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Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()

Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to...

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Autores principales: Pandurangan, Arun Prasad, Shakeel, Shabih, Butcher, Sarah Jane, Topf, Maya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Academic Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988922/
https://www.ncbi.nlm.nih.gov/pubmed/24333899
http://dx.doi.org/10.1016/j.jsb.2013.12.003
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author Pandurangan, Arun Prasad
Shakeel, Shabih
Butcher, Sarah Jane
Topf, Maya
author_facet Pandurangan, Arun Prasad
Shakeel, Shabih
Butcher, Sarah Jane
Topf, Maya
author_sort Pandurangan, Arun Prasad
collection PubMed
description Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2 and 6.1 Å resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog – EV71 capsid – in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by ∼5° counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting.
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spelling pubmed-39889222014-04-17 Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change() Pandurangan, Arun Prasad Shakeel, Shabih Butcher, Sarah Jane Topf, Maya J Struct Biol Article Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2 and 6.1 Å resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog – EV71 capsid – in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by ∼5° counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting. Academic Press 2014-03 /pmc/articles/PMC3988922/ /pubmed/24333899 http://dx.doi.org/10.1016/j.jsb.2013.12.003 Text en © 2013 The Authors http://creativecommons.org/licenses/by-nc-nd/3.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).
spellingShingle Article
Pandurangan, Arun Prasad
Shakeel, Shabih
Butcher, Sarah Jane
Topf, Maya
Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()
title Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()
title_full Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()
title_fullStr Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()
title_full_unstemmed Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()
title_short Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()
title_sort combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change()
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988922/
https://www.ncbi.nlm.nih.gov/pubmed/24333899
http://dx.doi.org/10.1016/j.jsb.2013.12.003
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