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Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM

In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas t...

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Autores principales: Simpkin, Adam J., Winn, Martyn D., Rigden, Daniel J., Keegan, Ronan M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8561737/
https://www.ncbi.nlm.nih.gov/pubmed/34726166
http://dx.doi.org/10.1107/S2059798321009165
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author Simpkin, Adam J.
Winn, Martyn D.
Rigden, Daniel J.
Keegan, Ronan M.
author_facet Simpkin, Adam J.
Winn, Martyn D.
Rigden, Daniel J.
Keegan, Ronan M.
author_sort Simpkin, Adam J.
collection PubMed
description In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (<8 Å) data sets.
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spelling pubmed-85617372021-11-18 Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM Simpkin, Adam J. Winn, Martyn D. Rigden, Daniel J. Keegan, Ronan M. Acta Crystallogr D Struct Biol Ccp-EM In crystallography, the phase problem can often be addressed by the careful preparation of molecular-replacement search models. This has led to the development of pipelines such as MrBUMP that can automatically identify homologous proteins from an input sequence and edit them to focus on the areas that are most conserved. Many of these approaches can be applied directly to cryo-EM to help discover, prepare and correctly place models (here called cryo-EM search models) into electrostatic potential maps. This can significantly reduce the amount of manual model building that is required for structure determination. Here, MrBUMP is repurposed to fit automatically obtained PDB-derived chains and domains into cryo-EM maps. MrBUMP was successfully able to identify and place cryo-EM search models across a range of resolutions. Methods such as map segmentation are also explored as potential routes to improved performance. Map segmentation was also found to improve the effectiveness of the pipeline for higher resolution (<8 Å) data sets. International Union of Crystallography 2021-10-20 /pmc/articles/PMC8561737/ /pubmed/34726166 http://dx.doi.org/10.1107/S2059798321009165 Text en © Adam J. Simpkin et al. 2021 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Ccp-EM
Simpkin, Adam J.
Winn, Martyn D.
Rigden, Daniel J.
Keegan, Ronan M.
Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM
title Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM
title_full Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM
title_fullStr Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM
title_full_unstemmed Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM
title_short Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM
title_sort redeployment of automated mrbump search-model identification for map fitting in cryo-em
topic Ccp-EM
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8561737/
https://www.ncbi.nlm.nih.gov/pubmed/34726166
http://dx.doi.org/10.1107/S2059798321009165
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