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.

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.

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.

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.

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.

Determination of the refractive indices of ionic liquids by ellipsometry, and their application as immersion liquids.

In principle, ionic liquids (ILs) can serve as stable and less harmful high-refractive-index liquids (n>1.60). However, detailed information on their complex refractive indices and dispersions is rare. Therefore, we determined the optical constants of six commercially available low-index ILs (n ca. 1.4) and two high-index ILs (n max. 2.38) synthesized by us utilizing spectroscopic ellipsometry. Furthermore, we tested the ILs as immersion liquids for different photonic crystals. Analysis of the optical properties of these photonic crystals after infiltration demonstrates potential applications of ILs in optofluidics and as index-matching liquids.

Kinetics of ozone decomposition in porous In2O3 monoliths.

The performance of many chemical gas-phase reactions is strongly influenced by the interaction of reactants with interfaces. Nanoporous materials, which exhibit pore diameters up to 100 nm and high specific surface areas, can be utilized to reduce the amount of cost-intensive materials (e.g. noble metals). However, due to limitations in material transport and reaction kinetics detailed knowledge of the diffusion and the kinetics of a chemical reaction is necessary to improve the performance of chemical processes in industry and research. To experimentally study the diffusion and reaction kinetics of gaseous species inside such pores, the chemoresistive behavior of certain metal oxides such as In2O3 can be utilized. In this work, we present a model system based on hierarchically porous monolithic indium oxide (In2O3) which allows the determination of kinetic effects by utilizing its gas transducing properties. The experimental data obtained by electrical measurements are compared to two diffusion and diffusion-reaction models. Using these methods, the rate constant of ozone decomposition in porous In2O3 is estimated. The results are the basis for a suitable material design for semiconducting gas sensors, on the nano-, meso- and macroscale, which helps in understanding the underlying mechanisms of diffusion and reaction.

Surface-modified CAU-10 MOF materials as humidity sensors: impedance spectroscopic study on water uptake.

Metal-organic frameworks (MOFs) are crystalline microporous materials with tunable chemical and physical properties. By combining various metal clusters with different interconnecting organic linkers, the pore structure, crystallinity, as well as the surface properties can be modified. In the present work, modification of the organic linker molecules is utilized to synthesize CAU-10 type MOFs with variable affinity of the pore surface to water. In principle, this should influence the accessibility of the pores for water vapor and therefore offer a tool to control its sorption properties. For a deeper understanding we studied the water sorption characteristics and compared the results to the conductive and dielectric properties studied by impedance spectroscopy. Spectra in a wide frequency range from 1 mHz to 1 MHz were recorded. Data analysis is performed using the Havriliak-Negami model. The MOFs are also tested as sensitive layers for capacitive humidity sensing by correlating the change in permittivity of the materials with the amount of physisorbed water. Such an MOF-based sensor was tested with respect to environmental monitoring and compared to a commonly used commercial humidity sensor.

Mesoporous materials as gas sensors.

Ordered mesoporous materials have great potential in the field of gas sensing. Today various template-assisted synthesis methods facilitate the preparation of silica (SiO2) as well as numerous metal oxides with well-defined, uniform and regular pore systems. The unique nanostructural properties of such materials are particularly useful for their application as active layers in gas sensors based on various operating principles, such as capacitive, resistive, or optical sensing. This review summarizes the basic aspects of materials synthesis, discusses some structural properties relevant in gas sensing, and gives an overview of the literature on ordered mesoporous gas sensors.

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.

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.

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.

Photoreduction of mesoporous In2O3: mechanistic model and utility in gas sensing.

A model is proposed for the drop in electronic resistance of n-type semiconducting indium oxide (In(2)O(3)) upon illumination with light (350 nm, 3.5 eV) as well as for the (light-enhanced) sensitivity of In(2)O(3) to oxidizing gases. Essential features of the model are photoreduction and a rate-limiting oxygen-diffusion step. Ordered, mesoporous In(2)O(3) with a high specific surface area serves as a versatile system for experimental studies. Analytical techniques comprise conductivity measurements under a controlled atmosphere (synthetic air, pure N(2)) and temperature-resolved in-situ Fourier transform infrared (FTIR) spectroscopy. IR measurements reveal that oxygen vacancies form a donor level 0.18 eV below the conduction band.

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 high temperature capacitive humidity sensor based on mesoporous silica.

Capacitive sensors are the most commonly used devices for the detection of humidity because they are inexpensive and the detection mechanism is very specific for humidity. However, especially for industrial processes, there is a lack of dielectrics that are stable at high temperature (>200 °C) and under harsh conditions. We present a capacitive sensor based on mesoporous silica as the dielectric in a simple sensor design based on pressed silica pellets. Investigation of the structural stability of the porous silica under simulated operating conditions as well as the influence of the pellet production will be shown. Impedance measurements demonstrate the utility of the sensor at both low (90 °C) and high (up to 210 °C) operating temperatures.

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.

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.