Cell Reports Physical Science最新文献

The capacity of temporal interference (TI) stimulation to target deep brain regions without affecting nearby surface electrodes remains uncertain. Using artifact-free optical recording, we compare excitation patterns and thresholds in hippocampal neurons stimulated by "pure" and amplitude-modulated sine waves, representing TI waveforms near electrodes and at the target, respectively. We show that pure 2- and 20-kHz sine waves induce repetitive firing at rates that increase up to 60-90 Hz with stronger electric fields. Beyond this limit, action potentials merge into sustained depolarization, resulting in an excitation block. Modulating the sine waves at 20 Hz aligns firing with amplitude "beats" and prevents the excitation block but does not lower excitation thresholds. Thus, off-target TI effects appear unavoidable, though the patterns of neuronal excitation and downstream effects may differ from those at the target. We further analyze membrane charging and relaxation kinetics at nanoscale resolution and confirm an excitation mechanism independent of envelope extraction.

Computational simulations of biomolecules provide a wealth of information about the thermodynamic landscape of biologically important systems, kinetics of important cellular processes, and the biophysical basis of life. Despite the ubiquity of molecular simulations in biophysical literature, major challenges persist for new practitioners entering the field, and even for experienced computational scientists, in maintaining and distributing their simulation outcomes. Here, we summarize critical obstacles encountered when performing biomolecular simulations and provide best practices for performing simulations that are robust, reproducible, and hypothesis-driven. We also discuss practices that promote improved reproducibility and accessibility using reliable tools and databases.

Innate immune responses rely on a critical adaptor protein, MYD88, to bridge extracellular inflammatory signals and transcription factor networks inside the cell. Dysregulation of MYD88 is associated with immunodeficiencies, autoimmunity, and cancer. Here, we identify a stretch of guanine/cytosine-rich DNA in the MYD88 promoter capable of adopting stable G-quadruplex and i-Motif structures. Molecular characterization of the i-motif reveals a unique folding pattern with asymmetric lateral loop sizes, a transition pH in line with previously documented i-motifs, and in vitro recognition by the chromatin insulator/transcription factor (CTCF). In exploring the transcriptional role and therapeutic potential of the MYD88 structures, we show the known G-quadruplex ligand, TMPyP4, destabilizes the i-motif, stabilizes the G-quadruplex, and promotes MYD88 expression. A ligand, 33353, from the National Cancer Institute (NCI) Diversity Set, also differentially interacts with the two structures yet represses MYD88. This work discovers DNA structures in MYD88 that can be pharmacologically leveraged for their ability to control gene expression.

Energy conservation is crucial to life's origin and evolution. The common ancestor of all cells used ATP synthase to convert proton gradients into ATP. However, pumps generating proton gradients and lipids maintaining proton gradients are not universally conserved across all lineages. A solution to this paradox is that ancestral ATP synthase could harness naturally formed geochemical ion gradients with simpler environmentally provided precursors preceding both proton pumps and biogenic membranes. This runs counter to traditional views that phospholipid bilayers are required to maintain proton gradients. Here, we show that fatty acid membranes can maintain sufficient proton gradients to synthesize ATP by ATP synthase under the steep pH and temperature gradients observed in hydrothermal vent systems. These findings shed substantial light on early membrane bioenergetics, uncovering a functional intermediate in the evolution of chemiosmotic ATP synthesis during protocellular stages postdating the ATP synthase's origin but preceding the advent of enzymatically synthesized cell membranes.

Multidrug efflux pumps confer not only antibiotic resistance to bacteria but also cell proliferation. In gram-negative bacteria, the ATP-binding cassette (ABC)-family transporter MacB, the adaptor protein MacA, and the outer membrane protein TolC form the MacA₆:MacB₂:TolC₃ assembly to extrude antibiotics and virulence factors. Here, using quantitative single-molecule single-cell imaging, we uncover that, in E. coli cells, there is a large excess of MacB (and TolC) driving the limiting adaptor protein MacA mostly into the MacAB-TolC assembly. Moreover, the excess MacB transporters can dynamically cluster around the assembly, and MacA can dynamically disassemble from the MacAB-TolC assembly, leading to an adaptor protein shuttling mechanism for efficient substrate sequestration from the periplasm toward efflux. We further show that both MacB clustering and MacAB-TolC assembly can be perturbed chemically or physically via microfluidics-based extrusion loading for compromised antibiotic tolerance. These insights may provide opportunities for countering the activities of multidrug efflux systems for antimicrobial treatments.

Alzheimer's disease (AD) is caused by the assembly of amyloid-beta (Aβ) peptides into oligomers and fibrils. Endogenous Aβ aggregation may be assisted by cell membranes, which can accelerate the nucleation step enormously, but knowledge of membrane-assisted aggregation is still very limited. Here, we used extensive molecular dynamics (MD) simulations to structurally and energetically characterize key intermediates along the membrane-assisted aggregation pathways of Aβ40. Reinforcing experimental observations, the simulations reveal unique roles of GM1 ganglioside and cholesterol in stabilizing membrane-embedded β sheets and of Y10 and K28 in the ordered release of a small oligomeric seed into solution. The same seed leads to either an open-shaped or R-shaped fibril, with significant stabilization provided by inter- or intra-subunit interfaces between a straight β sheet (residues Q15-D23) and a bent β sheet (residues A30-V36). This work presents a comprehensive picture of membrane-assisted aggregation of Aβ40, with broad implications for developing AD therapies and rationalizing disease-specific polymorphisms of amyloidogenic proteins.

Large language models (LLMs) have significantly impacted various domains of our society, including recent applications in complex fields such as biology and chemistry. These models, built on sophisticated neural network architectures and trained on extensive datasets, are powerful tools for designing, optimizing, and generating molecules. This review explores the role of LLMs in discovering and designing antibiotics, focusing on peptide molecules. We highlight advancements in drug design and outline the challenges of applying LLMs in these areas.

Porphyrinic metal-organic frameworks (MOFs) offer high surface areas and tunable catalytic and optoelectronic properties, making them versatile candidates for applications in phototherapy, drug delivery, photocatalysis, electronics, and energy storage. However, a key challenge for industrial integration is the rapid, cost-effective production of suitable sizes. This study introduces Zr(IV) alkoxides as metal precursors, achieving ultrafast (∼minutes) and high-yield (>90%) synthesis of three well-known Zr-based porphyrinic MOF nanocrystals: MOF-525, PCN-224, and PCN-222, each with distinct topologies. By adjusting linker-to-metal and modulator-to-metal ratios, we attain precise control over single-phase formation. Demonstrating alkoxides' potential, we synthesized nanosized PCN-224 at room temperature within seconds using a continuous multifluidic method. This advancement greatly simplifies porphyrinic MOF production, enabling broader industrial and scientific applications.

Small molecules that can reduce the neurotoxic beta-amyloid (Aβ) aggregates in the brain provide a potential treatment for Alzheimer disease (AD). Most screening methods for small-molecule hits focus on the overall Aβ aggregations without a specific target, such as the very first association step (i.e., nucleation) en route to the Aβ oligomers. Located in the middle of a full-length Aβ peptide, Aβ_19-20 (diphenylalanine or FF) nucleates the neurotoxic Aβ oligomer formation. Here, we innovate a single-molecule screen method in optical tweezers by targeting the nucleation process in Aβ aggregation, namely FF-dimerization. With a 121-compound National Institutes of Health (NIH) library, we identify 12 inhibitors and 8 stimulants that can inhibit/promote Aβ_19-20 dimerization significantly. The representative hits are subjected to the thioflavin T and cell toxicity assays to confirm their inhibiting or stimulating activities. By replacing FF with longer Aβ sequences, our single-molecule platform may identify more specific and potent small molecules to fight AD.

Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes from specific subgraphs. In this work, we introduce a GNN-based framework (graph-partitioned GNN [GP-GNN]) to partition the GNN graph to focus on the most relevant subgraphs. Our approach jointly learns task-dependent graph partitions and node representations, making it particularly effective when critical features reside within initially unidentified subgraphs. Protein liquid-liquid phase separation (LLPS) is a problem especially well-suited to GP-GNNs because intrinsically disordered regions (IDRs) are known to function as protein subdomains in it, playing a key role in the phase separation process. In this study, we demonstrate how GP-GNN accurately predicts LLPS by partitioning protein graphs into task-relevant subgraphs consistent with known IDRs. Our model achieves state-of-the-art accuracy in predicting LLPS and offers biological insights valuable for downstream investigation.