ArticleThe journal of physical chemistry. B2024
Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.
Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- High-speed atomic force microscopy of membrane proteins: From dynamic imaging to integrative structural biology.Current opinion in structural biology · 2026Review
- AFM-Fold: Rapid reconstruction of protein conformations from AFM images.Biophysical journal · 2026Article
- Large-Scale Structural Dynamics in the Tail Fiber Modulate the Infective Transition of the T7 Bacteriophage.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Structural Dynamics of the Afamin/Wnt3a Complex Mediated by the Afamin Hydrophobic Pocket.Nano letters · 2026Article
- Estimating Protein Conformational States from High-Speed AFM Images with Molecular Dynamics and Deep Learning.Journal of chemical information and modeling · 2026Article
- MET Enhances Amivantamab Binding to EGFR and Antibody-Dependent Cellular Toxicity.Cancer science · 2026Article
- Visualizing the Functional Dynamics of P-Glycoprotein and Its Modulation by Elacridar via High-Speed Atomic Force Microscopy.International journal of molecular sciences · 2025Article
- Article
- Deciphering conformational dynamics in AFM data using fast nonlinear NMA and FFT-based search with AFMFit.Communications biology · 2025Article
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Authors and funding
3 authors.
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Abstract
Observing a single biomolecule performing its function is fundamental in biophysics as it provides important information for elucidating the mechanism. High-speed atomic force microscopy (HS-AFM) is a unique and powerful technique that allows the observation of biomolecular motion in a near-native environment. However, the spatial resolution of HS-AFM is limited by the physical size of the cantilever tip, which restricts the ability to obtain atomic details of molecules. In this study, we propose a novel computational algorithm designed to derive atomistic models of conformational dynamics from AFM images. Our method uses normal-mode analysis to describe the expected motions of the molecule, allowing these motions to be represented with a limited number of coordinates. This approach mitigates the problem of overinterpretation inherent in the analysis of AFM images with limited resolution. We demonstrate the effectiveness of our algorithm, NMFF-AFM, using synthetic data sets for three proteins that undergo significant conformational changes. NMFF-AFM is a fast and user-friendly program that requires minimal setup and has the potential to be a valuable tool for biophysical studies using HS-AFM.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.