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A structural biology compatible file format for atomic force microscopy
Yining Jiang1,2, Zhaokun Wang2,3, Simon Scheuring4,5
1Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
Nature Communications
|February 15, 2025
Summary
Atomic force microscopy (AFM) data can now be converted into 3D-density files, enabling integration with other structural biology techniques. This advancement allows for visualization and analysis alongside cryo-EM, X-ray crystallography, and NMR, enhancing protein structure determination.
Area of Science:
- Structural Biology
- Biophysics
- Computational Biology
Background:
- Established structural biology methods like cryo-EM, X-ray crystallography, and NMR provide crucial protein structure data.
- Atomic force microscopy (AFM) has historically lacked direct integration with these established structural biology techniques.
- Localization AFM (LAFM) has emerged, offering high-resolution structural insights from AFM data.
Purpose of the Study:
- To develop a pipeline for transforming AFM data into a format compatible with standard structural biology visualization and analysis tools.
- To enable the integration of AFM data with established structural biology methods for enhanced protein structure determination.
- To create a standardized file format for AFM data that facilitates comparison and cross-verification with other structural data.
Main Methods:
- Development of a computational pipeline to convert AFM data into 3D-density files (.afm).
- Utilizing 3D-LAFM densities as force fields for molecular dynamics flexible fitting (MDFF).
- Demonstrating the visualization and analysis capabilities of the .afm file format for both conventional and LAFM images.
Main Results:
- Successful transformation of AFM data into .afm files, readable by common structural biology software.
- Demonstrated use of 3D-LAFM densities to guide MDFF, yielding structural models of previously unresolved states.
- The .afm format allows for direct 3D/2D visualization and analysis of AFM images, facilitating comparison with other structural data.
Conclusions:
- The developed pipeline and .afm file format bridge the gap between AFM and traditional structural biology methods.
- This integration allows AFM to be routinely used alongside cryo-EM, X-ray crystallography, and NMR for protein structure studies.
- The .afm format is anticipated to become a standard for AFM data deposition, promoting data sharing and cross-validation within the structural biology community.
