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Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images

Amyot, Romain ; Marchesi, Arin ; Franz, Clemens M ; Casuso, Ignacio ; Flechsig, Holger Onufriev, Alexey

PLoS computational biology, 2022-03, Vol.18 (3), p.e1009970-e1009970 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images
Autor: Amyot, Romain ; Marchesi, Arin ; Franz, Clemens M ; Casuso, Ignacio ; Flechsig, Holger
Onufriev, Alexey
Assuntos: Algorithms ; Atomic force microscopy ; Biology and Life Sciences ; Biomolecules ; Computer and Information Sciences ; Computer applications ; Computer Simulation ; Engineering and Technology ; Filaments ; Image reconstruction ; Lattices ; Methods ; Microscopes ; Microscopy ; Microscopy, Atomic Force - methods ; Molecular machines ; Molecular structure ; Nanotechnology ; Observations ; Optimization ; Physical Sciences ; Proteins ; Proteins - chemistry ; Research and Analysis Methods ; Simulation ; Software ; Topography
É parte de: PLoS computational biology, 2022-03, Vol.18 (3), p.e1009970-e1009970
Notas: new_version
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The authors have declared that no competing interests exist.
Current address: Dipartimento di Medicina Sperimentale e Clinica, Università Politecnica delle Marche, Ancona, Italy
Descrição: 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.
Editor: United States: Public Library of Science
Idioma: Inglês

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Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images

Amyot, Romain ; Marchesi, Arin ; Franz, Clemens M ; Casuso, Ignacio ; Flechsig, Holger Onufriev, Alexey

United States: Public Library of Science

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