Open AccessSimulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images
Author(s) -
Romain Amyot,
Arin Marchesi,
Clemens M. Franz,
Ignacio Casuso,
Holger Flechsig
Publication year - 2022
Publication title -
plos computational biology/plos computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.628
H-Index - 182
eISSN - 1553-7358
pISSN - 1553-734X
DOI - 10.1371/journal.pcbi.1009970
Subject(s) - atomic force microscopy , biomolecule , resolution (logic) , nanotechnology , computer science , molecular dynamics , microscopy , image resolution , materials science , biological system , chemistry , physics , artificial intelligence , optics , computational chemistry , biology
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, the scanning tip probes only the molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework to reconstruct 3D atomistic structures from AFM surface scans, employing simulation AFM and automatized fitting to experimental images. We provide applications to AFM images ranging from single molecular machines, protein filaments, to large-scale assemblies of 2D protein lattices, and demonstrate how the obtained full atomistic information advances the molecular understanding beyond the original topographic AFM image. We show that simulation AFM further allows for quantitative molecular feature assignment within measured AFM topographies. Implementation of the developed methods into the versatile interactive interface of the BioAFMviewer software, freely available at www.bioafmviewer.com , presents the opportunity for the broad Bio-AFM community to employ the enormous amount of existing structural and modeling data to facilitate the interpretation of resolution-limited AFM images.