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Flexible Fitting to Infer Atomistic-Precision Models of Large-Amplitude Conformational Dynamics in Biomolecules from High-Speed Atomic Force Microscopy Imaging
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Abstract
High-speed atomic force microscopy (HS-AFM) experiments allow direct observation of biomolecular dynamics at the single-molecule level, acquiring a large amount of topographic imaging data that visualizes changes in the molecular surface during functional activity over an extended period of time. Since images have no atomistic resolution, a major challenge has been to develop post-experimental computational methods to infer atomistic information from measurements. The recently developed NMFF-AFM flexible fitting method provides a computationally efficient approach promising to infer atomistic-precision models of conformational dynamics from resolution-limited AFM imaging data. We report the software integration of this method into the well-established BioAFMviewer platform and demonstrate its first applications to experimental HS-AFM imaging data. To facilitate applications, we developed a direct workflow from raw experimental AFM data to the visualization and analysis of fitting results. The presented applications to experimental data of a single protein domain, a protein complex, and a megadalton-sized protein filament demonstrate the versatility of NMFF-AFM modeling to reproduce large-amplitude conformational motions of biomolecular dynamics from HS-AFM imaging. As a first step toward automated large-scale analysis of AFM imaging data, we furthermore demonstrate reconstruction of an atomistic molecular movie of protein dynamics, involving large-amplitude conformational transitions, from a measured HS-AFM movie sequence. Implementation of flexible fitting within the stand-alone user-friendly interactive BioAFMviewer software provides the opportunity for a broad range of applications to facilitate the understanding of resolution-limited HS-AFM measurements.
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- Amyot, R.; Miyashita, O.; Wu, X.; Takeda, K.; Kodera, N.; Konno, H.; Tama, F.; Flechsig, H. Flexible fitting to infer atomistic-precision models of large-amplitude conformational dynamics in biomolecules from high-speed atomic force microscopy imaging bioRxiv 2025 https://www.biorxiv.org/content/10.1101/2025.05.14.653975v1.abstract 10.1101/2025.05.14.653975. (accessed September 10, 2025). · DOI · Paper page
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Metadata
- Authors
- Amyot, R., Miyashita, O., Wu, X., Takeda, K., Kodera, N., Konno, H., Tama, F., & Flechsig, H.
- Affiliations
- Kanazawa University (JP)
- RIKEN Center for Computational Science (JP)
- Nagoya University (JP)
- Corresponding author
- Tama, Florence
- Flechsig, Holger
- ORCID
- Venue
- ACS Nano
- Publisher
- American Chemical Society (ACS)
- Published
- 2025-09-18
- Volume
- 19
- Issue
- 38
- Pages
- 34065-34079
- ISSN
- 1936-0851 (ISSN-L)
- 1936-086X
- PMC
- PMC12490010
- OpenAlex
- W4414323111
- Cited by
- 13
- References
- 37
- Citations by year
- 2026: 11 · 2025: 2
- FWCI
- 4.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- ACS Nano (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- Institutional Repositories DataBase (IRDB) (submittedVersion)
- Funders
- Ministry of Education, Culture, Sports, Science and Technology (JPMXP1020230119)
- Japan Society for the Promotion of Science (24H02260, 25K01631)
- Kanazawa University
- Topics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Keywords
- flexible fitting, high-speed atomic force microscopy, conformational dynamics, biomolecular dynamics, protein dynamics, protein complexes, protein filaments, molecular movies
- MeSH terms
- Models, Molecular, Protein Conformation, Proteins, Software, Microscopy, Atomic Force, Molecular Dynamics Simulation
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