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Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality
[Image: see text] Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid–liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in ce...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9208010/ https://www.ncbi.nlm.nih.gov/pubmed/35678499 http://dx.doi.org/10.1021/acs.jpclett.2c01093 |
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author | Sumikama, Takashi Federici Canova, Filippo Gao, David Z. Penedo, Marcos Miyazawa, Keisuke Foster, Adam S. Fukuma, Takeshi |
author_facet | Sumikama, Takashi Federici Canova, Filippo Gao, David Z. Penedo, Marcos Miyazawa, Keisuke Foster, Adam S. Fukuma, Takeshi |
author_sort | Sumikama, Takashi |
collection | PubMed |
description | [Image: see text] Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid–liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe. |
format | Online Article Text |
id | pubmed-9208010 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-92080102022-06-21 Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality Sumikama, Takashi Federici Canova, Filippo Gao, David Z. Penedo, Marcos Miyazawa, Keisuke Foster, Adam S. Fukuma, Takeshi J Phys Chem Lett [Image: see text] Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid–liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe. American Chemical Society 2022-06-09 2022-06-16 /pmc/articles/PMC9208010/ /pubmed/35678499 http://dx.doi.org/10.1021/acs.jpclett.2c01093 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Sumikama, Takashi Federici Canova, Filippo Gao, David Z. Penedo, Marcos Miyazawa, Keisuke Foster, Adam S. Fukuma, Takeshi Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality |
title | Computed Three-Dimensional Atomic Force Microscopy
Images of Biopolymers Using the Jarzynski Equality |
title_full | Computed Three-Dimensional Atomic Force Microscopy
Images of Biopolymers Using the Jarzynski Equality |
title_fullStr | Computed Three-Dimensional Atomic Force Microscopy
Images of Biopolymers Using the Jarzynski Equality |
title_full_unstemmed | Computed Three-Dimensional Atomic Force Microscopy
Images of Biopolymers Using the Jarzynski Equality |
title_short | Computed Three-Dimensional Atomic Force Microscopy
Images of Biopolymers Using the Jarzynski Equality |
title_sort | computed three-dimensional atomic force microscopy
images of biopolymers using the jarzynski equality |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9208010/ https://www.ncbi.nlm.nih.gov/pubmed/35678499 http://dx.doi.org/10.1021/acs.jpclett.2c01093 |
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