Amorphous Co(OH)2 nanocages achieving efficient photo-induced charge transfer for significant SERS activity

Boosting substrate-molecule interactions, especially the strong vibronic coupling and efficient photo-induced charge transfer (PICT) transitions, are critical issues to improve surface-enhanced Raman scattering (SERS) sensitivity of non-metal substrates. Here, by...

A Novel Live Imaging-Based Assay for Visualising Species-Specific Interactions in Gametic Adhesion Molecules

Successful gametic fusion requires species-specific membrane adhesion. However, the interaction of adhesion molecules in gametes is difficult to study in real time through low-throughput microscopic observation. Therefore, we developed a novel live imaging-based adhesion molecule (LIAM) assay to study gametic adhesion molecule interactions in cultured cells. First, we modified a fusion assay previously established for fusogens introduced into cultured cells, and confirmed that our live imaging technique could visualise cell-to-cell fusion in the modified fusion assay. Next, instead of fusogen, we introduced adhesion molecules including a mammalian gametic adhesion molecule pair, IZUMO and JUNO, and detected their temporal accumulation at the contact interfaces of adjacent cells. Accumulated IZUMO or JUNO was translocated to the opposite cells; the mutation in amino acids required for their interaction impaired accumulation and translocation. By using the novel LIAM assay, we investigated the species specificity of IZUMO and JUNO of mouse, human, hamster, and pig in all combinations. IZUMO and JUNO accumulation and translocation were observed in conspecific, and some interspecific, combinations, suggesting potentially interchangeable combinations of IZUMO and JUNO from different species.

Inductive inference of novel protein-molecule interactions using Heterogeneous Graph Transformer (HGT) AutoEncoder

Protein-molecule interactions are promoted by the physicochemical characteristics of the actors involved, but structural information alone does not capture expression patterns, localization and pharmacokinetics. In this work we propose an integrative strategy for protein-molecule interaction discovery that combines different layers of information through the use of convolutional operators on graph, and frame the problem as missing link prediction task on an heterogeneous graph constituted by three node types: 1) molecules 2) proteins 3) diseases. Physicochemical information of the actors are encoded using shallow embedding techniques (SeqVec, Mol2Vec, Doc2Vec respectively) and are supplied as feature vectors to a Graph AutoEncoer (GAE) that uses a Heterogeneous Graph Transformer (HGT) in the encoder module. We show in this work that HGT Autoencoder can be used to accurately recapitulate the protein-molecule interactions set and propose novel relationships in inductive settings that are grounded in biological and functional information extracted from the graph.

Dihedral Angle Measurements for Structure Determination by Biomolecular Solid-State NMR Spectroscopy

In structural studies of immobilized, aggregated and self-assembled biomolecules, solid-state NMR (ssNMR) spectroscopy can provide valuable high-resolution structural information. Among the structural restraints provided by magic angle spinning (MAS) ssNMR the canonical focus is on inter-atomic distance measurements. In the current review, we examine the utility of ssNMR measurements of angular constraints, as a complement to distance-based structure determination. The focus is on direct measurements of angular restraints via the judicious recoupling of multiple anisotropic ssNMR parameters, such as dipolar couplings and chemical shift anisotropies. Recent applications are highlighted, with a focus on studies of nanocrystalline polypeptides, aggregated peptides and proteins, receptor-substrate interactions, and small molecule interactions with amyloid protein fibrils. The review also examines considerations of when and where ssNMR torsion angle experiments are (most) effective, and discusses challenges and opportunities for future applications.

Molecular synthesis in ices triggered by dissociative electron attachment to carbon monoxide

Chemical reactions in mixed molecular ices as relevant in the context of astrochemistry can be initiated by electron-molecule interactions. Dissociative electron attachment (DEA) as initiating step is identified from the enhancement of product yields upon irradiation at particular electron energies. Herein, we show that DEA to CO leads to the formation of HCN in mixed CO/$$\hbox {NH}_{{3}}$$ NH 3 ice at electron energies around 11 eV and 16 eV. We propose that this reaction proceeds via insertion of the neutral C fragment into a N–H bond. In the case of CO/$$\hbox {H}_{{2}}$$ H 2 O and CO/$$\hbox {CH}_{{3}}$$ CH 3 OH ices, a resonant enhancement of the yields of HCOOH and $$\hbox {CH}_{{3}}$$ CH 3 OCHO, respectively, is observed around 10 eV. In both ices, both molecular constituents exhibit DEA processes in this energy range so that the energy-dependent product yield alone does not uniquely identify the relevant DEA channel. However, we demonstrate by comparing with earlier results on mixed ices where CO is replaced by $$\hbox {C}_{{2}}\hbox {H}_{{4}}$$ C 2 H 4 that DEA to CO is again responsible for the enhanced product formation. In this case, $$\hbox {O}^{\cdot -}$$ O · - activates $$\hbox {H}_{{2}}$$ H 2 O or $$\hbox {CH}_{{3}}$$ CH 3 OH which leads to the formation of larger products. We thus show that DEA to CO plays an important role in electron-induced syntheses in molecular ices. Graphical abstract

Resolving sub-angstrom ambient motion through reconstruction from vibrational spectra

Metal/organic-molecule interactions underpin many key chemistries but occur on sub-nm scales where nanoscale visualisation techniques tend to average over heterogeneous distributions. Single molecule imaging techniques at the atomic scale have found it challenging to track chemical behaviour under ambient conditions. Surface-enhanced Raman spectroscopy can optically monitor the vibrations of single molecules but understanding is limited by the complexity of spectra and mismatch between theory and experiment. We demonstrate that spectra from an optically generated metallic adatom near a molecule of interest can be inverted into dynamic sub-Å metal-molecule interactions using a comprehensive model, revealing anomalous diffusion of a single atom. Transient metal-organic coordination bonds chemically perturb molecular functional groups > 10 bonds away. With continuous improvements in computational methods for modelling large and complex molecular systems, this technique will become increasingly applicable to accurately tracking more complex chemistries.

Digging Deeper: Advancements in Visualization of Inhibitory Synapses in Neurodegenerative Disorders

Recent research has provided strong evidence that neurodegeneration may develop from an imbalance between synaptic structural components in the brain. Lately, inhibitory synapses communicating via the neurotransmitters GABA or glycine have come to the center of attention. Increasing evidence suggests that imbalance in the structural composition of inhibitory synapses affect deeply the ability of neurons to communicate effectively over synaptic connections. Progressive failure of synaptic plasticity and memory are thus hallmarks of neurodegenerative diseases. In order to prove that structural changes at synapses contribute to neurodegeneration, we need to visualize single-molecule interactions at synaptic sites in an exact spatial and time frame. This visualization has been restricted in terms of spatial and temporal resolution. New developments in electron microscopy and super-resolution microscopy have improved spatial and time resolution tremendously, opening up numerous possibilities. Here we critically review current and recently developed methods for high-resolution visualization of inhibitory synapses in the context of neurodegenerative diseases. We present advantages, strengths, weaknesses, and current limitations for selected methods in research, as well as present a future perspective. A range of new options has become available that will soon help understand the involvement of inhibitory synapses in neurodegenerative disorders.