Kanazawa Univesity NanoLSI Podcast:Dynamic 3D structure extraction from HS-AFM images

Transcript of this podcast

 Hello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by  Holger Flechsig and Toshio Ando at the Kanazawa University NanoLSI.

 The research described in this podcast was published in the journal Current Opinion in Structural Biology in April 2023

 Kanazawa University NanoLSI website
  https://nanolsi.kanazawa-u.ac.jp/en/

 Dynamic 3D structure extraction from high-speed atomic force microscopy images
 
 By allowing the direct observation of biomolecules in dynamic action, high-speed atomic force microscopy or AFM has opened a new avenue to dynamic structural biology. A vast number of successful applications within the past 15 years have provided unique insights into essential biological processes at the nanoscale – visualizing, for example, how molecular motors execute their specific functions.

 Some intrinsic limitations of AFM imaging are that only the surface topography can be acquired, and that the AFM tip is too large to resolve details below the nanometer scale. To facilitate the interpretation and understanding of high-speed AFM observations, post-experimental analysis and computational methods play an increasingly important role.

 In their review paper published in the Current Opinion in Structural Biology journal Holger Flechsig a computational scientist at the NanoLSI at Kanazawa University and Toshio Ando, a Distinguished Professor at NanoLSI, provide an overview of developments in this topical field of interdisciplinary research. Computational modeling and simulations already allow the reconstruction of 3D conformations with atomistic resolution from topographic resolution-limited AFM images. Furthermore, quantitative analysis methods allow for example automated recognition of biomolecular shape changes from topographic images, or feature assignment including the identification of amino acid residues on the molecular surface.

So how is all this implemented?

The developed computational methods are often implemented in open-access software, allowing for convenient applications by the broad Bio-AFM community to complement experimental observations. In that regard, the BioAFMviewer software project initiated at Kanazawa University in 2020 has gained significant attention and plays an important role in a plethora of collaboration projects.

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

Reference
Holger Flechsig and Toshio Ando. Protein dynamics by the combination of high-speed AFM and computational modeling

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