The developed software provides the computational package towards this goal. The BioAFMviewer computationally emulates AFM scanning of any biomolecular structure to generate graphical images that resemble the outcome of AFM experiments. This makes the comparison of all available structural data and computational molecular movies to AFM results possible. The BioAFMviewer has a versatile interactive interface with rich functionality. An integrated 3D viewer visualizes the molecular structure while synchronized computational scanning with adjustable tip-shape geometry and spatial resolution generates the corresponding simulated AFM graphics. Obtained results can be conveniently exported as images or movies.

To demonstrate the great potential of simulated AFM scanning in supporting the analysis and interpretation of experimental data, the authors provide several applications to high-speed AFM observations of proteins. As an example, for the gene scissor related CRISPR-associated protein 9 endonuclease (Cas9), simulated scanning allows to disambiguate the domain arrangement seen in the high-speed AFM image and clarify their orientation with respect to the bound nucleotide strand. The authors furthermore demonstrate how the BioAFMviewer can transform molecular movies of proteins, obtained for example from molecular modeling, into corresponding simulated AFM movies. Therefore, simulated AFM experiments are possible and can be compared to the movies recorded in high-speed AFM experiments to better understand the resolution-limited observed conformational dynamics.

The BioAFMviewer has a user-friendly interface and no expert knowledge is required to use it. The software is already used by AFM groups worldwide, and it is expected to become a standard platform used by the broad community of Bio-AFM experimentalists. Beyond that, it also provides the interface for researchers from the fields of computational biology and bioinformatics to foster their interdisciplinary collaborations.

The BioAFMviewer software package is currently available for the Windows 10 operating system.

The BioAFMviewer software project was initiated by Holger Flechsig, who is an Assistant Professor of the Nano Life Science Institute at Kanazawa University, Japan, where world-leading AFM experiments of biological matter are performed. The first author, Romain Amyot has developed the software package and continues to work on future applications. Besides that, he also performs high-speed AFM experiments of proteins as a postdoctoral researcher at the Aix-Marseille University, France.

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Materials provided by Kanazawa University. Note: Content may be edited for style and length.

Journal Reference:

1. Romain Amyot, Holger Flechsig. BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics. PLOS Computational Biology, 2020; 16 (11): e1008444 DOI: 10.1371/journal.pcbi.1008444