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A structural biology compatible file format for atomic force microscopy

Author

Listed:
  • Yining Jiang

    (Weill Cornell Graduate School of Medical Sciences
    Department of Anesthesiology)

  • Zhaokun Wang

    (Department of Anesthesiology
    Weill Cornell Graduate School of Medical Sciences)

  • Simon Scheuring

    (Department of Anesthesiology
    Department of Physiology and Biophysics)

Abstract

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

Suggested Citation

  • Yining Jiang & Zhaokun Wang & Simon Scheuring, 2025. "A structural biology compatible file format for atomic force microscopy," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56760-7
    DOI: 10.1038/s41467-025-56760-7
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    References listed on IDEAS

    as
    1. Yining Jiang & Batiste Thienpont & Vinay Sapuru & Richard K. Hite & Jeremy S. Dittman & James N. Sturgis & Simon Scheuring, 2022. "Membrane-mediated protein interactions drive membrane protein organization," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Shifra Lansky & John Michael Betancourt & Jingying Zhang & Yining Jiang & Elizabeth D. Kim & Navid Paknejad & Crina M. Nimigean & Peng Yuan & Simon Scheuring, 2023. "A pentameric TRPV3 channel with a dilated pore," Nature, Nature, vol. 621(7977), pages 206-214, September.
    3. Maofu Liao & Erhu Cao & David Julius & Yifan Cheng, 2013. "Structure of the TRPV1 ion channel determined by electron cryo-microscopy," Nature, Nature, vol. 504(7478), pages 107-112, December.
    4. Nicolas Reyes & Christopher Ginter & Olga Boudker, 2009. "Transport mechanism of a bacterial homologue of glutamate transporters," Nature, Nature, vol. 462(7275), pages 880-885, December.
    5. George R. Heath & Ekaterina Kots & Janice L. Robertson & Shifra Lansky & George Khelashvili & Harel Weinstein & Simon Scheuring, 2021. "Localization atomic force microscopy," Nature, Nature, vol. 594(7863), pages 385-390, June.
    6. Toru Niina & Yasuhiro Matsunaga & Shoji Takada, 2021. "Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure," PLOS Computational Biology, Public Library of Science, vol. 17(7), pages 1-24, July.
    7. Raghavendar Reddy Sanganna Gari & Joel José Montalvo‐Acosta & George R. Heath & Yining Jiang & Xiaolong Gao & Crina M. Nimigean & Christophe Chipot & Simon Scheuring, 2021. "Correlation of membrane protein conformational and functional dynamics," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    8. Yi-Chih Lin & Christophe Chipot & Simon Scheuring, 2020. "Annexin-V stabilizes membrane defects by inducing lipid phase transition," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    9. George R. Heath & Simon Scheuring, 2018. "High-speed AFM height spectroscopy reveals µs-dynamics of unlabeled biomolecules," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    10. Fang Jiao & François Dehez & Tao Ni & Xiulian Yu & Jeremy S. Dittman & Robert Gilbert & Christophe Chipot & Simon Scheuring, 2022. "Perforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    11. Alma P. Perrino & Atsushi Miyagi & Simon Scheuring, 2021. "Single molecule kinetics of bacteriorhodopsin by HS-AFM," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
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