Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.
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 suc...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-03-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1009970 |
| _version_ | 1828413848082710528 |
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| author | Romain Amyot Arin Marchesi Clemens M Franz Ignacio Casuso Holger Flechsig |
| author_facet | Romain Amyot Arin Marchesi Clemens M Franz Ignacio Casuso Holger Flechsig |
| author_sort | Romain Amyot |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T13:15:54Z |
| format | Article |
| id | doaj.art-bc59ff1b08f34d7298a14456d81771e8 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-10T13:15:54Z |
| publishDate | 2022-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-bc59ff1b08f34d7298a14456d81771e82022-12-22T01:47:32ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582022-03-01183e100997010.1371/journal.pcbi.1009970Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.Romain AmyotArin MarchesiClemens M FranzIgnacio CasusoHolger FlechsigAtomic 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.https://doi.org/10.1371/journal.pcbi.1009970 |
| spellingShingle | Romain Amyot Arin Marchesi Clemens M Franz Ignacio Casuso Holger Flechsig Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. PLoS Computational Biology |
| title | Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. |
| title_full | Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. |
| title_fullStr | Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. |
| title_full_unstemmed | Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. |
| title_short | Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. |
| title_sort | simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution limited experimental images |
| url | https://doi.org/10.1371/journal.pcbi.1009970 |
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