478 papers
This paper presents a rapid and universal pipeline that combines an AI-driven in silico screening tool (NOAH) with a de novo designed fusion protein (ARK1) to eliminate the need for extensive experimental construct optimization, enabling high-resolution cryo-EM structure determination of challenging GPCRs in various states for drug discovery.
This study utilizes novel liposomal nano-sensors to map osmotic pressure gradients within *E. coli* biofilms in real time, revealing a radially increasing distribution that drives biofilm expansion, morphology, and nutrient transport through mechanical forces and water uptake.
This paper demonstrates that adding the mild non-ionic detergent n-decyl-{beta}-D-maltopyranoside (DM) immediately before vitrification effectively suppresses air-water interface interactions, thereby reducing protein denaturation and preferred orientation to enable high-resolution cryo-EM reconstructions across diverse macromolecular systems.
This paper presents a self-consistent free-energy framework that simultaneously determines membrane shape and osmotic pressure by coupling bending elasticity with solute entropy, revealing that global free-energy competition—not the classical linear Helfrich criterion—governs vesicle stability and yields critical pressures consistent with simulations across various vesicle sizes.
This paper introduces and validates a fluorescence correlation spectroscopy (FCS) based excitation scan assay to quantitatively compare the brightness and photostability of various fluorescent reporters in living systems, demonstrating that mNeonGreen outperforms mEGFP and providing a broadly applicable method for optimizing fluorescent tag selection.
This paper introduces an efficient, state-of-the-art detection scheme for 3D single-molecule localization microscopy that utilizes steerable filters to localize double helix point-spread functions with minimal computational cost and is implemented as a plug-in for the open-source PYME software.
This study reveals that the human chromatin remodeler BRG1 undergoes liquid-like condensation via its C-terminal intrinsically disordered region to form dynamic nucleolar condensates, which orchestrate rRNA-dependent mobility and spatiotemporally enrich rDNA binding to organize remodeling activity.
This paper presents a two-stage physics-based computational framework that combines weighted ensemble simulations with the RiteWeight reweighting algorithm to harmonize diverse AI-generated protein structure ensembles into a consistent, atomically-detailed equilibrium state.
This paper demonstrates the feasibility of a novel two-array temporal interference stimulation approach that, supported by fast optimization algorithms and hardware validation, achieves superior deep-brain focality with fewer electrodes and significantly reduced computational time compared to conventional multi-pair methods.
This study demonstrates that multiple sequence alignment perturbation strategies significantly enhance AlphaFold3's ability to sample alternative protein conformational states, often outperforming AlphaFold2 and matching the BioEmu model.
This study employs an integrated computational framework to reveal that broadly neutralizing SARS-CoV-2 antibodies achieve escape-proof efficacy by targeting minimally frustrated, evolutionarily constrained epitope cores, whereas immune escape occurs in neutrally frustrated peripheral regions that serve as energetic playgrounds for mutation.
This study utilizes molecular dynamics simulations to demonstrate that the transmembrane domain of the SARS-CoV-2 spike protein is not merely a static anchor but dynamically regulates the kinetics of S2 conformational transitions and is allosterically coupled to the conformational state of the S1 subunit.
This study utilizes mass spectrometry-based glycoproteomics and molecular dynamics simulations to demonstrate that site-specific O-glycans on lacritin modulate its structural flexibility and multimerization by influencing the conformation and solvent accessibility of key crosslinking residues (Lys101 and Lys104), thereby regulating its biological functions in tear fluid.
By combining experiments, simulations, and analytical models, this study reveals how the interplay between surface tension, filament bending energy, and wetting effects governs the shape deformations of biomolecular condensates containing filaments, providing a physical framework for understanding their role in cytoskeletal organization.
This paper presents a homogenization approach that rigorously links microscopic reaction-diffusion models to efficient macroscopic continuum equations for cytokine signaling, effectively capturing cellular uptake and volume exclusion while recovering classical Yukawa-type solutions under radial symmetry.
This study demonstrates that existing ion force fields do not transfer directly to OPC water without significant deviations, leading the authors to propose the new MS/G-LB(OPC) force field, which combines specific cation and anion parameters to accurately reproduce experimental hydration free energies, structural properties, and activity derivatives.
This paper identifies and corrects a fundamental bias in chromatin contact map preprocessing caused by whole-matrix percentile clipping, introducing a statistically consistent framework and a deep learning tool (CCUT) that enables physically interpretable, quantitative reconstruction of genome architecture aligned with polymer physics and loop extrusion models.
This paper demonstrates that receptor-mediated endocytosis, traditionally viewed as a signal attenuation mechanism, paradoxically enhances directional information in autonomous cell-cell attraction by reshaping self-generated extracellular chemical gradients to maximize relative surface anisotropy through an optimal balance between signal depletion and contrast enhancement.
This study reveals that the transcription factor YY1 forms mechanically distinct DNA condensates in a concentration-dependent manner, where moderately high concentrations yield weakly-linked, liquid-like assemblies scaffolded by immobile DNA, while high concentrations drive strongly-linked, solid-like condensates through zinc finger-mediated bridging.
This study elucidates the structural basis by which the lead compound CN045 inhibits M1 muscarinic and H3 histamine receptors to promote oligodendrocyte progenitor cell differentiation, revealing stronger and more stable binding to M1 through computational simulations to guide the development of remyelination therapies for multiple sclerosis.