Extraction of dynamic 3D structures from HS-AFM images

April 28, 2023

(Nanowerk News) Allowing the direct observation of biomolecules in dynamic action, high-speed AFM has opened a new pathway to dynamic structural biology. A large number of successful applications in the last 15 years provide unique insights into essential biological processes at the nanoscale – visualizing, for example, how molecular motors carry out their specific functions.

An intrinsic limitation in AFM imaging is that only surface topography can be obtained, and the AFM tip is too large to resolve detail below the nanometer scale. In order to facilitate the interpretation and understanding of HS-AFM observations, post-experimental analysis and computational methods are playing an increasingly important role.

In their review paper published in Current Opinion in Structural Biology(“Protein dynamics with a combination of high-speed AFM and computational modeling”), Holger Flechsig (NanoLSI, Computational Science), and Toshio Ando (Distinguished Professor of NanoLSI) provide an overview of developments in this topical interdisciplinary research area.

Computational modeling and simulation have made it possible to reconstruct 3D conformations with atomistic resolution from AFM images with topographically limited resolution. In addition, quantitative analytical methods allow for example the automatic recognition of changing biomolecular shapes from topographical images, or the assignment of features including the identification of amino acid residues on the surface of molecules.

The computational methods developed are often implemented in open access software, enabling convenient application by the extensive Bio-AFM community to complement experimental observations. In that regard, the software project BioAFMviewer started at Kanazawa University in 2020 has received significant attention and played an important role in many collaborative projects.

Combining high-speed AFM and computational modeling will enhance understanding of how proteins function in atomistic detail. An ambitious future goal is the application of molecular modeling to reconstruct atomistic-level 3D molecular films from high-speed AFM topographical films.

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