Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL

X-ray imaging of virus particles at the European XFEL could eventually allow their complete structures to be solved, potentially approaching the resolution of other structural virology methods. To achieve this ambitious goal with today's technologies, about 1 ml of purified virus suspension containing at least 1012 particles per millilitre is required. Such large amounts of concentrated suspension have never before been obtained for enveloped viruses. Tick-borne encephalitis virus (TBEV) represents an attractive model system for the development of enveloped virus purification and concentration protocols, given the availability of large amounts of inactivated virus material provided by vaccine-manufacturing facilities. Here, the development of a TBEV vaccine purification and concentration scheme is presented combined with a quality-control protocol that allows substantial amounts of highly concentrated non-aggregated suspension to be obtained. Preliminary single-particle imaging experiments were performed for this sample at the European XFEL, showing distinct diffraction patterns.

Permeation of Nanoparticles into Pulmonary Surfactant Monolayer: In Situ X-ray Standing Wave Studies

High-resolution X-ray techniques were applied to examine the effects of gold nanoparticles (size <5 nm) on natural pulmonary surfactant and pure DPPC monolayers preliminarily formed on water subphase in a Langmuir trough. Hydrophobic and hydrophilic nanoparticles were delivered from nanoaerosol using electrodeposition method. Grazing incidence diffraction, X-ray reflectivity, and X-ray standing wave measurements allow to monitor the changes in molecular organization of lipid monolayer and to locate the position of gold nanoparticles. X-ray experiments were performed over a period of 9-14 h. The obtained results evidenced that, on a long time scale, the deposition of nanoparticles, even at low doses, can induce pronounced alterations in lipid monolayer. The presented data can help to elucidate the mechanism of pulmonary translocation of inhaled nanoparticles that is of special interest for biomedical investigations of potential risk of nanoaerosols for human health.

Disturbance in Mammalian Cognition Caused by Accumulation of Silver in Brain

The influence of daily prolonged administration of silver nanoparticles on the cognitive functions of a model mammal was studied. The accumulation of silver in the whole brain and the hippocampus, cerebellum, cortex and residual brain tissue of the mouse was investigated by highly precise and representative neutron activation analysis, and histological studies were conducted. Here, we show that long-term memory impairments were caused by the accumulation of silver nanoparticles in the brain and its subregions, such as the hippocampus, cerebellum and cortex, in a step-like manner by disturbance of hippocampal cell integrity. Three different approaches allowed us to observe this phenomenon and discover the reasons it occurred.

Necessary conditions for STDP-based pattern recognition learning in a memristive spiking neural network

This work is aimed to study experimental and theoretical approaches for searching effective local training rules for unsupervised pattern recognition by high-performance memristor-based Spiking Neural Networks (SNNs). First, the possibility of weight change using Spike-Timing-Dependent Plasticity (STDP) is demonstrated with a pair of hardware analog neurons connected through a (CoFeB)_x(LiNbO₃)_1-x nanocomposite memristor. Next, the learning convergence to a solution of binary clusterization task is analyzed in a wide range of memristive STDP parameters for a single-layer fully connected feedforward SNN. The memristive STDP behavior supplying convergence in this simple task is shown also to provide it in the handwritten digit recognition domain by the more complex SNN architecture with a Winner-Take-All competition between neurons. To investigate basic conditions necessary for training convergence, an original probabilistic generative model of a rate-based single-layer network with independent or competing neurons is built and thoroughly analyzed. The main result is a statement of "correlation growth-anticorrelation decay" principle which prompts near-optimal policy to configure model parameters. This principle is in line with requiring the binary clusterization convergence which can be defined as the necessary condition for optimal learning and used as the simple benchmark for tuning parameters of various neural network realizations with population-rate information coding. At last, a heuristic algorithm is described to experimentally find out the convergence conditions in a memristive SNN, including robustness to a device variability. Due to the generality of the proposed approach, it can be applied to a wide range of memristors and neurons of software- or hardware-based rate-coding single-layer SNNs when searching for local rules that ensure their unsupervised learning convergence in a pattern recognition task domain.

Synchrotron radiation diffraction in a single crystal of paratellurite investigated with a new experimental scheme

First results are presented for synchrotron radiation diffraction in a paratellurite (TeO₂) single crystal investigated with a new experimental scheme consisting of a standard monochromator and a relatively narrow slit for collimation and monochromatization of an incident beam. The Bragg case reflection geometry is used. The monochromator, a pair of Si crystals, maintains the initial direction of the beam propagation. The theory is developed for a precise description of the instrumental function in such a scheme. A new rocking curve registration technique with use of an adaptive bending piezoactuator is applied for the first time with the aim to record the narrow diffraction peaks with high accuracy. A sample is attached to one edge of the bidomain lithium niobate single crystal piezoactuator used. The piezoactuator is bent under the influence of an electric field and it changes the angular position of the sample with a very small step. The experimental curves are compared with the calculated diffraction rocking curves of a perfect paratellurite crystal, both the theoretical one and the one calculated taking into account the instrumental function. An instrumental function account allows a complete coincidence of the simulated curves with the experimental results to be obtained if the experimental curve does not coincide with the theoretical rocking curve. A small discrepancy between the theory and the experimental data has been discovered in cases where the incident beam is sufficiently collimated and monochromated. This indicates the presence of a certain number of lattice defects in the sample under study.

Self-adaptive STDP-based learning of a spiking neuron with nanocomposite memristive weights

Neuromorphic systems consisting of artificial neurons and memristive synapses could provide a much better performance and a significantly more energy-efficient approach to the implementation of different types of neural network algorithms than traditional hardware with the Von-Neumann architecture. However, the memristive weight adjustment in the formal neuromorphic networks by the standard back-propagation techniques suffers from poor device-to-device reproducibility. One of the most promising approaches to overcome this problem is to use local learning rules for spiking neuromorphic architectures which potentially could be adaptive to the variability issue mentioned above. Different kinds of local rules for learning spiking systems are mostly realized on a bio-inspired spike-time-dependent plasticity (STDP) mechanism, which is an improved type of classical Hebbian learning. Whereas the STDP-like mechanism has already been shown to emerge naturally in memristive devices, the demonstration of its self-adaptive learning property, potentially overcoming the variability problem, is more challenging and has yet to be reported. Here we experimentally demonstrate an STDP-based learning protocol that ensures self-adaptation of the memristor resistive states, after only a very few spikes, and makes the plasticity sensitive only to the input signal configuration, but neither to the initial state of the devices nor their device-to-device variability. Then, it is shown that the self-adaptive learning of a spiking neuron with memristive weights on rate-coded patterns could also be realized with hardware-based STDP rules. The experiments have been carried out with nanocomposite-based (Co₄₀Fe₄₀B₂₀) _х (LiNbO_3-y )_100-х memristive structures, but their results are believed to be applicable to a wide range of memristive devices. All the experimental data were supported and extended by numerical simulations. There is a hope that the obtained results pave the way for building up reliable spiking neuromorphic systems composed of partially unreliable analog memristive elements, with a more complex architecture and the capability of unsupervised learning.

Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin

Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins. Here, we solved the symmetry-free cryo-EM structures of a single-ring chaperonin encoded by the gene 246 of bacteriophage OBP Pseudomonas fluorescens, in the nucleotide-free, ATPγS-, and ADP-bound states, with resolutions of 4.3 Å, 5.0 Å, and 6 Å, respectively. The structure of OBP chaperonin reveals a unique subunit arrangement, with three pairs of subunits and one unpaired subunit. Each pair combines subunits in two possible conformations, differing in nucleotide-binding affinity. The binding of nucleotides results in the increase of subunits' conformational variability. Due to its unique structural and functional features, OBP chaperonin can represent a new group.

The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme

The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl₂ and CuCl₂) as precipitants and the three-dimensional structures were determined at 1.35 Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu⁺², Ni⁺² and Na⁺¹ cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.Communicated by Ramaswamy H. Sarma.

The Enhancement of Metal-Binding Properties in Hemoglobin: The Role of Mild Damaging Factors

X-ray studies revealed the considerable enhancement of metal-binding properties in human hemoglobin under exposure to mild damaging factors (in the presence of 0.09 M urea or upon heating for 30 min at 50 °C). Changes in the element composition of the hemoglobin monolayer, formed on the water subphase in the Langmuir trough, have been monitored in real time by the total external reflection X-ray fluorescence measurements. X-ray absorption spectroscopy has been applied to study the local environment of zinc ions bound on hemoglobin molecules. According to these data, each zinc ion is coordinated by four ligands, two of which are cysteine and histidine. The oxidative stress has been found to accelerate extensively the enhancement of metal-binding ability in protein. A two-stage mechanism has been proposed as a possible explanation of the observed phenomenon: First, in the presence of the mild damaging agents, protein molecules can undergo a transition from the native conformation to a more labile intermediate state that increases the accessibility of amino acid residues (in particular cysteine). At the second stage, oxidation of cysteine and the subsequent activation of cysteine SH groups can affect markedly the protein-metal interaction. The presented investigations provide a deeper insight into the pathogenesis of metabolic disorders that excessive concentrations of the endogenic toxicants might trigger in an organism.

Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium Thermobaculum terrenum by small-angle X-ray scattering

The pre-crystallization solution of the transaminase from Thermobaculum terrenum (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric composition of the protein were observed after the addition of the precipitant. Comparison of the observed oligomers with the crystal structure of TaTT (PDB ID 6GKR) shows that dodecamers may act as building blocks in the growth of transaminase single crystals. Correlating of these results to the similar X-ray studies of other proteins suggests that SAXS may be a valuable tool for searching optimum crystallization conditions. AbbreviationSAXSsmall-angle X-ray scatteringTatransaminaseTaTTtransaminase from Thermobaculum terrenumPLPpyridoxal-5'-phosphateR-PEAR-(þ)-1-phenylethylamineBCATbranched-chain amino acid aminotransferaseDAATD-aminoacid aminotransferaseR-TAR-amine:pyruvate transaminaseCommunicated by Ramaswamy H. Sarma.

Octamer formation in lysozyme solutions at the initial crystallization stage detected by small-angle neutron scattering

Solutions of lysozyme in heavy water were studied by small-angle neutron scattering (SANS) at concentrations of 40, 20 and 10 mg ml^-1 with and without the addition of precipitant, and at temperatures of 10, 20 and 30°C. In addition to the expected protein monomers, dimeric and octameric species were identified in solutions at the maximum concentration and close to the optimal conditions for crystallization. An optimal temperature for octamer formation was identified and both deviation from this temperature and a reduction in protein concentration led to a significant decrease in the volume fractions of octamers detected. In the absence of precipitant, only monomers and a minor fraction of dimers are present in solution.

Cytochrome c Complexes with Cardiolipin Monolayer Formed under Different Surface Pressure

The formation of the complex of cytochrome c (Cytc) with a phospholipid cardiolipin (CL) in mitochondria is a crucial event in apoptosis development. There are two viewpoints on the structure of the complex. (1) Cytc is bound on the surface of the lipid bilayer. (2) The complex is a hydrophobic nanoparticle Cytc-CL formed by Cytc molten globule, covered by CL monolayer.1 In the present work, we attempted to bridge the gap between these two structures. We investigated the interaction between Cytc and Langmuir monolayers of CL. The surface pressure increase during incorporation of Cytc into CL monolayer obeys the equation: π = π0 + Δπ∞[1 - exp(-βt)], where β is pseudo-first-order rate constant of Cytc binding, directly proportional to the initial Cytc concentration c0. Parameters Δπ∞ and the rate β measured in different conditions were virtually equal for natural bovine CL and peroxidation-resistant tetraoleoyl CL in all experiments. Surface area-surface pressure isotherms of Cytc alone and in combination with a CL monolayer were similar in shape. Apparently, the protein exposes hydrophilic groups to the water phase and hydrophobic to the air or to the hydrocarbon chains of CL. The 30% ethanol dramatically accelerated the adsorption of Cytc on the water surface. The protein-lipid surface films showed, in compression-expansion cycles, that hysteresis loops were observed always when Cytc present, reproducible in repeating cycles. Taken together, our data show that when incorporated in a lipid monolayer or after adsorption on the water-air interface, Cytc undergoes conformational transition. In that, one part of the globule sphere becomes predominantly hydrophobic and the other, hydrophilic and charged ("stratified" Cytc). We hypothesize that in CL-containing bilayer membranes, Cytc incorporation into the lipid monolayer would result in membrane folding with subsequent formation of either catalytically reactive "bubbles" inside the bilayer, formed by Cytc-CL, or the appearance of hydrophilic pores. The role of lipid peroxidation catalyzed by Cytc-CL in the appearance of pores and apoptosis is also discussed.

High-synconformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures ofShewanella oneidensisMR-1 uridine phosphorylase in the free form and in complex with uridine

Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Expression of UP fromShewanella oneidensisMR-1 (SoUP) was performed inEscherichia coli. The high-resolution X-ray structure of SoUP was solved in the free form and in complex with uridine. A crystal of SoUP in the free form was grown under microgravity and diffracted to ultrahigh resolution. Both forms of SoUP contained sulfate instead of phosphate in the active site owing to the presence of ammonium sulfate in the crystallization solution. The latter can be considered as a good mimic of phosphate. In the complex, uridine adopts a high-synconformation with a nearly planar ribose ring and is present only in one subunit of the hexamer. A comparison of the structures of SoUP in the free form and in complex with the natural substrate uridine showed that the subunits of the hexamer are not identical, with the active sites having either an open or a closed conformation. In the monomers with the closed conformation, the active sites in which uridine is absent contain a glycerol molecule mimicking the ribose moiety of uridine.

CaCO₃ vaterite microparticles for biomedical and personal care applications

Among the polymorph modifications of calcium carbonate, the metastable vaterite is the most practically important. Vaterite particles are applied in regenerative medicine, drug delivery and a broad range of personal care products. This manuscript scopes to review the mechanism of the calcium carbonate crystal growth highlighting the factors stabilizing the vaterite polymorph in the most cost efficient synthesis routine. The size of vaterite particles is a crucial parameter for practical applications. The options for tuning the particle size are also discussed.

ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain

DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 Å shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.

Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus

DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential to maintain the integrity of the genome in DNA replication, recombination and repair. A recombinant ATP-dependent DNA ligase from the hyperthermophilic anaerobic archaeon Thermococcus sibiricus was expressed in Escherichia coli and purified. Crystals were grown by vapour diffusion using the hanging-drop method with 17%(w/v) PEG 4000 and 8.5%(v/v) 2-propanol as precipitants. A diffraction experiment was performed with a single crystal, which diffracted X-rays to 3.0 Å resolution. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.590, b = 87.540, c = 126.300 Å.

Expression, purification and crystallization of a thermostable short-chain alcohol dehydrogenase from the archaeon Thermococcus sibiricus

Alcohol dehydrogenases belong to the oxidoreductase family and play an important role in a broad range of physiological processes. They catalyze the cofactor-dependent reversible oxidation of alcohols to the corresponding aldehydes or ketones. The NADP-dependent short-chain alcohol dehydrogenase TsAdh319 from the thermophilic archaeon Thermococcus sibiricus was overexpressed, purified and crystallized. Crystals were obtained using the hanging-drop vapour-diffusion method using 25%(w/v) polyethylene glycol 3350 pH 7.5 as precipitant. The crystals diffracted to 1.68 A resolution and belonged to space group I222, with unit-cell parameters a = 55.63, b = 83.25, c = 120.75 A.

Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed

KillerRed is the only known fluorescent protein that demonstrates notable phototoxicity, exceeding that of the other green and red fluorescent proteins by at least 1,000-fold. KillerRed could serve as an instrument to inactivate target proteins or to kill cell populations in photodynamic therapy. However, the nature of KillerRed phototoxicity has remained unclear, impeding the development of more phototoxic variants. Here we present the results of a high resolution crystallographic study of KillerRed in the active fluorescent and in the photobleached non-fluorescent states. A unique and striking feature of the structure is a water-filled channel reaching the chromophore area from the end cap of the beta-barrel that is probably one of the key structural features responsible for phototoxicity. A study of the structure-function relationship of KillerRed, supported by structure-based, site-directed mutagenesis, has also revealed the key residues most likely responsible for the phototoxic effect. In particular, Glu(68) and Ser(119), located adjacent to the chromophore, have been assigned as the primary trigger of the reaction chain.

Overexpression, purification and crystallization of a thermostable DNA ligase from the archaeon Thermococcus sp. 1519

DNA ligases catalyze the sealing of 5'-phosphate and 3'-hydroxyl termini at single-strand breaks in double-stranded DNA and their function is essential to maintain the integrity of the genome in DNA metabolism. An ATP-dependent DNA ligase from the archaeon Thermococcus sp. 1519 was overexpressed, purified and crystallized. Crystals were obtained using the hanging-drop vapour-diffusion method employing 35%(v/v) Tacsimate pH 7.0 as a precipitant and diffracted X-rays to 3.09 A resolution. They belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 79.7, c = 182.6 A.

On the off-Bragg reflectivity enhancement in dynamical multiple diffraction of X-rays by an In(0.5)Ga(0.5)P/GaAs heteroepitaxial structure

The effect of dynamical interactions between reflections involved in 000/111/220 multiple diffraction by an In(0.5)Ga(0.5)P/GaAs heteroepitaxial structure was observed, which significantly increases the intensity of the (111) reflection in the region of the total (220) reflection from the substrate during Renninger-like scanning. The amplitude of the peak is roughly five times as great as the peak of detoured excitation for ideal GaAs. Possible applications of the observed feature in synchrotron-radiation-based studies are discussed.