Development of nanoparticles based on amphiphilic cyclodextrins for the delivery of active substances

Although amphiphilic cyclodextrin derivatives (ACDs) serve as valuable building blocks for nanomedicine formulations, their widespread production still encounters various challenges, limiting large-scale manufacturing. This work focuses on a robust alternative pathway using mineral base catalysis to transesterify β-cyclodextrin with long-chain vinyl esters, yielding ACD with modular and controlled hydrocarbon chain grafting. ACDs with a wide range of degrees of substitution (DS) were reliably synthesized, as indicated by extensive physicochemical characterization, including MALDI-TOF mass spectrometry. The influence of various factors, including the type of catalyst and the length of the hydrocarbon moiety of the vinyl ester, was studied in detail. ACDs were assessed for their ability to form colloidal suspensions by nanoprecipitation, with or without PEGylated phospholipid. Small-angle X-ray scattering and cryo-electron microscopy revealed the formation of nanoparticles with distinct ultrastructures depending on the DS: an onion-like structure for low and very high DS, and reversed hexagonal organization for DS between 4.5 and 6.1. We confirmed the furtivity of the PEGylated versions of the nanoparticles through complement activation experiments and that they were well tolerated in-vivo on a zebrafish larvae model after intravenous injection. Furthermore, a biodistribution experiment showed that the nanoparticles left the bloodstream within 10 h after injection and were phagocytosed by macrophages.

Grid batch-dependent tuning of glow discharge parameters

Sample preparation on cryo-EM grids can give various results, from very thin ice and homogeneous particle distribution (ideal case) to unwanted behavior such as particles around the “holes” or complexes that do not entirely correspond to the one in solution (real life). We recently run into such a case and finally found out that variations in the 3D reconstructions were systematically correlated with the grid batches that were used. We report the use of several techniques to investigate the grids' characteristics, namely TEM, SEM, Auger spectroscopy and Infrared Interferometry. This allowed us to diagnose the origin of grid preparation problems and to adjust glow discharge parameters. The methods used for each approach are described and the results obtained on a common specific case are reported.

Role of aIF5B in archaeal translation initiation

In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNA_i^Met, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.

Crystallization within Intermediate Amorphous Phases Determines the Polycrystallinity of Nanoparticles from Coprecipitation

Intense research on nanocrystals synthesized in solution is motivated by their original physical properties, which are determined by their sizes and shapes on various scales. However, morphology control on the nanoscale is limited by our understanding of crystallization, which is challenged by the now well-established prevalence of noncrystalline intermediates. In particular, the impact of such intermediates on the final sizes and crystal quality remains unclear because the characterization of their evolution on the nanometer and millisecond scales with nonperturbative analyses has remained a challenge. Here we use in situ X-ray scattering to show that the nucleation and growth of YVO₄:Eu nanocrystals is spatially restrained within amorphous, nanometer-scaled intermediates. The reactivity and size of these amorphous intermediates determine (i) the mono versus polycrystalline character of final crystals and (ii) the size of final crystals. This implies that designing amorphous intermediates themselves that form in <6 ms is one of the keys to controlled bottom-up syntheses of optimized nanoparticles.

Discriminative and quantitative analysis of norepinephrine and epinephrine by surface-enhanced Raman spectroscopy with gold nanoparticle suspensions

Surface-enhanced Raman spectroscopy (SERS) is a powerful analytical technique capable of increasing the Raman signal of an analyte using specific nanostructures. The close contact between those nanostructures, usually a suspension of nanoparticles, and the molecule of interest produces an important exaltation of the intensity of the Raman signal. Even if the exaltation leads to an improvement of Raman spectroscopy sensitivity, the complexity of the SERS signal and the numbers of parameters to be controlled allow the use of SERS for detection rather than quantification. The aim of this study was to develop a robust discriminative and quantitative analysis in accordance with pharmaceutical standards. In this present work, we develop a discriminative and quantitative analysis based on the previous optimized parameters obtained by the design of experiments fixed for norepinephrine (NOR) and extended to epinephrine (EPI) which are two neurotransmitters with very similar structures. Studying the short evolution of the Raman signal intensity over time coupled with chemometric tools allowed the identification of outliers and their removal from the data set. The discriminant analysis showed an excellent separation of EPI and NOR. The comparative analysis of the data showed the superiority of the multivariate analysis after logarithmic transformation. The quantitative analysis allowed the development of robust quantification models from several gold nanoparticle batches with limits of quantification of 32 µg/mL for NOR and below 20 µg/mL for EPI even though no Raman signal is observable for such concentrations. This study improves SERS analysis over ultrasensitive detection for discrimination and quantification using a handheld Raman spectrometer.

Monazite LaPO4:Eu3+ nanorods as strongly polarized nano-emitters

Orientation analyses of macromolecules or artificial particles are vital for both fundamental research and practical bio-applications. An accurate approach is monitoring the polarization spectroscopy of lanthanide-doped nanocrystalline materials. However, nanomaterials are often far from ideal for the colloidal and polarization luminescence properties. In the present study, we synthesize well-dispersed LaPO₄:Eu³⁺ nanomaterials in an anisotropic rod shape. Microwave heating with excess addition of phosphate precursor invokes a rapid phase transition of rhabdophane into monazite. The colloidal stability of the nanorod suspension is outstanding, demonstrated by showing liquid crystalline behaviors. The monazite nanorods are also superior in luminescence efficiency with limited defects. The emission spectrum of Eu³⁺ consists of well-defined lines with prominent polarization dependencies for both the forced electric dipole transitions and the magnetic dipole transitions. All the results demonstrate that the synthesized monazite nanorods can serve as an accurate probe in orientation analyses and potential applications, such as in microfluidics and biological detections.

New Insights into the Reactivity of Detonation Nanodiamonds during the First Stages of Graphitization

The present study aims to compare the early stages of graphitization of the same DND source for two annealing atmospheres (primary vacuum, argon at atmospheric pressure) in an identical set-up. DND samples are finely characterized by a combination of complementary techniques (FTIR, Raman, XPS, HR-TEM) to highlight the induced modifications for temperature up to 1100 °C. The annealing atmosphere has a significant impact on the graphitization kinetics with a higher fraction of sp²-C formed under vacuum compared to argon for the same temperature. Whatever the annealing atmosphere, carbon hydrogen bonds are created at the DND surface during annealing according to FTIR. A “nano effect”, specific to the <10 nm size of DND, exalts the extreme surface chemistry in XPS analysis. According to HR-TEM images, the graphitization is limited to the first outer shell even for DND annealed at 1100 °C under vacuum.

Nuclear Magnetic Resonance Spectroscopy: A Multifaceted Toolbox to Probe Structure, Dynamics, Interactions, and Real-Time In Situ Release Kinetics in Peptide-Liposome Formulations

Liposomal formulations represent attractive biocompatible and tunable drug delivery systems for peptide drugs. Among the tools to analyze their physicochemical properties, nuclear magnetic resonance (NMR) spectroscopy, despite being an obligatory technique to characterize molecular structure and dynamics in chemistry as well as in structural biology, yet appears to be rather sparsely used to study drug-liposome formulations. In this work, we exploited several facets of liquid-state NMR spectroscopy to characterize liposomal delivery systems for the apelin-derived K14P peptide and K14P modified by Nα-fatty acylation. Various liposome compositions and preparation modes were analyzed. Using NMR, in combination with cryo-electron microscopy and dynamic light scattering, we determined structural, dynamic, and self-association properties of these peptides in solution and probed their interactions with liposomes. Using ³¹P and ¹H NMR, we characterized membrane fluidity and thermotropic phase transitions in empty and loaded liposomes. Based on diffusion and ¹H NMR experiments, we localized and quantified peptides with respect to the interior/exterior of liposomes and changes over time and upon thermal treatments. Finally, we assessed the release kinetics of several solutes and compared various formulations. Taken together, this work shows that NMR has the potential to assist the design of peptide/liposome systems and more generally drug delivery systems.

SERS characterization of aggregated and isolated bacteria deposited on silver-based substrates

Surface-enhanced Raman scattering (SERS), based on the enhancement of the Raman signal of molecules positioned within a few nanometres from a structured metal surface, is ideally suited to provide bacterial-specific molecular fingerprints which can be used for analytical purposes. However, for some complex structures such as bacteria, the generation of reproducible SERS spectra is still a challenging task. Among the various factors influencing the SERS variability (such as the nature of SERS-active substrate, Raman parameters and bacterial specificity), we demonstrate in this study that the environment of Gram-positive and Gram-negative bacteria deposited on ultra-thin silver films also impacts the origin of the SERS spectra. In the case of densely packed bacteria, the obtained SERS signatures were either characteristic of the secretion of adenosine triphosphate for Staphylococcus aureus (S. aureus) or the cell wall and the pili/flagella for Escherichia coli (E. coli), allowing for an easy discrimination between the various strains. In the case of isolated bacteria, SERS mapping together with principal component analysis revealed some variabilities of the spectra as a function of the bacteria environment and the bactericidal effect of the silver. However, the variability does not preclude the SERS signatures of various E. coli strains to be discriminated.

Rapid and sensitive identification of uropathogenic Escherichia coli using a surface-enhanced-Raman-scattering-based biochip

Rapid, selective and sensitive sensing of bacteria remains challenging. We report on a highly sensitive and reproducible surface-enhanced Raman spectroscopy (SERS)-based sensing approach for the detection of uropathogenic Escherichia coli (E. coli) bacteria in urine. The assay is based on the specific capture of the bacteria followed by interaction with cetyltrimethylammonium bromide (CTAB)-stabilised gold nanorods (Au NRS) as SERS markers. High sensitivity up to 10 CFU mL^-1 is achieved by optimizing the capture interface based on hydrogenated amorphous silicon a-Si:H thin films. The integration of CH₃O-PEG750 onto a-Si:H gives the sensing interface an efficient anti-fouling character, while covalent linkage of antibodies directed against the major type-1 fimbrial pilin FimA of the human pathogen E. coli results in the specific trapping of fimbriated E. coli onto the SERS substrate and their spectral fingerprint identification.

Elaboration of Superparamagnetic and Bioactive Multicore-Shell Nanoparticles (γ-Fe2O3@SiO2-CaO): A Promising Material for Bone Cancer Treatment

The past few decades have seen the development of new bone cancer therapies, triggered by the discovery of new biomaterials. When the tumoral area is small and accessible, the common clinical treatment implies the tumor mass removal followed by bone reconstruction or consolidation with a bioceramic or a metallic scaffold. Even though the treatment also involves chemotherapy or radiotherapy, resurgence of cancer cells remains possible. We have thus designed a new kind of heterostructured nanobiomaterial, composed of SiO₂-CaO bioactive glass as the shell and superparamagnetic γ-Fe₂O₃ iron oxide as the core in order to combine the benefits of bone repair thanks to the glass bioactivity and cancer cell destruction through magnetic hyperthermia. These multifunctional core-shell nanoparticles (NPs) have been obtained using a two-stage procedure, involving the coprecipitation of 11 nm sized iron oxide NPs followed by their encapsulation inside a bioactive glass shell by sol-gel chemistry. The as-produced spherical multicore-shell NPs show a narrow size distribution of 73 ± 7 nm. Magnetothermal loss measurements by calorimetry under an alternating magnetic field and in vitro bioactivity assessment performed in simulated body fluid showed that these heterostructures exhibit a good heating capacity and a fast mineralization process (hydroxyapatite forming ability). In addition, their in vitro cytocompatibility, evaluated in the presence of human mesenchymal stem cells during 3 and 7 days, has been demonstrated. These first findings suggest that γ-Fe₂O₃@SiO₂-CaO heterostructures are a promising biomaterial to fill bone defects resulting from bone tumor resection, as they have the ability to both repair bone tissue and act as thermoseeds for cancer therapy.

Toward a Chemical Control of Colloidal YVO4 Nanoparticles Microstructure

Rare-earth-doped oxides are a class of compounds that have been largely studied in the context of the development of luminescent nanocrystals for various applications including fluorescent labels for bioimaging, MRI contrast agents, luminescent nanocomposite coatings, etc. Elaboration of colloidal suspensions is usually achieved through coprecipitation. Particles exhibit emission properties that are similar to the bulk counterparts, although altered by crystalline defects or surface quenching species. Focusing on YVO₄:Eu, one of the first reported systems, the aim of this work is to revisit the elaboration of nanoparticles obtained through a simple aqueous coprecipitation route. The objective is more precisely to get a better understanding of the parameters affecting the particles' internal microstructure, a feature that is poorly controlled and characterized. We show that the hydroxyl concentration in the precursor solution has a drastic effect on the particles' microstructure. Moreover, discrepancies in the reported particle structure are shown to possibly arise from the carbonation of the strongly basic orthovanadate precursor. For this study, SAXS/WAXS is shown to be a powerful tool to characterize the multiscale structure of the particles. It could be shown that playing on the precursor composition, it may be varied between almost monocrystalline nanocrystals to particles exhibiting a hierarchical microstructure well described by a surface fractal model. This work provides a new methodology for the characterization of nanoparticles microstructure and opens new directions for its optimization in view of applications.

Strain engineering of photo-induced phase transformations in Prussian blue analogue heterostructures

Heterostructures based on Prussian blue analogues (PBA) combining photo- and magneto-striction have shown a large potential for the development of light-induced magnetization switching. However, studies of the microscopic parameters that control the transfer of the mechanical stresses across the interface and their propagation in the magnetic material are still too scarce to efficiently improve the elastic coupling. Here, this coupling strength is tentatively controlled by strain engineering in heteroepitaxial PBA core-shell heterostructures involving the same Rb0.5Co[Fe(CN)6]0.8·zH2O photostrictive core and isostructural shells of similar thickness and variable mismatch with the core lattice. The shell deformation and the optical electron transfer at the origin of photostriction are monitored by combined in situ and real time synchrotron X-ray powder diffraction and X-ray absorption spectroscopy under visible light irradiation. These experiments show that rather large strains, up to +0.9%, are developed within the shell in response to the tensile stresses associated with the expansion of the core lattice upon illumination. The shell behavior is, however, complex, with contributions in dilatation, in compression or unchanged. We show that a tailored photo-response in terms of strain amplitude and kinetics with potential applications for a magnetic manipulation using light requires a trade-off between the quality of the interface (which needs a small lattice mismatch i.e. a small a-cubic parameter for the shell) and the shell rigidity (decreased for a large a-parameter). A shell with a high compressibility that is further increased by the presence of misfit dislocations will show a decrease in its mechanical retroaction on the photo-switching properties of the core particles.

Lanthanoid-Doped Phosphate/Vanadate Mixed Hollow Particles as Ratiometric Luminescent Sensors

Rare earth (RE) phosphates and vanadates are structurally similar compositions that display distinct but complementary luminescent properties. The properties of these phosphors can be combined in REPO₄-REVO₄ heterostructures during the development of new sensing technologies for biological applications. This work presents the synthesis of hollow RE phosphate/vanadate colloidal particles and evaluates their applicability as luminescent markers. Hydrothermal treatments of RE hydroxycarbonate particles in the presence of the PO₄^3- and VO₄^3- precursors afforded the final REPO₄-REVO₄ solids in a two-step template synthesis. We converted precursor hydroxycarbonate particles into the final heterostructures and characterized their structure and morphology. According to our detailed study into the spectroscopic properties of Eu³⁺-doped particles and their luminescence response to several species, the presence of the phosphate and vanadate phases in a single particle provided different chemical environments and enabled the design of a ratiometric approach to detect H₂O₂. These results open new perspectives for the development of new intracellular luminescent markers.

Fluorescence correlation spectroscopy as a sensitive and useful tool for revealing potential overlaps between the epitopes of monoclonal antibodies on viral particles

Although the enzyme-linked immunosorbent assay (ELISA) is well established for quantitating epitopes on inactivated virions used as vaccines, it is less suited for detecting potential overlaps between the epitopes recognized by different antibodies raised against the virions. We used fluorescent correlation spectroscopy (FCS) to detect the potential overlaps between 3 monoclonal antibodies (mAbs 4B7-1H8-2E10, 1E3-3G4, 4H8-3A12-2D3) selected for their ability to specifically recognize poliovirus type 3. Competition of the Alexa488-labeled mAbs with non-labeled mAbs revealed that mAbs 4B7-1H8-2E10 and 4H8-3A12-2D3 compete strongly for their binding sites on the virions, suggesting an important overlap of their epitopes. This was confirmed by the cryo-electron microscopy (cryo EM) structure of the poliovirus type 3 complexed with the corresponding antigen-binding fragments (Fabs) of the mAbs, which revealed that Fabs 4B7-1H8-2E10 and 4H8-3A12-2D3 epitopes share common amino acids. In contrast, a less efficient competition between mAb 1E3-3G4 and mAb 4H8-3A12-2D3 was observed by FCS, and there was no competition between mAbs 1E3-3G4 and 4B7-1H8-2E10. The Fab 1E3-3G4 epitope was found by cryoEM to be close to but distinct from the epitopes of both Fabs 4H8-3A12-2D3 and 4B7-1H8-2E10. Therefore, the FCS data additionally suggest that mAbs 4H8-3A12-2D3 and 4B7-1H8-2E10 bind in a different orientation to their epitopes, so that only the former sterically clashes with the mAb 1E3-3G4 bound to its epitope. Our results demonstrate that FCS can be a highly sensitive and useful tool for assessing the potential overlap of mAbs on viral particles.

Reversible switching of the interparticle distance in DNA-templated gold nanoparticle dimers

We produce gold nanoparticle dimers with a surface-to-surface distance that varies reversibly by a factor of 3 when hybridizing or removing a single target DNA strand. The dimers are built on one DNA template that features a stem-loop enabling the interparticle distance change. Using electrophoresis, we reach 90% sample purities and demonstrate that this chemical process is reversible in solution at room temperature for a low molar excess of the target DNA strand. The kinetics of the reaction is asymmetric due to steric hindrance in the stem-loop opening process. Furthermore, a statistical analysis of cryo-electron microscopy measurements allows us to provide the first quantitative analysis of distance changes in chemically switchable nanoparticle assemblies.

Fast characterisation of cell-derived extracellular vesicles by nanoparticles tracking analysis, cryo-electron microscopy, and Raman tweezers microspectroscopy

The joint use of 3 complementary techniques, namely, nanoparticle tracking analysis (NTA), cryo-electron microscopy (Cryo-EM) and Raman tweezers microspectroscopy (RTM), is proposed for a rapid characterisation of extracellular vesicles (EVs) of various origins. NTA is valuable for studying the size distribution and concentration, Cryo-EM is outstanding for the morphological characterisation, including observation of vesicle heterogeneity, while RTM provides the global chemical composition without using any exogenous label. The capabilities of this approach are evaluated on the example of cell-derived vesicles of Dictyostelium discoideum, a convenient general model for eukaryotic EVs. At least 2 separate species differing in chemical composition (relative amounts of DNA, lipids and proteins, presence of carotenoids) were found for each of the 2 physiological states of this non-pathogenic microorganism, that is, cell growth and starvation-induced aggregation. These findings demonstrate the specific potency of RTM. In addition, the first Raman spectra of human urinary exosomes are reported, presumably constituting the primary step towards Raman characterisation of EVs for the purpose of human diseases diagnoses.

Optical and topological characterization of gold nanoparticle dimers linked by a single DNA double strand

We demonstrate that symmetric or asymmetric gold nanoparticle dimers with substantial scattering cross sections and plasmon coupling can be produced with a perfectly controlled chemical environment and a high purity using a single DNA linker as short as 7 nm. A statistical analysis of the optical properties and morphology of single dimers is performed using darkfield and cryo-electron microscopies. These results, correlated to Mie theory calculations, indicate that the particle dimers are stretched in water by electrostatic interactions.

Nanoscale topography of hepatitis B antigen particles by atomic force microscopy

Hepatitis B virus envelope is mainly composed of three forms of the same protein expressed from different start codons of the same open reading frame. The smaller form named S protein corresponds to the C-terminal common region and represents about 80% of the envelope proteins. It is mainly referred as hepatitis B virus surface antigen (HBsAg). Over expressed in the host cell, this protein can be produced as spherical and tubular self-organized particles. Highly immunogenic, these particles are used in licensed hepatitis B vaccines. In this study we have combined transmission electron microscopy and atomic force microscopy to determine the shape and size of HBsAg particles produced from the yeast Hansenula polymorpha. Tapping mode atomic force microscopy in liquid allows structural details of the surface to be delineated with a resolution in the nanometer range. Particles were decorated by closely packed spike-like structures protruding from particle surface. Protrusions appeared uniformly distributed at the surface and an average number of 75 protrusions per particle were calculated. Importantly, we demonstrated that proteins mainly contribute to the topography of the protrusions.

Evidence of double-walled Al-Ge imogolite-like nanotubes. a cryo-TEM and SAXS investigation

It has been recently discovered that the synthesis of Al-Ge imogolite-like nanotubes is possible at high concentration. Despite this initial success, the structure of these Al-Ge imogolite-like nanotubes remains not completely understood. Using high resolution cryo-TEM and Small Angle X-ray Scattering, we unravel their mesoscale structure in two contrasted situations. On the one hand, Al-Ge imogolite nanotubes synthesized at 0.25 M are double-walled nanotubes of 4.0 +/- 0.1 nm with an inner tube of 2.4 +/- 0.1 nm. Moreover, SAXS data also suggest that the two concentric tubes have an equal length and identical wall structure. On the other hand, at higher concentration (0.5M), both SAXS and cryo-TEM data confirm the formation of single-walled nanotubes of 3.5 +/- 0.15 nm. Infrared spectroscopy confirms the imogolite structure of the tubes. This is the first evidence of any double-walled imogolite or imogolite-like nanotubes likely to renew interest in these materials and associated potential applications.

Nanovesicles released by Dictyostelium cells: a potential carrier for drug delivery

Nanovesicles released by Dictyostelium discoideum cells grown in the presence of the DNA-specific dye Hoechst 33342 have been previously shown to mediate the transfer of the dye into the nuclei of Hoechst-resistant cells. The present investigation extends this work by conducting experiments in the presence of hypericin, a fluorescent therapeutic photosensitizer assayed for antitumoral photodynamic therapy. Nanovesicles released by Dictyostelium cells exhibit an averaged diameter between 50 and 150 nm, as measured by transmission cryoelectron microscopy. A proteomic analysis reveals a predominance of actin and actin-related proteins. The detection of a lysosomal membrane protein (LIMP II) indicates that these vesicles are likely generated in the late endosomal compartment. The use of the hypericin-containing nanovesicles as nanodevices for in vitro drug delivery was investigated by fluorescence microscopy. The observed signal was almost exclusively located in the perinuclear area of two human cell lines, skin fibroblasts (HS68) and cervix carcinoma (HeLa) cells. Studies by confocal microscopy with specific markers of cell organelles, provided evidence that hypericin was accumulated in the Golgi apparatus. All these data shed a new light on in vitro drug delivery by using cell-released vesicles as carriers.

Transformation of vivianite by anaerobic nitrate-reducing iron-oxidizing bacteria

In phosphate-rich environments, vivianite (Fe(II)(3)(PO(4))(2), 8H(2)O) is an important sink for dissolved Fe(II) and is considered as a very stable mineral due to its low solubility at neutral pH. In the present study, we report the mineralogical transformation of vivianite in cultures of the nitrate-reducing iron-oxidizing bacterial strain BoFeN1 in the presence of dissolved Fe(II). Vivianite was first transformed into a greenish phase consisting mostly of an amorphous mixed valence Fe-phosphate. This precipitate became progressively orange and the final product of iron oxidation consisted of an amorphous Fe(III)-phosphate. The sub-micrometer analysis by scanning transmission X-ray microscopy of the iron redox state in samples collected at different stages of the culture indicated that iron was progressively oxidized at the contact of the bacteria and at a distance from the cells in extracellular minerals. Iron oxidation in the extracellular minerals was delayed by a few days compared with cell-associated Fe-minerals. This led to strong differences of Fe redox in between these two types of minerals and finally to local heterogeneities of redox within the sample. In the absence of dissolved Fe(II), vivianite was not significantly transformed by BoFeN1. Whereas Fe(II) oxidation at the cell contact is most probably directly catalyzed by the bacteria, vivianite transformation at a distance from the cells might result from oxidation by nitrite. In addition, processes leading to the export of Fe(III) from bacterial oxidation sites to extracellular minerals are discussed including some involving colloids observed by cryo-transmission electron microscopy in the culture medium.

The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications

The three-dimensional structure of the hexameric (alphabeta)(6) 1.2-MDa complex formed by glutamate synthase has been determined at subnanometric resolution by combining cryoelectron microscopy, small angle x-ray scattering, and molecular modeling, providing for the first time a molecular model of this complex iron-sulfur flavoprotein. In the hexameric species, interprotomeric alpha-alpha and alpha-beta contacts are mediated by the C-terminal domain of the alpha subunit, which is based on a beta helical fold so far unique to glutamate synthases. The alphabeta protomer extracted from the hexameric model is fully consistent with it being the minimal catalytically active form of the enzyme. The structure clarifies the electron transfer pathway from the FAD cofactor on the beta subunit, to the FMN on the alpha subunit, through the low potential [4Fe-4S](1+/2+) centers on the beta subunit and the [3Fe-4S](0/1+) cluster on the alpha subunit. The (alphabeta)(6) hexamer exhibits a concentration-dependent equilibrium with alphabeta monomers and (alphabeta)(2) dimers, in solution, the hexamer being destabilized by high ionic strength and, to a lower extent, by the reaction product NADP(+). Hexamerization seems to decrease the catalytic efficiency of the alphabeta protomer only 3-fold by increasing the K(m) values measured for l-Gln and 2-OG. However, it cannot be ruled out that the (alphabeta)(6) hexamer acts as a scaffold for the assembly of multienzymatic complexes of nitrogen metabolism or that it provides a means to regulate the activity of the enzyme through an as yet unknown ligand.

Radiation-induced synthesis and cryo-TEM characterization of silver nanoshells on linoleate spherical micelles

We combine the self-assembly properties of amphiphilic molecules with the radiolysis method to produce specific sizes and shapes of metallic nano-objects. Radiolysis is used to synthesize core--shell structures consisting of nanometric linoleate spherical micelles as the core and silver as the shell. The validity of the technique is asserted by cryoelectron microscopy, which is an adequate technique for low density contrasts and core--shell structures. The shells are found to be homogeneous with a size of a few nanometers. Images are used to bring forward the hypothesis of the fabrication process.

3D electron microscopy of biological nanomachines: principles and applications

Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.

How ATP hydrolysis controls filament assembly from profilin-actin: implication for formin processivity

Formins catalyze rapid filament growth from profilin-actin, by remaining processively bound to the elongating barbed end. The sequence of elementary reactions that describe filament assembly from profilin-actin at either free or formin-bound barbed ends is not fully understood. Specifically, the identity of the transitory complexes between profilin and actin terminal subunits is not known; and whether ATP hydrolysis is directly or indirectly coupled to profilin-actin assembly is not clear. We have analyzed the effect of profilin on actin assembly at free and FH1-FH2-bound barbed ends in the presence of ADP and non-hydrolyzable CrATP. Profilin blocked filament growth by capping the barbed ends in ADP and CrATP/ADP-Pi states, with a higher affinity when formin is bound. We confirm that, in contrast, profilin accelerates depolymerization of ADP-F-actin, more efficiently when FH1-FH2 is bound to barbed ends. To reconcile these data with effective barbed end assembly from profilin-MgATP-actin, the nature of nucleotide bound to both terminal and subterminal subunits must be considered. All data are accounted for quantitatively by a model in which a barbed end whose two terminal subunits consist of profilin-ATP-actin cannot grow until ATP has been hydrolyzed and Pi released from the penultimate subunit, thus promoting the release of profilin and allowing further elongation. Formin does not change the activity of profilin but simply uses it for its processive walk at barbed ends. Finally, if profilin release from actin is prevented by a chemical cross-link, formin processivity is abolished.

A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas

In a context of automation of cryo-electron microscopy, we developed a novel method for improving visibility of diffraction rings in the power spectra of cryo-electron micrographs of vitreous ice (without carbon film or high concentration of diffracting material). We used these enhanced spectra to semi-automatically detect and remove micrographs and/or local areas introducing errors in the global 3D map (drifted and charged areas) or those unable to increase global signal-to-noise ratio (non-diffracting areas). Our strategy also allows a detection of micrographs/areas with a strong astigmatism. These images should be removed when using algorithms that do not correct astigmatism. Our sorting method is simple and fast since it uses the normalized cross-correlation between enhanced spectra and their copies rotated by 90 degrees. It owes its success mainly to the novel pre-processing of power spectra. The improved visibility also allows an easier visual check of accuracy of sorting. We show that our algorithm can even improve the visibility of diffraction rings of cryo-electron micrographs of pure water. Moreover, we show that this visibility depends strongly on ice thickness. This algorithm is implemented in the Xmipp (open-source image processing package) and is freely available for implementation in any other software package.

Analysis of tetramethylrhodamine-labeled actin polymerization and interaction with actin regulatory proteins

The hydrolysis of ATP accompanying actin polymerization destabilizes the filament, controls actin assembly dynamics in motile processes, and allows the specific binding of regulatory proteins to ATP- or ADP-actin. However, the relationship between the structural changes linked to ATP hydrolysis and the functional properties of actin is not understood. Labeling of actin Cys374 by tetramethylrhodamine (TMR) has been reported to make actin non-polymerizable and enabled the crystal structures of ADP-actin and 5'-adenylyl beta,gamma-imidodiphosphate-actin to be solved. TMR-actin has also been used to solve the structure of actin in complex with the formin homology 2 domain of mammalian Dia1. To understand how the covalent modification of actin by TMR may affect the structural changes linked to ATP hydrolysis and to evaluate the functional relevance of crystal structures of TMR-actin in complex with actin-binding proteins, we have analyzed the assembly properties of TMR-actin and its interaction with regulatory proteins. We show that TMR-actin polymerized in very short filaments that were destabilized by ATP hydrolysis. The critical concentrations for assembly of TMR-actin in ATP and ADP were only an order of magnitude higher than those for unlabeled actin. The functional interactions of actin with capping proteins, formin, actin-depolymerizing factor/cofilin, and the VCA-Arp2/3 filament branching machinery were profoundly altered by TMR labeling. The data suggest that TMR labeling hinders the intramolecular movements of actin that allow its specific adaptative recognition by regulatory proteins and that determine its function in the ATP- or ADP-bound state.

Divalent ion-dependent swelling of Tomato Bushy Stunt Virus: A multi-approach study

Time-resolved small-angle X-ray and neutron scattering (SAXS and SANS) in solution were used to study the swelling reaction of TBSV upon chelation of its constituent calcium at mildly basic pH. SAXS intensities comprise contribution from the protein capsid and the RNA moiety, while neutron scattering, recorded in 72% D2O, is essentially due to the protein capsid. Cryo-electron micrographs of compact and swollen virus were used to produce 3D reconstructions of the initial and final conformations of the virus at a resolution of 13 A and 19 A, respectively. While compact particles appear to be very homogeneous in size, solutions of swollen particles exhibit some size heterogeneity. A procedure has been developed to compute the SAXS pattern from the 3D reconstruction for comparison with experimental data. Cryo-electron microscopy thereby provides an invaluable starting (and ending) point for the analysis of the time-resolved swelling process using the scattering data.

Aggregation and gelation of micellar casein particles

Micellar casein particles (submicelles) are formed by removing calcium phosphate from native casein. The submicelles aggregate and eventually form a gel with a rate that increases strongly with increasing temperature and casein concentration. At low casein concentrations the gel is very weak and collapses under its own weight so that a precipitate is formed. The structure of the aggregates is studied using light scattering and cryo-electron microscopy. It is found that the aggregates have a self-similar structure with fractal dimension 2. The viscoelastic properties of the gel are studied by frequency scans of the loss and storage moduli during the gelation process. The bonds between the submicelles probably involve calcium phosphate complexes.

Oligomeric Assemblies of the Escherichia coli MalT Transcriptional Activator Revealed by Cryo-electron Microscopy and Image Processing

MalT, the dedicated transcriptional activator of the maltose regulon in Escherichia coli, is the prototype for a family of large (approximately 100 kDa) transcriptional activators. MalT self-association plays a key role in recognition of the target promoters, which contain several MalT sites that are cooperatively bound by the activator. The unliganded form of MalT is monomeric. The protein self-associates only in the presence of both ATP (or AMP-PNP, a non-hydrolysable analog of ATP) and maltotriose, the inducer. Here, we report cryo-electron microscopy analyses of MalT multimeric forms. We show that, in the presence of maltotriose and AMP-PNP, MalT associates into novel, polydisperse, curved homopolymers. The building block, corresponding to a MalT monomer, comprises an outer globular domain connected by a peduncle to an inner domain that mediates self-association. Image analyses highlight the significant conformational flexibility of these polymeric forms. In the presence of a DNA fragment containing a MalT-controlled promoter, malPp500, MalT forms homopolymers with a much smaller radius of curvature and a different conformation. We propose that MalT binding to the target promoters involves the assembly of a MalT homo-oligomer that is governed by the array of MalT sites present.

Unusual IgM fibrillar deposits in glomerulonephritis: ultrastructural and diffraction studies in a case report

Morphological examination of 2 renal biopsy specimens obtained from a 69-year-old woman with a nephrotic syndrome, high blood pressure, and a reduced glomerular filtration rate revealed, in ultrastructural study, a type of a glomerulonephritis with fibrillar deposits in a subendothelial position which were unusual in their immunoglobulin components (mainly IgM). The fibrillar components were of irregular size, 13 to 18 nm in diameter and presented a very particular "barbed wire" morphological aspect, not hitherto described. Diffraction studies and image analysis, revealed spiraled fibrils with regular alternating elements that we suggest may correspond to IgM molecules. The clinical (isolated renal symptoms) and laboratory (traces of 3 monoclonal components in the serum and 2 normal bone marrow biopsy specimens) data provided no evidence of hematopoietic malignancy, viral hepatitis or cryoglobulinemia.

Type IV-like pili formed by the type II secreton: specificity, composition, bundling, polar localization, and surface presentation of peptides

The secreton or type II secretion machinery of gram-negative bacteria includes several type IV pilin-like proteins (the pseudopilins) that are absolutely required for secretion. We previously reported the presence of a bundled pilus composed of the pseudopilin PulG on the surface of agar-grown Escherichia coli K-12 cells expressing the Klebsiella oxytoca pullulanase (Pul) secreton genes at high levels (N. Sauvonnet, G. Vignon, A. P. Pugsley, and P. Gounon, EMBO J. 19:2221-2228, 2000). We show here that PulG is the only pseudopilin in purified pili and that the phenomenon is not restricted to the Pul secreton reconstituted in E. coli or to PulG. For example, high-level expression of the endogenous E. coli gsp secreton genes caused production of bundled pili composed of the pseudopilin GspG, and the Pul secreton was able to form pili composed of PulG-like proteins from secreton systems of other bacteria. PulG derivatives in which the C terminus was extended by the addition of eight different peptides were also assembled into pili and functioned in secretion. Three of the C-terminal peptides were shown to be exposed along the entire length of the assembled pili. Hence, the C terminus of PulG may represent a permissive site for the insertion of immunogenic epitopes or other peptide sequences. One of these PulG variants, with a six-histidine tag at its C terminus, formed nonpolar, nonbundled pili, suggesting that bundle formation and polar localization are not correlated with the ability of PulG to function in secretion. We propose that the PulG pilus is an artifactual manifestation of a periplasmic "pseudopilus" and that cycles of pseudopilus extension and retraction within the periplasm propel pullulanase through secretin channels in the outer membrane. Abnormally long pili that extend beyond the outer membrane are produced only when pilus length control and retraction are deregulated by overproduction of the major pseudopilus subunit (PulG).

Helical structure of the needle of the type III secretion system of Shigella flexneri

Gram-negative bacteria commonly interact with animal and plant hosts using type III secretion systems (TTSSs) for translocation of proteins into eukaryotic cells during infection. 10 of the 25 TTSS-encoding genes are homologous to components of the bacterial flagellar basal body, which the TTSS needle complex morphologically resembles. This indicates a common ancestry, although no TTSS sequence homologues for the genes encoding the flagellum are found. We here present an approximately 16-A structure of the central component, the needle, of the TTSS. Although the needle subunit is significantly smaller and shares no sequence homology with the flagellar hook and filament, it shares a common helical architecture ( approximately 5.6 subunits/turn, 24-A helical pitch). This common architecture implies that there will be further mechanistic analogies in the functioning of these two bacterial systems.

Specificity of the interaction of RocR with the rocG-rocA intergenic region in Bacillus subtilis

In Bacillus subtilis, expression of the rocG gene, encoding glutamate dehydrogenase, and the rocABC operon, involved in arginine catabolism, requires SigL (sigma(54))-containing RNA polymerase as well as RocR, a positive regulator of the NtrC/NifA family. The RocR protein was purified and shown to bind specifically to the intergenic region located between rocG and the rocABC operon. DNaseI footprinting experiments were used to define the RocR-binding site as an 8 bp inverted repeat, separated by one base pair, forming an imperfect palindrome which is present twice within the rocG-rocABC intergenic region, acting as both a downstream activating sequence (DAS) and an upstream activating sequence (UAS). Point mutations in either of these two sequences significantly lowered expression of both rocG and rocABC. This bidirectional enhancer element retained partial activity even when moved 9 kb downstream of the rocA promoter. Electron microscopy experiments indicated that an intrinsically curved region is located between the UAS/DAS region and the promoter of the rocABC operon. This curvature could facilitate interaction of RocR with sigma(54)-RNA polymerase at the rocABC promoter.

Bcl-2 and Bax modulate adenine nucleotide translocase activity

Bcl-2 is a prosurvival factor that reportedly prevents the nonspecific permeabilization of mitochondrial membranes, yet enhances specific ADP/ATP exchange by these organelles. Here, we show that Bcl-2 enhances the ADP/ATP exchange in proteoliposomes containing the purified adenine nucleotide translocase (ANT) in isolated mitochondria and mitoplasts, as well as in intact cells in which mitochondrial matrix ATP was monitored continuously using a specific luciferase-based assay system. Conversely, Bax, which displaces Bcl-2 from ANT in apoptotic cells, inhibits ADP/ATP exchange through a direct action on ANT. The Bax-mediated inhibition of ADP/ATP exchange can be separated from Bax-stimulated formation of nonspecific pores by ANT. Chemotherapy-induced apoptosis caused an inhibition of ANT activity, which preceded the loss of the mitochondrial transmembrane potential and could be prevented by overexpression of Bcl-2. These data are compatible with a model of mitochondrial apoptosis regulation in which ANT interacts with either Bax or Bcl-2, which both influence ANT function in opposing manners. Bcl-2 would maintain the translocase activity at high levels, whereas Bax would inhibit the translocase function of ANT.

Structure and composition of the Shigella flexneri "needle complex", a part of its type III secreton

Type III secretion systems (TTSSs or secretons), essential virulence determinants of many Gram-negative bacteria, serve to translocate proteins directly from the bacteria into the host cytoplasm. Electron microscopy (EM) indicates that the TTSSs of Shigella flexneri are composed of: (1) an external needle; (2) a transmembrane domain; and (3) a cytoplasmic bulb. EM analysis of purified and negatively stained parts 1, 2 and a portion of 3 of the TTSS, together termed the "needle complex" (NC), produced an average image at 17 A resolution in which a base, an outer ring and a needle, inserted through the ring into the base, could be discerned. This analysis and cryoEM images of NCs indicated that the needle and base contain a central 2-3 nm canal. Five major NC components, MxiD, MxiG, MxiJ, MxiH and MxiI, were identified by N-terminal sequencing. MxiG and MxiJ are predicted to be inner membrane proteins and presumably form the base. MxiD is predicted to be an outer membrane protein and to form the outer ring. MxiH and MxiI are small hydrophilic proteins. Mutants lacking either of these proteins formed needleless secretons and were unable to secrete Ipa proteins. As MxiH was present in NCs in large molar excess, we propose that it is the major needle component. MxiI may cap at the external needle tip.

The human Rad52 protein exists as a heptameric ring

The RAD52 epistasis group was identified in yeast as a group of genes required to repair DNA damaged by ionizing radiation [1]. Genetic evidence indicates that Rad52 functions in Rad51-dependent and Rad51-independent recombination pathways [2] [3] [4]. Consistent with this, purified yeast and human Rad52 proteins have been shown to promote single-strand DNA annealing [5] [6] [7] and to stimulate Rad51-mediated homologous pairing [8] [9] [10] [11]. Electron microscopic examinations of the yeast [12] and human [13] Rad52 proteins have revealed their assembly into ring-like structures in vitro. Using both conventional transmission electron microscopy and scanning transmission electron microscopy (STEM), we found that the human Rad52 protein forms heptameric rings. A three-dimensional (3D) reconstruction revealed that the heptamer has a large central channel. Like the hexameric helicases such as Escherichia coli DnaB [14] [15], bacteriophage T7 gp4b [16] [17], simian virus 40 (SV40) large T antigen [18] and papilloma virus E1 [19], the Rad52 rings show a distinctly chiral arrangement of subunits. Thus, the structures formed by the hexameric helicases may be a more general property of other proteins involved in DNA metabolism, including those, such as Rad52, that do not bind and hydrolyze ATP.

The tripartite type III secreton of Shigella flexneri inserts IpaB and IpaC into host membranes

Bacterial type III secretion systems serve to translocate proteins into eukaryotic cells, requiring a secreton and a translocator for proteins to pass the bacterial and host membranes. We used the contact hemolytic activity of Shigella flexneri to investigate its putative translocator. Hemolysis was caused by formation of a 25-A pore within the red blood cell (RBC) membrane. Of the five proteins secreted by Shigella upon activation of its type III secretion system, only the hydrophobic IpaB and IpaC were tightly associated with RBC membranes isolated after hemolysis. Ipa protein secretion and hemolysis were kinetically coupled processes. However, Ipa protein secretion in the immediate vicinity of RBCs was not sufficient to cause hemolysis in the absence of centrifugation. Centrifugation reduced the distance between bacterial and RBC membranes beyond a critical threshold. Electron microscopy analysis indicated that secretons were constitutively assembled at 37 degrees C before any host contact. They were composed of three parts: (a) an external needle, (b) a neck domain, and (c) a large proximal bulb. Secreton morphology did not change upon activation of secretion. In mutants of some genes encoding the secretion machinery the organelle was absent, whereas ipaB and ipaC mutants displayed normal secretons.

Brownian dynamics simulation of DNA condensation

DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.

DNA bending induced by the archaebacterial histone-like protein MC1

The conformational changes induced by the binding of the histone-like protein MC1 to DNA duplexes have been analyzed by dark-field electron microscopy and polyacrylamide gel electrophoresis. Visualisation of the DNA molecules by electron microscopy reveals that the binding of MC1 induces sharp kinks. Linear DNA duplexes (176 bp) which contained a preferential site located at the center were used for quantitative analysis. Measurements of the angle at the center of all duplexes, at a fixed DNA concentration, as a function of the MC1 concentration, were very well fitted by a simple model of an isotropic flexible junction and an equilibrium between the two conformations of DNA with bound or unbound MC1. This model amounts to double-folded Gaussian distributions and yields an equilibrium deflection angle of theta0=116 degrees for the DNA with bound MC1. It allowed measurements of the fraction of DNA with bound MC1 to be taken as a function of MC1 concentrations and yields an equilibrium dissociation constant of Kd=100 nM. It shows that the flexibility of DNA is reduced by the binding of MC1 and the formation of a kink. The equilibrium dissociation constant value was corroborated by gel electrophoresis. Control of the model by the computation of the reduced chi2 shows that the measurements are consistent and that electron microscopy can be used to quantify precisely the DNA deformations induced by the binding of a protein to a preferential site.

[Complementarity of microscopies in the structural analysis of DNA minicircles associated to protein MC1]

Electron microscopy of DNA, either free or complexed with ligands, allows the analysis of local conformational variations along individual molecules. Electron microscopy is unique, in that it has the capacity to determine the average behaviour of a population of molecules observed individually, and can thus provide a better appreciation of variability within the series of molecules than biophysical or biochemical methods. Very encouraging results have been obtained by cryoelectron and near-field microscopies, especially atomic force microscopy, in parallel with traditional techniques for visualizing DNA molecules adsorbed onto a support film. Differences in sample processing procedures and image formation modes render these 3 types of microscopies complementary. The torsional stress of a DNA molecule together with a local curvature induced by the protein MC1 from archaebacteria, can be detected within minicircles comprising 207 base pairs.

Architecture of native human alpha 2-macroglobulin studied by cryoelectron microscopy and three-dimensional reconstruction

The architecture of the native human alpha 2-macroglobulin was studied by cryoelectron microscopy and image processing techniques. The lip, padlock, doughnut, and four-petaled flower views of this homotetrameric proteinase inhibitor were observed in the frozen-hydrated specimen, and a new view, termed eye view, was also characterized. The present three-dimensional reconstruction demonstrates that all these electron microscope views derive from a single three-dimensional structure. The molecule is composed of two horizontal bodies and of two oblique arches, which border a large central cavity. The polymorphism and the flexibility of the native alpha 2-macroglobulin are discussed.