2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching

Abstract In this study, we develop an approach termed “2D hybrid analysis” for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In...

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Autores principales:	Atsushi Matsumoto, Naoyuki Miyazaki, Junichi Takagi, Kenji Iwasaki
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6d905341f689497fa32f72555a18ce27
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spelling	oai:doaj.org-article:6d905341f689497fa32f72555a18ce272021-12-02T12:32:30Z2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching10.1038/s41598-017-00337-y2045-2322https://doaj.org/article/6d905341f689497fa32f72555a18ce272017-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00337-yhttps://doaj.org/toc/2045-2322Abstract In this study, we develop an approach termed “2D hybrid analysis” for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.Atsushi MatsumotoNaoyuki MiyazakiJunichi TakagiKenji IwasakiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Atsushi Matsumoto Naoyuki Miyazaki Junichi Takagi Kenji Iwasaki 2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching
description	Abstract In this study, we develop an approach termed “2D hybrid analysis” for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.
format	article
author	Atsushi Matsumoto Naoyuki Miyazaki Junichi Takagi Kenji Iwasaki
author_facet	Atsushi Matsumoto Naoyuki Miyazaki Junichi Takagi Kenji Iwasaki
author_sort	Atsushi Matsumoto
title	2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching
title_short	2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching
title_full	2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching
title_fullStr	2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching
title_full_unstemmed	2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching
title_sort	2d hybrid analysis: approach for building three-dimensional atomic model by electron microscopy image matching
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/6d905341f689497fa32f72555a18ce27
work_keys_str_mv	AT atsushimatsumoto 2dhybridanalysisapproachforbuildingthreedimensionalatomicmodelbyelectronmicroscopyimagematching AT naoyukimiyazaki 2dhybridanalysisapproachforbuildingthreedimensionalatomicmodelbyelectronmicroscopyimagematching AT junichitakagi 2dhybridanalysisapproachforbuildingthreedimensionalatomicmodelbyelectronmicroscopyimagematching AT kenjiiwasaki 2dhybridanalysisapproachforbuildingthreedimensionalatomicmodelbyelectronmicroscopyimagematching
_version_	1718394039223451648

2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching

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