Beyond Dimerization: Harnessing Tetrameric Coiled-Coils for Nanostructure Assembly.

Versatile DNA and polypeptide-based structures have been designed based on complementary modules. However, polypeptides can also form higher oligomeric states. We investigated the introduction of tetrameric modules as a substitute for coiled-coil dimerization units used in previous modular nanostructures.

: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing.

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are becoming the preferred methodologies for investigating subcellular and macromolecular structures in native or near-native environments. Although cryo-ET is amenable to a wide range of biological problems, these problems often have data-processing requirements that need to be individually optimized, precluding the notion of a one-size-fits-all processing pipeline. Cryo-ET data processing is also becoming progressively more complex due to the increasing number of packages for each processing step.

Critical Evaluation of Childs Method for the NMR Spectroscopic Scaling of Effective Lewis Acidity: Limitations and Resolution of Earlier Discrepancies.

Quantifying Lewis acidity is essential for understanding and optimizing the performance of Lewis acids in diverse applications. Next to the widely accepted Gutmann-Beckett (GB) method, using triethyl phosphine oxide (TEPO) as a probe, the Childs method-employing trans-crotonaldehyde (TCA)-gained attention as an NMR-based technique for measuring effective Lewis acidity (eLA). Despite its steady use, the robustness of Childs method and its correlation with other measures remain underexplored.

Serialized on-grid lift-in sectioning for tomography (SOLIST) enables a biopsy at the nanoscale.

Cryo-focused ion beam milling has substantially advanced our understanding of molecular processes by opening windows into cells. However, applying this technique to complex samples, such as tissues, has presented considerable technical challenges. Here we introduce an innovative adaptation of the cryo-lift-out technique, serialized on-grid lift-in sectioning for tomography (SOLIST), addressing these limitations.

A Benchmark Study of DFT-Computed p-Block Element Lewis Pair Formation Enthalpies Against Experimental Calorimetric Data.

The quantification of Lewis acidity is of fundamental and applied importance in chemistry. While the computed fluoride ion affinity (FIA) is the most widely accepted thermodynamic metric, only sparse experimental values exist. Accordingly, a benchmark of methods for computing Lewis pair formation enthalpies, also with a broader set of Lewis bases against experimental data, is missing.

TOMOMAN: a software package for large scale cryo-electron tomography data preprocessing, community data sharing, and collaborative computing.

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are becoming the preferred methodologies for investigating subcellular and macromolecular structures in native or near-native environments. While cryo-ET is amenable to a wide range of biological problems, these problems often have data processing requirements that need to be individually optimized, precluding the notion of a one-size-fits-all processing pipeline. Cryo-ET data processing is also becoming progressively more complex due to an increasing number of packages for each processing step.

How to Deal with Charge in the Ranking of Lewis Acidity: Critical Evaluation of an Extensive Set of Cationic Lewis Acids.

The quantification of Lewis acidity is of fundamental and applied importance in chemistry. However, if neutral and charged Lewis acids are compared, a coherent ranking has been elusive, and severe uncertainties were accepted. With this study, we present a systematic computational analysis of Lewis base affinities of 784 mono-, di- and tricationic Lewis acids and their comparison with 149 representative neutral Lewis acids.

Predicting Lewis Acidity: Machine Learning the Fluoride Ion Affinity of p-Block-Atom-Based Molecules.

"How strong is this Lewis acid?" is a question researchers often approach by calculating its fluoride ion affinity (FIA) with quantum chemistry. Here, we present FIA49k, an extensive FIA dataset with 48,986 data points calculated at the RI-DSD-BLYP-D3(BJ)/def2-QZVPP//PBEh-3c level of theory, including 13 different p-block atoms as the fluoride accepting site. The FIA49k dataset was used to train FIA-GNN, two message-passing graph neural networks, which predict gas and solution phase FIA values of molecules excluded from training with a mean absolute error of 14 kJ mol (r=0.

Pharmaceutical Interventions for Inpatients with Liver Cirrhosis and Liver Transplantation: A Systematic Review of Experimental Studies.

Liver cirrhosis, which is considered one of the leading causes of death in the world, can lead to severe complications, and is often followed by a liver transplantation. These patients take an average of nine medications daily. If not managed adequately, it can be accompanied by serious drug-related problems.

Recent advances in plant endomembrane research and new microscopical techniques.

The endomembrane system consists of various membrane-bound organelles including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN), endosomes, and the lysosome/vacuole. Membrane trafficking between distinct compartments is mainly achieved by vesicular transport. As the endomembrane compartments and the machineries regulating the membrane trafficking are largely conserved across all eukaryotes, our current knowledge on organelle biogenesis and endomembrane trafficking in plants has mainly been shaped by corresponding studies in mammals and yeast.

Trialkoxysilane Exchange: Scope, Mechanism, Cryptates and pH-Response.

The dynamic covalent chemistry (DCvC) of the Si-O bond holds unique opportunities, but has rarely been employed to assemble discrete molecular architectures. This may be due to the harsh conditions required to initiate exchange reactions at silicon in aprotic solvents. Herein, we provide a comprehensive experimental and computational account on the reaction of trialkoxysilanes with alcohols and identify mild conditions for rapid exchange in aprotic solvents.

Multishot tomography for high-resolution in situ subtomogram averaging.

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.

In situ structural analysis reveals membrane shape transitions during autophagosome formation.

Autophagosomes are unique organelles that form de novo as double-membrane vesicles engulfing cytosolic material for destruction. Their biogenesis involves membrane transformations of distinctly shaped intermediates whose ultrastructure is poorly understood. Here, we combine cell biology, correlative cryo-electron tomography (cryo-ET), and extensive data analysis to reveal the step-by-step structural progression of autophagosome biogenesis at high resolution directly within yeast cells.

In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains.

The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the entry of large intraflagellar transport (IFT) trains, which carry cargo proteins required for ciliary assembly and maintenance. However, the native architecture of the ciliary base and the process of IFT train assembly remain unresolved.

Synthesis and Characterization of Hypercoordinated Silicon Anions: Catching Intermediates of Lewis Base Catalysis.

Anionic hypercoordinated silicates with weak donors were proposed as key intermediates in numerous silicon-based reactions. However, their short-lived nature rendered even spectroscopic observations highly challenging. Here, we characterize hypercoordinated silicon anions, including the first bromido-, iodido-, formato-, acetato-, triflato- and sulfato-silicates.

What Distinguishes the Strength and the Effect of a Lewis Acid: Analysis of the Gutmann-Beckett Method.

IUPAC defines Lewis acidity as the thermodynamic tendency for Lewis pair formation. This strength property was recently specified as global Lewis acidity (gLA), and is gauged for example by the fluoride ion affinity. Experimentally, Lewis acidity is usually evaluated by the effect on a bound molecule, such as the induced P NMR shift of triethylphosphine oxide in the Gutmann-Beckett (GB) method.

Sample Preparation by 3D-Correlative Focused Ion Beam Milling for High-Resolution Cryo-Electron Tomography.

Cryo-electron tomography (cryo-ET) has become the method of choice for investigating cellular ultrastructure and molecular complexes in their native, frozen-hydrated state. However, cryo-ET requires that samples are thin enough to not scatter or block the incident electron beam. For thick cellular samples, this can be achieved by cryo-focused ion beam (FIB) milling.

In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli.

Ribosomes comprise a large (LSU) and a small subunit (SSU) which are synthesized independently in the nucleolus before being exported into the cytoplasm, where they assemble into functional ribosomes. Individual maturation steps have been analyzed in detail using biochemical methods, light microscopy and conventional electron microscopy (EM). In recent years, single particle analysis (SPA) has yielded molecular resolution structures of several pre-ribosomal intermediates.

Autophagy ENDing unproductive phase-separated endocytic protein deposits.

Selective disposal of a wide range of cellular entities by macroautophagy/autophagy is achieved through a special class of proteins called autophagy receptors, which link corresponding cargo to the membrane-bound autophagosomal protein Atg8/LC3. In pursuit of novel autophagy receptors and their cargo, we uncovered a previously undescribed autophagy pathway for removal of aberrant clathrin-mediated endocytosis (CME) protein condensates in . Of these CME proteins, Ede1 functions as an autophagy receptor, harboring distinct Atg8-binding domains and driving phase separation into condensates.

A streamlined workflow for automated cryo focused ion beam milling.

Cryo-electron tomography (cryo-ET) is an emerging technique to study the cellular architecture and the structure of proteins at high resolution in situ. Most biological specimens are too thick to be directly investigated and are therefore thinned by milling with a focused ion beam under cryogenic conditions (cryo-FIB). This procedure is prone to contaminations, which makes it a tedious process, often leading to suboptimal results.

Membrane imaging in the plant endomembrane system.

Recent studies on membrane imaging in the plant endomembrane system by 2-D/3-D CLSM and TEM provide future perspectives of whole-cell ET and cryo-FIB-aided cryo-ET analysis.

Multidimensional Lewis Acidity: A Consistent Data Set of Chloride, Hydride, Methide, Water and Ammonia Affinities for 183 p-Block Element Lewis Acids.

The computed fluoride ion affinity (FIA) is a widely applied descriptor to gauge Lewis acidity. Like every other single-parameter Lewis acidity scale, the FIA metric suffers from the one-dimensionality, that prohibits addressing Lewis acidity by the multidimensionality it inherently requires (i. e.

A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits.

Autophagy eliminates cytoplasmic content selected by autophagy receptors, which link cargo to the membrane-bound autophagosomal ubiquitin-like protein Atg8/LC3. Here, we report a selective autophagy pathway for protein condensates formed by endocytic proteins in yeast. In this pathway, the endocytic protein Ede1 functions as a selective autophagy receptor.

Architecture of the centriole cartwheel-containing region revealed by cryo-electron tomography.

Centrioles are evolutionarily conserved barrels of microtubule triplets that form the core of the centrosome and the base of the cilium. While the crucial role of the proximal region in centriole biogenesis has been well documented, its native architecture and evolutionary conservation remain relatively unexplored. Here, using cryo-electron tomography of centrioles from four evolutionarily distant species, we report on the architectural diversity of the centriole's proximal cartwheel-bearing region.