there is competition between the polysaccharide II synthesis pathway and peptidoglycan synthesis that probably exists in other Gram-positive bacteria. A better understanding of these mechanisms allows us to define the Lcp proteins as a therapeutic target for potential design of novel antibiotics against pathogenic Gram-positive bacteria.

Correction: Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures.

Correction for 'Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures' by Marco Deiana et al., Nanoscale, 2021, 13, 13795-13808, https://doi.org/10.1039/D1NR02855C.

Ni-Centered Coordination-Induced Spin-State Switching Triggered by Electrical Stimulation.

We herein report the synthesis and magnetic properties of a Ni(II)-porphyrin tethered to an imidazole ligand through a flexible electron-responsive mechanical hinge. The latter is capable of undergoing a large amplitude and fully reversible folding motion under the effect of electrical stimulation. This redox-triggered movement is exploited to force the axial coordination of the appended imidazole ligand onto the square-planar Ni(II) center, resulting in a change in its spin state from low spin (S = 0) to high spin (S = 1) proceeding with an 80% switching efficiency. The driving force of this reversible folding motion is the π-dimerization between two electrogenerated viologen cation radicals. The folding motion and the associated spin state switching are demonstrated on the grounds of NMR, (spectro)electrochemical, and magnetic data supported by quantum calculations.

Assembly of Aggregation-Induced Emission Active Bola-Amphiphilic Macromolecules into Luminescent Nanoparticles Optimized for Two-Photon Microscopy In Vivo.

The (Z) and (E)-isomers of an extended tetraphenylethylene-based chromophore with optimized two-photon-induced luminescence properties are separated and functionalized with water-solubilizing pendant polymer groups, promoting their self-assembly in physiological media in the form of small, colloidal stable organic nanoparticles. The two resulting fluorescent suspensions are then evaluated as potential two-photon luminescent contrast agents for intravital epifluorescence and two-photon fluorescence microscopy. Comparisons with previously reported works involving similar fluorophores devoid of polymer side chains illustrate the benefits of later functionalization regarding the control of the self-assembly of the nano-objects and ultimately their biocompatibility toward the imaged organism.

Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures.

Light-activated functional materials capable of remote control over duplex and G-quadruplex (G4) nucleic acids formation at the cellular level are still very rare. Herein, we report on the photoinduced macrocyclisation of a helicenoid quinoline derivative of binaphthol that selectively provides easy access to an unprecedented class of extended heteroaromatic structures with remarkable photophysical and DNA/RNA binding properties. Thus, while the native bisquinoline precursor shows no DNA binding activity, the new in situ photochemically generated probe features high association constants to DNA and RNA G4s. The latter inhibits DNA synthesis by selectively stabilizing G4 structures associated with oncogenic promoters and telomere repeat units. Finally, the light sensitive compound is capable of in cellulo photoconversion, localizes primarily in the G4-rich sites of cancer cells, competes with a well-known G4 binder and shows a clear nuclear co-localization with the quadruplex specific antibody BG4. This work provides a benchmark for the future design and development of a brand-new generation of light-activated target-selective G4-binders.

Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration.

In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy. This study highlights the importance of a large conformational sampling to reconcile characteristic time in NMR with molecular dynamics simulations, where sampling in the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complex-peptide or lanthanide complex-protein interaction or self-assembly processes.

High-Performance Porous Ionic Liquids for Low-Pressure CO2 Capture*.

Porous ionic liquids are non-volatile, versatile materials that associate porosity and fluidity. New porous ionic liquids, based on the ZIF-8 metal-organic framework and on phosphonium acetate or levulinate salts, were prepared and show an increased capacity to absorb carbon dioxide at low pressures. Porous suspensions based on phosphonium levulinate ionic liquid absorb reversibly 103 % more carbon dioxide per mass than pure ZIF-8 at 1 bar and 303 K. We show how the rational combination of MOFs with ionic liquids can greatly enhance low pressure CO2 absorption, paving the way towards a new generation of high-performance, readily available liquid materials for effective low pressure carbon capture.

The Ser/Thr Kinase PrkC Participates in Cell Wall Homeostasis and Antimicrobial Resistance in Clostridium difficile.

Clostridium difficile is the leading cause of antibiotic-associated diarrhea in adults. During infection, C. difficile must detect the host environment and induce an appropriate survival strategy. Signal transduction networks involving serine/threonine kinases (STKs) play key roles in adaptation, as they regulate numerous physiological processes. PrkC of C. difficile is an STK with two PASTA domains. We showed that PrkC is membrane associated and is found at the septum. We observed that deletion of prkC affects cell morphology with an increase in mean size, cell length heterogeneity, and presence of abnormal septa. A ΔprkC mutant was able to sporulate and germinate but was less motile and formed more biofilm than the wild-type strain. Moreover, a ΔprkC mutant was more sensitive to antimicrobial compounds that target the cell envelope, such as the secondary bile salt deoxycholate, cephalosporins, cationic antimicrobial peptides, and lysozyme. This increased susceptibility was not associated with differences in peptidoglycan or polysaccharide II composition. However, the ΔprkC mutant had less peptidoglycan and released more polysaccharide II into the supernatant. A proteomic analysis showed that the majority of C. difficile proteins associated with the cell wall were less abundant in the ΔprkC mutant than the wild-type strain. Finally, in a hamster model of infection, the ΔprkC mutant had a colonization delay that did not significantly affect overall virulence.

Redox-Induced Molecular Metamorphism Promoting a Sol/Gel Phase Transition in a Viologen-Based Coordination Polymer.

We have developed a strategy enabling control over the organization of ditopic molecular tectons within a palladium-based self-assembled system. The key electron-responsive sub-unit is a viologen-based mechanical hinge that can toggle under electric stimulation between a folded and a stretched position, the driving force of the folding motion being the π-dimerisation of the electrogenerated viologen cation radicals. The title ditopic tecton features two planar, N2-type, triazole/pyridine-based bidentate binding units, providing the tecton with the ability to chelate two palladium ions both in its folded and in its elongated conformations. Association of this ditopic redox-responsive tecton with palladium to form 1D self-assembled architectures undergoing large scale reorganizations in solution under electric stimulation, has been established on the ground of spectroscopic, electrochemical, spectro-electrochemical and rheological data. Our result reveal that addition of metal leads to a significant stabilization of the π-dimer species in solution and that the redox-triggered reorganisation of the tectons comes along in suitable conditions with a macroscopic sol/gel-type phase transition.

"Polymultivalent" Polymer-Peptide Cluster Conjugates for an Enhanced Targeting of Cells Expressing αvß3 Integrins.

A new class of "polymultivalent" ligands combining several ligand clusters and a water-soluble biocompatible polymer is introduced. These original conjugates bear two levels of multivalency. They are prepared by covalent coupling of a controlled number of tetrameric cRGD peptide clusters along a well-defined copolymer synthesized by RAFT polymerization. The presence of multiple copies of peptide clusters on the same polymer backbone resulted in a much-higher relative potency than the free cluster reference. Thanks to the "polymultivalency", up to ∼2 orders of magnitude potency enhancement was reached in a competitive cell adhesion assay (nanomolar-range IC50 values). In addition, confocal microscopy and flow cytometry demonstrated that fluorescent "polymultivalent" conjugates (emitting in the far-red/near-infrared region) were able to specifically and selectively label cells expressing αvß3-integrin, the natural receptor of cRGD.

Keto-polymethines: a versatile class of dyes with outstanding spectroscopic properties for in cellulo and in vivo two-photon microscopy imaging.

The synthesis of keto-heptamethine derivatives has been expanded to various new symmetrical and asymmetrical structures, including an unprecedented di-anionic keto-polymethine. The spectroscopic behavior of these new dyes has been systematically and thoroughly investigated, revealing that the formation of hydrogen bond interactions with protic solvents is responsible for a dramatic enhancement of the fluorescence quantum yield in the far-red spectral region. The existence of these strong hydrogen-bond interactions was further confirmed by molecular dynamics simulations. These bis-dipolar polymethines exhibit large two-photon absorption (TPA) cross-sections (σ2 in GM) in the near-infrared, making them ideal candidates for NIR-to-NIR two-photon microscopy imaging applications. We demonstrate that the molecular engineering of the hydrophilic/hydrophobic balance enables targeting of different cellular components, such as cytoplasm or cell membranes. Addition of appropriate substituents provides the molecule with high-water-solubility, affording efficient two-photon probes for angiography.

Paramagnetic DOSY: An Accurate Tool for the Analysis of the Supramolecular Interactions between Lanthanide Complexes and Proteins.

Diffusion ordered NMR is implemented to determine accurately the mobility of paramagnetic tris-dipicolinate lanthanide complexes that are versatile probes of protein structure. It is shown that diffusion coefficient ratios can be measured with an accuracy of 1 % using a standard BPPLED pulse sequence, which allows for observing significant, though weak, variations when different species are interacting with the paramagnetic compound. We demonstrate that this approach is complementary to classical chemical shift titration experiments, and that it can be applied successfully to probe the supramolecular dynamic interactions between lanthanide complexes and small molecules on the one hand, or to determine rapidly their affinity for a targeted protein.

Electron-Triggered Metamorphism in Porphyrin-Based Self-Assembled Coordination Polymers.

Viologen-centered electron transfer is used to trigger a complete dissociation of a porphyrin-based supramolecular architecture. In the oxidized state, self-assembly is induced by iterative association of individual porphyrin-based tectons. Dissociation of the self-assembled species is actuated upon changing the redox state of the bipyridium units involved in the tectons from their dicationic state to their radical cation state, the driving force of the disassembling process being the formation of an intramolecularly locked conformation partly stabilized by π-dimerization of both viologen cation radicals.

Mediating gel formation from structurally controlled poly(electrolytes) through multiple "head-to-body" electrostatic interactions.

Tuning the chain-end functionality of a short-chain cationic homopolymer, owing to the nature of the initiator used in the atom transfer radical polymerization (ATRP) polymerization step, can be used to mediate the formation of a gel of this poly(electrolyte) in water. While a neutral end group gives a solution of low viscosity, a highly homogeneous gel is obtained with a phosphonate anionic moiety, as characterized by rheometry and diffusion nuclear magnetic resonance (NMR). This novel type of supramolecular control over poly(electrolytic) gel formation could find potential use in a variety of applications in the field of electro-active materials.

Rare earth fluoride nanoparticles obtained using charge transfer complexes: a versatile and efficient route toward colloidal suspensions and monolithic transparent xerogels.

Crystalline rare earth fluoride nanoparticles were synthesized by reacting rare earth ions with charge-transfer complexes, in solution, under mild conditions. An infrared study showed that these intermediate complexes are made up of solvent molecules (amide: N,N-dimethylformamide, 1-methyl-2-pyrrolidinone, etc.) and fluoride ions coming from hydrofluoric acid. The size and shape of the particles can be controlled through the process parameters. The complete study of the particles obtained through this process is carried out in this document, especially for the YbF(3) system. However, the process can easily be extended to the whole series of rare earth elements. We also show the ability of these objects to be transferred from an aqueous medium to an organic phase thanks to their surface modification. Finally, transparent monolithic xerogels of rare earth fluoride have been developed starting from the prepared colloidal solutions.

Protein expression from synthetic genes: selection of clones using GFP.

Construction of synthetic genes is today the most elegant way to optimize the heterologous expression of a recombinant protein. However, the selection of positive clones that incorporate the correct synthetic DNA fragments is a bottleneck as current methods of gene synthesis introduce 3.5 nucleotide deletions per kb. Furthermore, even when all predictable optimizations for protein production have been introduced into the synthetic gene, production of the protein is often disappointing: protein is produced in too low amounts or end up in inclusion bodies. We propose a strategy to overcome these two problems simultaneously by cloning the synthetic gene upstream of a reporter gene. This permits the selection of clones devoid of frame-shift mutations. In addition, beside nucleotide deletion, an average of three non-neutral mutations per kb are introduced during gene synthesis. Using a reporter protein downstream of the synthetic gene, allows the selection of clones with random mutations improving the expression or the folding of the protein of interest. The problem of errors found in synthetic genes is then turned into an advantage since it provides polymorphism useful for molecular evolution. The use of synthetic genes appears as an alternative to the error-prone PCR strategy to generate the variations necessary in protein engineering experiments.