Yersinia entomophaga Tc toxin is released by T10SS-dependent lysis of specialized cell subpopulations.

Disease-causing bacteria secrete numerous toxins to invade and subjugate their hosts. Unlike many smaller toxins, the secretion machinery of most large toxins remains enigmatic. By combining genomic editing, proteomic profiling and cryo-electron tomography of the insect pathogen Yersinia entomophaga, we demonstrate that a specialized subset of these cells produces a complex toxin cocktail, including the nearly ribosome-sized Tc toxin YenTc, which is subsequently exported by controlled cell lysis using a transcriptionally coupled, pH-dependent type 10 secretion system (T10SS). Our results dissect the Tc toxin export process by a T10SS, identifying that T10SSs operate via a previously unknown lytic mode of action and establishing them as crucial players in the size-insensitive release of cytoplasmically folded toxins. With T10SSs directly embedded in Tc toxin operons of major pathogens, we anticipate that our findings may model an important aspect of pathogenesis in bacteria with substantial impact on agriculture and healthcare.

Structure of the native myosin filament in the relaxed cardiac sarcomere.

The thick filament is a key component of sarcomeres, the basic units of striated muscle1. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other heart and muscle diseases2. Despite the central importance of the thick filament, its molecular organization remains unclear. Here we present the molecular architecture of native cardiac sarcomeres in the relaxed state, determined by cryo-electron tomography. Our reconstruction of the thick filament reveals the three-dimensional organization of myosin, titin and myosin-binding protein C (MyBP-C). The arrangement of myosin molecules is dependent on their position along the filament, suggesting specialized capacities in terms of strain susceptibility and force generation. Three pairs of titin-α and titin-ß chains run axially along the filament, intertwining with myosin tails and probably orchestrating the length-dependent activation of the sarcomere. Notably, whereas the three titin-α chains run along the entire length of the thick filament, titin-ß chains do not. The structure also demonstrates that MyBP-C bridges thin and thick filaments, with its carboxy-terminal region binding to the myosin tails and directly stabilizing the OFF state of the myosin heads in an unforeseen manner. These results provide a foundation for future research investigating muscle disorders involving sarcomeric components.

Aurophilic Molecules on Surfaces. Part II. (NapNC)AuCl on Au(111).

Although aurophilicity is a well-known phenomenon in structural gold chemistry and is found in many crystals of Au(I) complexes, its potential for self-assembly in thin films is not yet explored. This paper is Part II of a study, in which we investigated the ultrathin film formation of chlorido(2-naphthyl isonitrile) gold(I) on gold surfaces. Here, we present the data for the growth of (NapNC)AuCl on isotropic Au(111) surfaces. Already during physical vapor deposition, the condensation of ultrathin films is monitored by photoelectron emission microscopy (PEEM) and incremental and spectrally resolved changes in the optical reflectance (DDRS). Additional structural data obtained by scanning tunneling microscopy (STM) and low-energy electron diffraction (LEED) reveal that the "crossed swords" packing motif known from the bulk is also present in thin films.

Aurophilic Molecules on Surfaces. Part I. (NapNC)AuCl on Au(110).

Aurophilicity is a well-known phenomenon in structural gold chemistry and is found in many crystals of Au(I) complexes. However, these attractive dispersion forces between and within complexes containing Au(I) moieties have not been well studied in ultrathin films. In this paper, we elucidate the interaction of chlorido(2-naphthyl isonitrile)gold(I) on and with Au(110) surfaces. Already during physical vapor deposition, the condensation of ultrathin films is monitored by photoelectron emission microscopy (PEEM) and by incremental and spectrally resolved changes in the optical reflectance (DDRS). Additional structural data obtained by STM and LEED reveal that the "crossed swords" packing motif known from the bulk is also present in thin films. The molecular arrangement changes several times during thin-film deposition.

TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining.

Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volumes are still needed. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: an open source general picking model for cryogenic-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space that separates macromolecules according to their three-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network to locate new proteins.

Accelerated 2D Classification With ISAC Using GPUs.

A widely used approach to analyze single particles in electron microscopy data is 2D classification. This process is very computationally expensive, especially when large data sets are analyzed. In this paper we present GPU ISAC, a newly developed, GPU-accelerated version of the established Iterative Stable Alignment and Clustering (ISAC) algorithm for 2D images and generating class averages. While the previously existing implementation of ISAC relied on a computer cluster, GPU ISAC enables users to produce high quality 2D class averages from large-scale data sets on a single desktop machine equipped with affordable, consumer-grade GPUs such as Nvidia GeForce GTX 1080 TI cards. With only two such cards GPU ISAC matches the performance of twelve high end cluster nodes and, using high performance GPUs, is able to produce class averages from a million particles in between six to thirteen hours, depending on data set quality and box size. We also show GPU ISAC to scale linearly in all input dimensions, and thereby capable of scaling well with the increasing data load demand of future data sets. Further user experience improvements integrate GPU ISAC seamlessly into the existing SPHIRE GUI, as well as the TranSPHIRE on-the-fly processing pipeline. It is open source and can be downloaded at https://gitlab.gwdg.de/mpi-dortmund/sphire/cuISAC/.

Attenuation of Photoelectron Emission by a Single Organic Layer.

We report an in situ study of the thin-film growth of cobalt-phthalocyanine on Ag(100) surfaces using photoelectron emission microscopy (PEEM) and the Anderson method. Based on the Fowler-DuBridge theory, we were able to correlate the evolution of the mean electron yield acquired with PEEM for coverages up to two molecular layers of cobalt-phthalocyanine to the global work function changes measured with the Anderson method. For coverages above two monolayers, the transients measured with the Anderson method and those obtained with PEEM show different trends. We exploit this discrepancy to determine the inelastic mean free path of the low-energy electrons while passing through the third layer of CoPc.

Structures from intact myofibrils reveal mechanism of thin filament regulation through nebulin.

In skeletal muscle, nebulin stabilizes and regulates the length of thin filaments, but the underlying mechanism remains nebulous. In this work, we used cryo-electron tomography and subtomogram averaging to reveal structures of native nebulin bound to thin filaments within intact sarcomeres. This in situ reconstruction provided high-resolution details of the interaction between nebulin and actin, demonstrating the stabilizing role of nebulin. Myosin bound to the thin filaments exhibited different conformations of the neck domain, highlighting its inherent structural variability in muscle. Unexpectedly, nebulin did not interact with myosin or tropomyosin, but it did interact with a troponin T linker through two potential binding motifs on nebulin, explaining its regulatory role. Our structures support the role of nebulin as a thin filament "molecular ruler" and provide a molecular basis for studying nemaline myopathies.

A trigonal coordination of Au(I) phosphane complexes stabilized by O-H ⋯ X (X = Cl-, Br-, I-) interactions.

In this work, we show that intramolecular hydrogen bonding can be used to stabilize tri-coordinated phosphane-gold(I) complexes. Two molecular structures of 2-(diphenylphosphino)benzoic acid (L) coordinated to a gold(I) atom were determined by single-crystal X-ray diffraction. The linear L-Au-Br shows a standard linear coordination and dimerizes via hydrogen bonds of the carboxylic acid. Upon addition of two additional phosphane ligands the complex [L3Au]X is formed which is stabilized by three intramolecular -C(O)O-H … X hydrogen bonds as proven by the X-ray structure of the respective chlorido-complex. X-ray powder diffractograms suggest the same structure also for X- = Br- and I-. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00706-021-02843-2.

The molecular basis for sarcomere organization in vertebrate skeletal muscle.

Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we determine the molecular architecture of native vertebrate skeletal sarcomeres by electron cryo-tomography. Our reconstruction reveals molecular details of the three-dimensional organization and interaction of actin and myosin in the A-band, I-band, and Z-disc and demonstrates that α-actinin cross-links antiparallel actin filaments by forming doublets with 6-nm spacing. Structures of myosin, tropomyosin, and actin at ~10 Å further reveal two conformations of the "double-head" myosin, where the flexible orientation of the lever arm and light chains enable myosin not only to interact with the same actin filament, but also to split between two actin filaments. Our results provide unexpected insights into the fundamental organization of vertebrate skeletal muscle and serve as a strong foundation for future investigations of muscle diseases.

Standard deviation of microscopy images used as indicator for growth stages.

Photoelectron emission microscopy (PEEM) and low energy electron microscopy (LEEM) can easily distinguish between organic molecules adsorbed in crystallites or in the wetting layers as well as the bare metal substrate due to their different electronic properties. Already before (and during) the condensation of such solid phases (2D islands or 3D crystallites), there is a dilute 2D gas phase. Such a 2D gas phase consists of molecules, which are highly mobile and diffuse across the surface. The individual molecules are too small to be resolved in PEEM/LEEM images. Here, we discuss, how image features below and above the resolution limit of a PEEM/LEEM affect the mean electron yield and its (normalized) standard deviation. We support our findings with two experimental examples: the deposition of cobalt phthalocyanine (CoPc) on Ag(100) and of perfluoro-pentacene on Ag(110). Our results demonstrate, how a spatial and temporal analysis of image series can be used to obtain information about molecular phases, which cannot be directly resolved in microscopy images.

TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM.

Single particle cryo-EM requires full automation to allow high-throughput structure determination. Although software packages exist where parts of the cryo-EM pipeline are automated, a complete solution that offers reliable on-the-fly processing, resulting in high-resolution structures, does not exist. Here we present TranSPHIRE: A software package for fully-automated processing of cryo-EM datasets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering, and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its picking model to adapt to any given data set live during processing. This elegant approach enables TranSPHIRE to process data more effectively, producing high-quality particle stacks. TranSPHIRE collects and displays all metrics and microscope settings to allow users to quickly evaluate data during acquisition. TranSPHIRE can run on a single work station and also includes the automated processing of filaments.

Recombination mechanisms of luminescence type gas sensors.

Luminescence type gas sensors based on organic luminophores are characterized by an excellent signal stability over the luminophores' lifetime. Even though the sensing material is prone to degradation due to photobleaching, evaluation of the dynamic optical response allows to minimize aging induced drift effects of the luminophore and the optoelectronic components. The gas dependent luminophore decay time is mostly independent of the excitation intensity, which is attributed to the monomolecular recombination in many organic luminophores. To improve the overall sensor lifetime and to utilize this luminescence based sensor concept for long-term sensing applications, new luminophores are needed. Potential candidates are inorganic, semiconducting materials, which, however, show more complex recombination behaviour than the organic luminophores mentioned before, involving also bimolecular recombination. In the scope of this work, the differences of mono- and bimolecular recombination are discussed by the use of a simple statistical model. The theoretical aspects are furthermore confirmed by dynamic luminescence measurements on manganese doped zinc sulfide (ZnS). The semiconducting ZnS is an oxygen sensitive luminophore, which shows both, mono- and bimolecular recombination, depending on the excitation energy.

Two particle-picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER.

Structure determination of filamentous molecular complexes involves the selection of filaments from cryo-EM micrographs. The automatic selection of helical specimens is particularly difficult, and thus many challenging samples with issues such as contamination or aggregation are still manually picked. Here, two approaches for selecting filamentous complexes are presented: one uses a trained deep neural network to identify the filaments and is integrated in SPHIRE-crYOLO, while the other, called SPHIRE-STRIPER, is based on a classical line-detection approach. The advantage of the crYOLO-based procedure is that it performs accurately on very challenging data sets and selects filaments with high accuracy. Although STRIPER is less precise, the user benefits from less intervention, since in contrast to crYOLO, STRIPER does not require training. The performance of both procedures on Tobacco mosaic virus and filamentous F-actin data sets is described to demonstrate the robustness of each method.

Proton Conduction in a Single Crystal of a Phosphonato-Sulfonate-Based Coordination Polymer: Mechanistic Insight.

The proton conduction properties of a phosphonato-sulfonate-based coordination polymer are studied by impedance spectroscopy using a single crystal specimen. Two distinct conduction mechanisms are identified. Water-mediated conductance along the crystal surface occurs by mass transport, as evidenced by a high activation energy (0.54 eV). In addition, intrinsic conduction by proton 'hopping' through the interior of the crystal with a low activation energy (0.31 eV) is observed. This latter conduction is anisotropic with respect to the crystal structure and seems to occur through a channel along the c axis of the orthorhombic crystal. Proton conduction is assumed to be mediated by sulfonate groups and non-coordinating water molecules that are part of the crystal structure.

Cellulose Nanocrystal-Templated Tin Dioxide Thin Films for Gas Sensing.

Porous tin dioxide is an important low-cost semiconductor applied in electronics, gas sensors, and biosensors. Here, we present a versatile template-assisted synthesis of nanostructured tin dioxide thin films using cellulose nanocrystals (CNCs). We demonstrate that the structural features of CNC-templated tin dioxide films strongly depend on the precursor composition. The precursor properties were studied by using low-temperature nuclear magnetic resonance spectroscopy of tin tetrachloride in solution. We demonstrate that it is possible to optimize the precursor conditions to obtain homogeneous precursor mixtures and therefore highly porous thin films with pore dimensions in the range of 10-20 nm (ABET = 46-64 m2 g-1, measured on powder). Finally, by exploiting the high surface area of the material, we developed a resistive gas sensor based on CNC-templated tin dioxide. The sensor shows high sensitivity to carbon monoxide (CO) in ppm concentrations and low cross-sensitivity to humidity. Most importantly, the sensing kinetics are remarkably fast; both the response to the analyte gas and the signal decay after gas exposure occur within a few seconds, faster than in standard SnO2-based CO sensors. This is attributed to the high gas accessibility of the very thin porous film.

Aggregation of Au(i)-complexes on amorphous substrates governed by aurophilicity.

In single crystals of 2-naphthylisonitrile-gold(i)-halide (halide = Cl, Br, I) complexes, AuAu distances are found to be significantly shorter than twice the van der Waals radius, indicating attractive interactions between gold atoms in adjacent molecules. In the particular case of the studied 2-naphthylisonitrile-gold(i) complexes, homodimers are the common structural motifs, in which the linearly coordinated gold exhibits a crossed swords arrangement with the Au atoms of two molecules being at the intersection point. The crossed swords motif is preserved upon physical vapour deposition of both the chlorine and bromine derivatives on amorphous substrates like glass and glassy carbon. The determined activation energies of desorption for the chlorine (0.9 eV) and the bromine (1.2 eV) derivative are comparable to that of unsubstituted naphthalene. Using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and ion scattering (RBS), we confirmed the chemical integrity of the molecules in thin films and revealed the orientation of the crossed swords dimers with respect to the substrate surface.

Evaluation of a TEM based Approach for Size Measurement of Particulate (Nano)materials.

An approach for the size measurement of particulate (nano)materials by transmission electron microscopy was evaluated. The approach combines standard operating procedures for specimen preparation, imaging, and image analysis, and it was evaluated on a series of certified reference materials and representative test materials with varying physical properties, including particle size, shape, and agglomeration state. The measurement of the median value of the minimal external particle diameter distribution was intra-laboratory validated. The validation study included an assessment of the limit of detection, working range, selectivity, precision, trueness, robustness, and ruggedness. An uncertainty that was associated to intermediate precision in the range of 1-7% and an expanded measurement uncertainty in the range of 7-20% were obtained, depending on the material and image analysis mode. No bias was observed when assessing the trueness of the approach on the certified reference materials ERM-FD100 and ERM-FD304. The image analysis method was validated in an inter-laboratory study by 19 laboratories, which resulted in a within-laboratory precision in the range of 2-8% and a between-laboratory precision of between 2% and 14%. The automation and standardization of the proposed approach significantly improves labour and cost efficiency for the accurate and precise size measurement of the particulate materials. The approach is shown to be implementable in many other electron microscopy laboratories.

SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM.

Selecting particles from digital micrographs is an essential step in single-particle electron cryomicroscopy (cryo-EM). As manual selection of complete datasets-typically comprising thousands of particles-is a tedious and time-consuming process, numerous automatic particle pickers have been developed. However, non-ideal datasets pose a challenge to particle picking. Here we present the particle picking software crYOLO which is based on the deep-learning object detection system You Only Look Once (YOLO). After training the network with 200-2500 particles per dataset it automatically recognizes particles with high recall and precision while reaching a speed of up to five micrographs per second. Further, we present a general crYOLO network able to pick from previously unseen datasets, allowing for completely automated on-the-fly cryo-EM data preprocessing during data acquisition. crYOLO is available as a standalone program under http://sphire.mpg.de/ and is distributed as part of the image processing workflow in SPHIRE.