Extracting Dynamic 3D Structures from HS-AFM Images

Allowing direct observation of biomolecules in dynamic action, high-speed AFM has opened a new avenue for dynamic structural biology. An overwhelming number of successful applications developed over the past 15 years provide unique insights into fundamental biological processes at the nanoscale – visualizing, for example, how molecular motors carry out their specific functions.

An intrinsic limitation of AFM imaging is that only superficial topography can be obtained, and the AFM tip is too large to resolve details below the nanometer scale. To facilitate interpretation and understanding of HS-AFM observations, post-experimental analysis and computational methods play an increasingly important role.

In their review paper published in Current opinion in structural biologyand Holger Flechsig (NanoLSI, Computational Science), and Toshio Ando (NanoLSI Distinguished Professor) provide an overview of developments in this topical area of ​​interdisciplinary research. Computational modeling and simulations already allow 3D conformations to be reconstructed with atomic resolution from topographically limited AFM images. Furthermore, quantitative analysis methods allow automated identification of biomolecular shape changes from topographic images, or feature customizations including identification of amino acid residues on the molecular surface.

The computational methods developed are often implemented in open access software, allowing convenient applications by the broad Bio-AFM community to complement experimental observations. In this regard, the BioAFMviewer software project that started at Kanazawa University in 2020 has received great attention and plays an important role in a large number of collaborative projects.

The combination of high-speed AFM and computational modeling will raise the level of understanding of how proteins function in atomic detail. An ambitious future goal is to apply molecular modeling to reconstruct 3D molecular films at the atomic level from high-speed AFM topographic films.