A structural biology compatible file format for atomic force microscopy

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 15, 2025

Cryogenic electron microscopy (cryo-EM), X-ray crystallography, and nuclear magnetic resonance (NMR) contribute structural data that are interchangeable, cross-verifiable, visualizable on common platforms, making them powerful tools for our understanding of protein structures. Unfortunately, atomic force (AFM) has so far failed to interface with these biology methods, despite the recent development localization AFM (LAFM) allows extracting high-resolution information from data. Here, we build LAFM develop a pipeline transforms into 3D-density files (.afm) readable by programs commonly used visualize, analyze, interpret We show 3D-LAFM densities can serve as fields steer molecular dynamics flexible fitting (MDFF) obtain models previously unresolved states based observations in close-to-native environment. Besides, .afm format enables direct 3D or 2D visualization analysis conventional images. anticipate file will find wide usage embed repertoire methods routinely community, allowing researchers deposit repositories comparison cross-verification other techniques.

Language: Английский

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AI-Enabled Compact and Efficient Dynamic Light Scattering System for Precise Microparticle Sizing

Applied Sciences, Journal Year: 2025, Volume and Issue: 15(4), P. 1900 - 1900

Published: Feb. 12, 2025

A cost-effective and efficient AI-DLS framework integrating dynamic light scattering (DLS) with artificial intelligence (AI) enables precise microparticle size characterization. compact DLS system was developed using a helium–neon laser, high-frequency photodetectors, optimized optical components, achieving significant miniaturization—4.5% volume, 16.7% weight, 25% cost of conventional systems. Advanced signal processing, such as Kalman filtering, improved data quality, while deep learning models (deep neural network (DNN), one-dimensional convolutional (1D-CNN), 2D-CNN Gramian angular field transformations) enhanced prediction accuracy. The model achieved exceptional results, mean absolute error 10 nm 99% matched the stability accuracy traditional instruments, reducing test time by 80%. This scalable, low-cost solution overcomes limitations, offering broad accessibility for scientific industrial

Language: Английский

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Mechanisms of pore geometry and apparent morphology on the wettability of coal-ionic liquids

Physics of Fluids, Journal Year: 2025, Volume and Issue: 37(2)

Published: Feb. 1, 2025

In order to investigate the mechanism of pore regulation on wetting performance coal-ionic liquids, and liquids at different temperatures were analyzed based contact angle, surface tension, low-field nuclear magnetic resonance, atomic force microscopy experiments. A method comprehensively analyzing through structure morphology was proposed. The findings demonstrated that properties ionic coal showed temperature selectivity, with containing Cl− preferring low [BMIM][BF4] contrary. After treatment, average diameter, roughness, porosity samples increased by 0.34–18.36 nm, 2.09–9.7 0.5929%–1.4313%, respectively, trend parameter change aligns characteristic change. addition, fitting results revealed increase in roughness had a negative correlation angle's size positive porosity, indicating can affect changing apparent coal. research are significant enhancing mine dust management capability.

Language: Английский

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Quantitative study on the interfacial performance of micron-fiber cord/elastomer

Composites Part B Engineering, Journal Year: 2025, Volume and Issue: unknown, P. 112625 - 112625

Published: May 1, 2025

Language: Английский

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Perspectives Toward an Integrative Structural Biology Pipeline With Atomic Force Microscopy Topographic Images

Journal of Molecular Recognition, Journal Year: 2024, Volume and Issue: 37(6)

Published: Sept. 27, 2024

After the recent double revolutions in structural biology, which include use of direct detectors for cryo-electron microscopy resulting a significant improvement expected resolution large macromolecule structures, and advent AlphaFold allows near-accurate prediction any protein field biology is now pursuing more ambitious targets, including several MDa assemblies. But complex target systems cannot be tackled using single biophysical technique. The integrative has emerged as global solution. aim to integrate data from multiple complementary techniques produce final three-dimensional model that obtained absence atomic force platforms not necessarily due its nm resolution, opposed Å x-ray crystallography, nuclear magnetic resonance, or electron microscopy. Rather issue was AFM topographic lacked interpretability. Fortunately, with introduction AFM-Assembly pipeline other similar tools, it possible into modeling platforms. advantages molecule techniques, such AFM, ability confirm experimentally assembled molecular models alternative conformations mimic inherent flexibility proteins complexes. review begins brief overview historical developments followed by an examination strengths limitations imaging, have hindered integration modern This discusses correction images, well principles behind pipeline. It also presents series challenges need addressed order improve incorporation platform.

Language: Английский

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Advances and Challenges in Interfacial Binding Forces for Electrocatalysts

ChemSusChem, Journal Year: 2024, Volume and Issue: unknown

Published: July 9, 2024

As a practical chemical energy conversion technology, electrocatalysis could be used in fields of and environmental protection. In recent years, significant research efforts have been devoted to the design development high-performance electrocatalysts because rational catalysts is crucial for enhancing electrocatalytic performance. Creating by forming interactions between different components at interface an important means controlling improving Therefore, several common interfacial binding forces synthesizing was systematically summarized this review first time. The discussion revolves around roles these play various reaction processes. Various characterization techniques capable proving existence also involved review. Finally, some prospects challenges designing researching materials through utilization were presented.

Language: Английский

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Pro-inflammatory S100A8 Protein Exhibits a Detergent-like Effect on Anionic Lipid Bilayers, as Imaged by High-Speed AFM

ACS Applied Materials & Interfaces, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 26, 2024

Neuronal cell death induced by membrane damage is one of the major hallmarks neurodegenerative diseases. Neuroinflammation precedes loss neurons; however, whether and how inflammation-related proteins contribute to integrity remains unknown. We employed a range biophysical tools, including high-speed atomic force microscopy, fluorescence spectroscopy, electrochemical impedance ascertain pro-inflammatory protein S100A8 induces alterations in biomimetic lipid membranes upon interaction. Our findings underscore crucial roles played divalent cations charge. found that apo-S100A8 selectively interacts with anionic composed phosphatidylserine (PS), causing disruption through detergent-like mechanism, primarily affecting regions where phospholipids are less tightly packed. Interestingly, introduction Ca2+ ions inhibited S100A8-induced disruption, suggesting disruptive effects most pronounced under conditions mimicking intracellular compartments, calcium levels low, PS concentrations inner leaflet high. Overall, our results present mechanistic basis for understanding molecular interactions between plasma membrane, emphasizing as potential contributor onset

Language: Английский

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Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy

Structure, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

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