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-1 (r2=0.93) from the SMILES string of the Lewis acid as the only input. The level of accuracy is notable, given the wide energetic range of 750 kJ mol-1 spanned by FIA49k. The model's value was demonstrated with four case studies, including predictions for molecules extracted from the Cambridge Structural Database and by reproducing results from catalysis research available in the literature. Weaknesses of the model are evaluated and interpreted chemically. FIA-GNN and the FIA49k dataset can be reached via a free web app (www.grebgroup.de/fia-gnn).

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. Evaluating vacuum fluoride ion affinities (FIA) reveals a charge-caused clustering that prohibits any meaningful ranking. Instead, solvation-corrected FIAsolv is identified as a metric that overcomes charge sensitivity in a balanced manner, allowing for a coherent evaluation of Lewis acidity across varying charge states. Analyzing the impact of molecular volume on solvation-induced FIA damping provides rationales for fundamental trends and guidelines for the choice or design of neutral and cationic Lewis acids in the condensed phase. Exploring alternative scales, explicit counteranion effects, and selected experimental case studies reaffirms the advantages of solvation-corrected FIAsolv as the most versatile and practical approach for the quantitative ranking of general (thermodynamic) Lewis acidity.

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. However, unique perspectives have emerged from plant cell biology research through the characterization of plant-specific regulators as well as the development and application of the state-of-the-art microscopical techniques. In this review, we summarize our current knowledge on the plant endomembrane system, with a focus on several distinct pathways: ER-to-Golgi transport, protein sorting at the TGN, endosomal sorting on multivesicular bodies, vacuolar trafficking/vacuole biogenesis, and the autophagy pathway. We also give an update on advanced imaging techniques for the plant cell biology research.

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. Substituent, solvent and salt effects are uncovered, understood and exploited for the construction of sila-orthoester cryptates. A sharp, divergent pH-response of the obtained cages renders this substance class attractive for future applications well beyond host-guest chemistry, for instance, in drug delivery.

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. The analysis uncovers an unexpectedly thin intermembrane distance that is dilated at the phagophore rim. Mapping of individual autophagic structures onto a timeline based on geometric features reveals a dynamical change of membrane shape and curvature in growing phagophores. Moreover, our tomograms show the organelle interactome of growing autophagosomes, highlighting a polar organization of contact sites between the phagophore and organelles, such as the vacuole and the endoplasmic reticulum (ER). Collectively, these findings have important implications for the contribution of different membrane sources during autophagy and for the forces shaping and driving phagophores toward closure without a templating cargo.

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. In this work, we used in situ cryo-electron tomography to reveal native structures of the transition zone region and assembling IFT trains at the ciliary base in Chlamydomonas. We combined this direct cellular visualization with ultrastructure expansion microscopy to describe the front-to-back stepwise assembly of IFT trains: IFT-B forms the backbone, onto which bind IFT-A, dynein-1b, and finally kinesin-2 before entry into the cilium.

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. This is enabled by a new, donor-free polymeric form of Lewis superacidic bis(perchlorocatecholato)silane 1. Spectroscopic, structural, and computational insights allow a reassessment of Gutmann's empirical rules for the role of silicon hypercoordination in synthesis and catalysis. The electronic perturbations of 1 exerted on the bound anions indicate pronounced substrate activation.

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 31 P NMR shift of triethylphosphine oxide in the Gutmann-Beckett (GB) method. This type of scaling was called effective Lewis acidity (eLA). Unfortunately, gLA and eLA often correlate poorly, but a reason for this is unknown. Hence, the strength and the effect of a Lewis acid are two distinct properties, but they are often granted interchangeably. The present work analyzes thermodynamic, NMR specific, and London dispersion effects on GB numbers for 130 Lewis acids by theory and experiment. The deformation energy of a Lewis acid is identified as the prime cause for the critical deviation between gLA and eLA but its correction allows a unification for the first time.

A modular platform for automated cryo-FIB workflows.

Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga+ ion beam currents required to maintain the structural integrity of vitreous specimens, common preparation protocols are time-consuming and labor intensive. The improved stability of new-generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available Python packages, and interfaces with three-dimensional correlative light and electron microscopy (CLEM) tools. SerialFIB enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM-guided lamella preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.

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. This protocol describes how to target specific cellular sites during FIB milling using a 3D-correlative approach, which combines three-dimensional fluorescence microscopy data with information from the FIB-scanning electron microscope. Using this technique, rare cellular events and structures can be targeted with high accuracy and visualized at molecular resolution using cryo-transmission electron microscopy (cryo-TEM).

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. It falls short, however, of revealing the spatiotemporal sequence of ribosome biogenesis in the cellular context. Here, we present our study on native nucleoli in Chlamydomonas reinhardtii, in which we follow the formation of LSU and SSU precursors by in situ cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). By combining both positional and molecular data, we reveal gradients of ribosome maturation within the granular component (GC), offering a new perspective on how the liquid-liquid-phase separation of the nucleolus supports ribosome biogenesis.

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 S. cerevisiae. Of these CME proteins, Ede1 functions as an autophagy receptor, harboring distinct Atg8-binding domains and driving phase separation into condensates. The aberrant CME condensates at the plasma membrane (PM) exhibit a drop-like structure surrounded by a fenestrated ER, which are engulfed in pieces in an Ede1-dependent manner by autophagy. Thus, our work suggests that aberrant CME is a target for autophagic degradation, with the scaffold protein Ede1 serving as a built-in autophagy receptor that monitors the assembly status of the CME machinery.

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. Here, we present new hardware that overcomes the current limitations. We developed a new glove box and a high vacuum cryo transfer system and installed a stage heater, a cryo-shield and a cryo-shutter in the FIB milling microscope. This reduces the ice contamination during the transfer and milling process and simplifies the handling of the sample. In addition, we tested a new software application that automates the key milling steps. Together, these improvements allow for high-quality, high-throughput cryo-FIB milling. This paves the way for new types of experiments, which have been previously considered infeasible.

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., reference Lewis base dependency). However, a systematic screening of computed affinities other than the FIA is much less developed. Herein, we extended our CCSD(T)/CBS benchmark of different density functionals and the DLPNO-CCSD(T) method for chloride (CIA), methide (MIA), hydride (HIA), water (WA), and ammonia (AA) affinities. The best performing methods are subsequently applied to yield nearly 800 affinities for 183 p-block element compounds of group 13-16 with an estimated accuracy of <10 kJ mol-1 . The study's output serves as a consistent library for qualitative analyses and a training set for future statistical approaches. A first holistic correlation analysis underscores the need for a multidimensional description of Lewis acidity.

Advanced cryo-tomography workflow developments - correlative microscopy, milling automation and cryo-lift-out.

Cryo-electron tomography (cryo-ET) is a groundbreaking technology for 3D visualisation and analysis of biomolecules in the context of cellular structures. It allows structural investigations of single proteins as well as their spatial arrangements within the cell. Cryo-tomograms provide a snapshot of the complex, heterogeneous and transient subcellular environment. Due to the excellent structure preservation in amorphous ice, it is possible to study interactions and spatial relationships of proteins in their native state without interference caused by chemical fixatives or contrasting agents. With the introduction of focused ion beam (FIB) technology, the preparation of cellular samples for electron tomography has become much easier and faster. The latest generation of integrated FIB and scanning electron microscopy (SEM) instruments (dual beam microscopes), specifically designed for cryo-applications, provides advances in automation, imaging and the preparation of high-pressure frozen bulk samples using cryo-lift-out technology. In addition, correlative cryo-fluorescence microscopy provides cellular targeting information through integrated software and hardware interfaces. The rapid advances, based on the combination of correlative cryo-microscopy, cryo-FIB and cryo-ET, have already led to a wealth of new insights into cellular processes and provided new 3D image data of the cell. Here we introduce our recent developments within the cryo-tomography workflow, and we discuss the challenges that lie ahead. LAY DESCRIPTION: This article describes our recent developments for the cryo-electron tomography (cryo-ET) workflow. Cryo-ET offers superior structural preservation and provides 3D snapshots of the interior of vitrified cells at molecular resolution. Before a cellular sample can be imaged by cryo-ET, it must be made accessible for transmission electron microscopy. This is achieved by preparing a 200-300 nm thin cryo-lamella from the cellular sample using a cryo-focused ion beam (cryo-FIB) microscope. Cryo-correlative light and electron microscopy (cryo-CLEM) is used within the workflow to guide the cryo-lamella preparation to the cellular areas of interest. We cover a basic introduction of the cryo-ET workflow and show new developments for cryo-CLEM, which facilitate the connection between the cryo-light microscope and the cryo-FIB. Next, we present our progress in cryo-FIB software automation to streamline cryo-lamella preparation. In the final section we demonstrate how the cryo-FIB can be used for 3D imaging and how bulk-frozen cellular samples (obtained by high-pressure freezing) can be processed using the newly developed cryo-lift-out technology.

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. Distinct domains within Ede1 bind Atg8 and mediate phase separation into condensates. Both properties are necessary for an Ede1-dependent autophagy pathway for endocytic proteins, which differs from regular endocytosis and does not involve other known selective autophagy receptors but requires the core autophagy machinery. Cryo-electron tomography of Ede1-containing condensates, at the plasma membrane and in autophagic bodies, shows a phase-separated compartment at the beginning and end of the Ede1-mediated selective autophagy route. Our data suggest a model for autophagic degradation of macromolecular protein complexes by the action of intrinsic autophagy receptors.

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. Our work reveals that the cartwheel central hub is constructed from a stack of paired rings with cartwheel inner densities inside. In both Paramecium and Chlamydomonas, the repeating structural unit of the cartwheel has a periodicity of 25 nm and consists of three ring pairs, with 6 radial spokes emanating and merging into a single bundle that connects to the microtubule triplet via the D2-rod and the pinhead. Finally, we identified that the cartwheel is indirectly connected to the A-C linker through the triplet base structure extending from the pinhead. Together, our work provides unprecedented evolutionary insights into the architecture of the centriole proximal region, which underlies centriole biogenesis.

An Extensive Set of Accurate Fluoride Ion Affinities for p-Block Element Lewis Acids and Basic Design Principles for Strong Fluoride Ion Acceptors.

The computed fluoride ion affinity (FIA) is a valuable descriptor to assess the Lewis acidity of a compound. Despite its widespread use, the varying accuracy of applied computational models hampers the broad comparability of literature data. Herein, we evaluate the performance of selected methods (like DLPNO-CCSD(T)) in FIA computations against CCSD(T)/CBS data and guide for the choice of suitable density functionals that allow the treatment of larger Lewis acids. Based on the benchmarked methods, we computed an extensive set of gas-phase and solvation corrected FIA, that is covering group 13-16 elements featuring moderate to strong electron-withdrawing substituents (190 entries). It permits an unbiased comparison of FIA over a significant fraction of the periodic table, serves as a source of reference for future synthetic or theoretical studies, and allows to derive some simple design principles for strong fluoride ion acceptors. Finally, the manuscript includes a tutorial section for the computation of FIA with and without the consideration of solvation.