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Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo

Subtomogram averaging (STA) is a powerful image processing technique in electron tomography used to determine the 3D structure of macromolecular complexes in their native environments. It is a fast growing technique with increasing importance in structural biology. The computational aspect of STA is...

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Detalles Bibliográficos
Autores principales: Scaramuzza, Stefano, Castaño-Díez, Daniel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8389376/
https://www.ncbi.nlm.nih.gov/pubmed/34437529
http://dx.doi.org/10.1371/journal.pbio.3001318
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author Scaramuzza, Stefano
Castaño-Díez, Daniel
author_facet Scaramuzza, Stefano
Castaño-Díez, Daniel
author_sort Scaramuzza, Stefano
collection PubMed
description Subtomogram averaging (STA) is a powerful image processing technique in electron tomography used to determine the 3D structure of macromolecular complexes in their native environments. It is a fast growing technique with increasing importance in structural biology. The computational aspect of STA is very complex and depends on a large number of variables. We noticed a lack of detailed guides for STA processing. Also, current publications in this field often lack a documentation that is practical enough to reproduce the results with reasonable effort, which is necessary for the scientific community to grow. We therefore provide a complete, detailed, and fully reproducible processing protocol that covers all aspects of particle picking and particle alignment in STA. The command line–based workflow is fully based on the popular Dynamo software for STA. Within this workflow, we also demonstrate how large parts of the processing pipeline can be streamlined and automatized for increased throughput. This protocol is aimed at users on all levels. It can be used for training purposes, or it can serve as basis to design user-specific projects by taking advantage of the flexibility of Dynamo by modifying and expanding the given pipeline. The protocol is successfully validated using the Electron Microscopy Public Image Archive (EMPIAR) database entry 10164 from immature HIV-1 virus-like particles (VLPs) that describe a geometry often seen in electron tomography.
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spelling pubmed-83893762021-08-27 Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo Scaramuzza, Stefano Castaño-Díez, Daniel PLoS Biol Methods and Resources Subtomogram averaging (STA) is a powerful image processing technique in electron tomography used to determine the 3D structure of macromolecular complexes in their native environments. It is a fast growing technique with increasing importance in structural biology. The computational aspect of STA is very complex and depends on a large number of variables. We noticed a lack of detailed guides for STA processing. Also, current publications in this field often lack a documentation that is practical enough to reproduce the results with reasonable effort, which is necessary for the scientific community to grow. We therefore provide a complete, detailed, and fully reproducible processing protocol that covers all aspects of particle picking and particle alignment in STA. The command line–based workflow is fully based on the popular Dynamo software for STA. Within this workflow, we also demonstrate how large parts of the processing pipeline can be streamlined and automatized for increased throughput. This protocol is aimed at users on all levels. It can be used for training purposes, or it can serve as basis to design user-specific projects by taking advantage of the flexibility of Dynamo by modifying and expanding the given pipeline. The protocol is successfully validated using the Electron Microscopy Public Image Archive (EMPIAR) database entry 10164 from immature HIV-1 virus-like particles (VLPs) that describe a geometry often seen in electron tomography. Public Library of Science 2021-08-26 /pmc/articles/PMC8389376/ /pubmed/34437529 http://dx.doi.org/10.1371/journal.pbio.3001318 Text en © 2021 Scaramuzza, Castaño-Díez https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Methods and Resources
Scaramuzza, Stefano
Castaño-Díez, Daniel
Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo
title Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo
title_full Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo
title_fullStr Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo
title_full_unstemmed Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo
title_short Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo
title_sort step-by-step guide to efficient subtomogram averaging of virus-like particles with dynamo
topic Methods and Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8389376/
https://www.ncbi.nlm.nih.gov/pubmed/34437529
http://dx.doi.org/10.1371/journal.pbio.3001318
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