474 papers
Through atomistic molecular dynamics simulations, this study reveals that the Dead End protein's tandem RRM domains utilize conformational plasticity and cooperative binding to maintain RNA sequence specificity, demonstrating that highly dynamic interfaces are essential for effective RNA regulation.
This study utilizes single-molecule conductance measurements in planar lipid bilayers to demonstrate that the cationic peptide protamine binds to and blocks the bacterial porin OmpF in a voltage- and concentration-dependent manner, with binding kinetics significantly influenced by peptide length.
This study demonstrates that TMPyP4 selectively stabilizes the HRAS2 i-motif DNA structure through specific binding interactions, as evidenced by comprehensive biophysical and thermodynamic analyses, highlighting its potential as a selective probe and therapeutic agent for targeting i-motif DNA in cancer.
This paper presents a scalable microfabrication pipeline for creating tunable, 3D-printed reflective micromirrors that adapt standard imaging chambers for single-objective light sheet microscopy, significantly improving signal-to-background ratios and nanoscale resolution compared to conventional widefield epi-illumination.
This study utilizes FragLite chemical fragments to map the cyclin T2 interaction landscape, successfully identifying known binding sites for CDK9, AFF4, and HIV-1 Tat while discovering and characterizing a novel BRD4 recruitment interface through integrated biophysical and computational analyses.
This study employs PIP2-assisted adaptive sampling to successfully model the thermodynamically stable open conformation of the TMEM16A ion channel and map the binding sites of various pore blockers, thereby establishing a novel lipid-stabilized framework for structure-specific drug development targeting diseases associated with channel overactivation.
This paper demonstrates that combining high-resolution structural priors with 2D template matching significantly improves the cryo-EM reconstruction of small macromolecular complexes, successfully resolving a previously intractable ~43 kDa protein kinase and predicting the method's potential to extend single-particle cryo-EM to targets well below 50 kDa.
This study utilizes molecular modeling and simulations to reveal that the NisFEG transporter employs a functional asymmetry where the NisG subunit drives ATP-hydrolysis-induced conformational changes while the NisE subunit primarily mediates nisin binding, explaining the evolutionary advantage of its distinct transmembrane chains in providing bacterial immunity.
This study presents a computational framework that integrates molecular dynamics simulations with machine learning classifiers to accurately predict KRAS mutation-induced drug resistance by identifying key conformational and solvent-exposure changes driven by specific residues.
This study presents the first MARTINI 3-compatible coarse-grained forcefield for 19 common peptoid residues, derived from all-atom reference simulations and integrated into the martinize2 tool, to enable efficient and accurate mesoscale modeling of peptoid structures, self-assembly, and interactions.
By integrating single-molecule optical tweezers, biochemical assays, and cryo-EM, this study reveals that the central coupler in ClpX facilitates intersubunit communication by positioning key residues to trigger ATP hydrolysis in neighboring subunits, thereby coupling chemical energy into rapid force generation for efficient protein unfolding.
This study utilizes high-resolution cryo-electron microscopy and proteomics to reveal the detailed structural architecture of the Shiga toxin-converting bacteriophage phi24B, characterizing its T=9 icosahedral capsid, complex tail assembly, and unique peripheral features that distinguish it from related podoviruses.
This study utilizes serial femtosecond crystallography and multiscale analyses to reveal that the prolonged action of insulin glargine is driven by a pH-dependent allosteric transition involving specific structural rearrangements and molten-like intermediate states, rather than simple isoelectric precipitation.
The paper introduces KinConfBench, a curated benchmark revealing that while state-of-the-art cofolding models can classify kinase conformations with moderate accuracy, they fail to capture ligand-induced structural diversity and suffer from severe "apo-drift," highlighting the need for new dynamical evaluation metrics beyond geometric pose fitting.
This paper introduces an uncompromised, multimodal, multiscale live-to-cryo correlative imaging workflow that integrates fluorescence, Raman, and electron microscopy techniques to reveal the hierarchical 3D structure and chemical composition of mineralized tissues in their near-native state, as demonstrated by characterizing the plywood-like collagen architecture and mineral platelet alignment in regenerating zebrafish scales.
This paper presents a mathematical model demonstrating that accumulated neurotoxicity, defined as the time-integrated concentration of soluble amyloid-beta oligomers, serves as a non-reversible surrogate for biological age that correlates non-linearly with plaque burden and explains the variability in cognitive decline through the critical influence of protein degradation efficiency and specific microscopic aggregation dynamics.
This paper introduces Spatial Spectral Single-Molecule Microscopy (S3M), a simplified imaging technique that utilizes commercially available color CMOS detectors to simultaneously recover molecular position and spectral fingerprints from single images without the need for complex optical beam splitting or registration.
Using NMR spectroscopy, this study elucidates the distinct roles of the three binding sites within the trivalent CpCBM92A protein, revealing how their cooperative interactions and specific preferences for glucan chain segments enable the cross-linking of scleroglucan chains.
Using cryo-ptychographic X-ray computed tomography alongside electron microscopy, this study reveals the 3D developmental stages of *Gephyrocapsa huxleyi* coccolith formation, demonstrating how intracellular confinement shapes crystal morphology and offering insights into biomineralisation pathways for advanced material design.
This paper presents a novel method that utilizes 3D single-molecule tracking data and hidden Markov modeling to accurately recover membrane interaction kinetics in rod-shaped bacteria by identifying membrane-associated motion through trajectory curvature, overcoming the limitations of conventional 2D analyses that rely on diffusion rate changes.