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Effects of cryo-EM cooling on structural ensembles

Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble i...

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Autores principales: Bock, Lars V., Grubmüller, Helmut
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8971465/
https://www.ncbi.nlm.nih.gov/pubmed/35361752
http://dx.doi.org/10.1038/s41467-022-29332-2
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author Bock, Lars V.
Grubmüller, Helmut
author_facet Bock, Lars V.
Grubmüller, Helmut
author_sort Bock, Lars V.
collection PubMed
description Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures.
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spelling pubmed-89714652022-04-20 Effects of cryo-EM cooling on structural ensembles Bock, Lars V. Grubmüller, Helmut Nat Commun Article Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures. Nature Publishing Group UK 2022-03-31 /pmc/articles/PMC8971465/ /pubmed/35361752 http://dx.doi.org/10.1038/s41467-022-29332-2 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Bock, Lars V.
Grubmüller, Helmut
Effects of cryo-EM cooling on structural ensembles
title Effects of cryo-EM cooling on structural ensembles
title_full Effects of cryo-EM cooling on structural ensembles
title_fullStr Effects of cryo-EM cooling on structural ensembles
title_full_unstemmed Effects of cryo-EM cooling on structural ensembles
title_short Effects of cryo-EM cooling on structural ensembles
title_sort effects of cryo-em cooling on structural ensembles
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8971465/
https://www.ncbi.nlm.nih.gov/pubmed/35361752
http://dx.doi.org/10.1038/s41467-022-29332-2
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