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Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography
An evaluation of systematic differences in local structure and conformation in the interior of protein tertiary structures determined by crystallography and by cryo-electron microscopy (cryo-EM) is reported. The expectation is that any consistent differences between the derived atomic models could p...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8733892/ https://www.ncbi.nlm.nih.gov/pubmed/35059214 http://dx.doi.org/10.1107/S2052252521011945 |
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author | Ravikumar, Ashraya Gopnarayan, Mrugsen Nagsen Subramaniam, Sriram Srinivasan, Narayanaswamy |
author_facet | Ravikumar, Ashraya Gopnarayan, Mrugsen Nagsen Subramaniam, Sriram Srinivasan, Narayanaswamy |
author_sort | Ravikumar, Ashraya |
collection | PubMed |
description | An evaluation of systematic differences in local structure and conformation in the interior of protein tertiary structures determined by crystallography and by cryo-electron microscopy (cryo-EM) is reported. The expectation is that any consistent differences between the derived atomic models could provide insights into variations in side-chain packing that result from differences in specimens prepared for analysis between these two methods. By computing an atomic packing score, which provides a quantitative measure of clustering of side-chain atoms in the core of the tertiary structures, it is found that, in general, for structures determined by cryo-EM, side chains are more dispersed than in structures determined by X-ray crystallography over a similar resolution range. This trend is also observed in the packing comparison at subunit interfaces. Similar trends were observed in the packing comparison at the core of tertiary structures of the same proteins determined by both X-ray and cryo-EM methods. It is proposed here that the reduced dispersion of side chains in protein crystals could be due to some level of dehydration in 3D crystals prepared for X-ray crystallography and also because the higher rate of freezing of protein samples for cryo-EM may enable preservation of a more native conformation. |
format | Online Article Text |
id | pubmed-8733892 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-87338922022-01-19 Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography Ravikumar, Ashraya Gopnarayan, Mrugsen Nagsen Subramaniam, Sriram Srinivasan, Narayanaswamy IUCrJ Research Papers An evaluation of systematic differences in local structure and conformation in the interior of protein tertiary structures determined by crystallography and by cryo-electron microscopy (cryo-EM) is reported. The expectation is that any consistent differences between the derived atomic models could provide insights into variations in side-chain packing that result from differences in specimens prepared for analysis between these two methods. By computing an atomic packing score, which provides a quantitative measure of clustering of side-chain atoms in the core of the tertiary structures, it is found that, in general, for structures determined by cryo-EM, side chains are more dispersed than in structures determined by X-ray crystallography over a similar resolution range. This trend is also observed in the packing comparison at subunit interfaces. Similar trends were observed in the packing comparison at the core of tertiary structures of the same proteins determined by both X-ray and cryo-EM methods. It is proposed here that the reduced dispersion of side chains in protein crystals could be due to some level of dehydration in 3D crystals prepared for X-ray crystallography and also because the higher rate of freezing of protein samples for cryo-EM may enable preservation of a more native conformation. International Union of Crystallography 2021-12-10 /pmc/articles/PMC8733892/ /pubmed/35059214 http://dx.doi.org/10.1107/S2052252521011945 Text en © A. Ravikumar et al. 2022 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 | Research Papers Ravikumar, Ashraya Gopnarayan, Mrugsen Nagsen Subramaniam, Sriram Srinivasan, Narayanaswamy Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography |
title | Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography |
title_full | Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography |
title_fullStr | Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography |
title_full_unstemmed | Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography |
title_short | Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography |
title_sort | comparison of side-chain dispersion in protein structures determined by cryo-em and x-ray crystallography |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8733892/ https://www.ncbi.nlm.nih.gov/pubmed/35059214 http://dx.doi.org/10.1107/S2052252521011945 |
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