Cargando…

Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8

The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre‐existing experimentally determined structures are used as search models. In favorable cases, ab...

Descripción completa

Detalles Bibliográficos
Autores principales: Flower, Thomas G., Hurley, James H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7980513/
https://www.ncbi.nlm.nih.gov/pubmed/33625752
http://dx.doi.org/10.1002/pro.4050
_version_ 1783667444389249024
author Flower, Thomas G.
Hurley, James H.
author_facet Flower, Thomas G.
Hurley, James H.
author_sort Flower, Thomas G.
collection PubMed
description The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre‐existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for MR. The ORF8 protein of SARS‐CoV‐2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all β‐sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.
format Online
Article
Text
id pubmed-7980513
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher John Wiley & Sons, Inc.
record_format MEDLINE/PubMed
spelling pubmed-79805132021-04-01 Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8 Flower, Thomas G. Hurley, James H. Protein Sci Accelerated Communications The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre‐existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for MR. The ORF8 protein of SARS‐CoV‐2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all β‐sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution. John Wiley & Sons, Inc. 2021-03-04 2021-04 /pmc/articles/PMC7980513/ /pubmed/33625752 http://dx.doi.org/10.1002/pro.4050 Text en © 2021 The Protein Society.
spellingShingle Accelerated Communications
Flower, Thomas G.
Hurley, James H.
Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8
title Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8
title_full Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8
title_fullStr Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8
title_full_unstemmed Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8
title_short Crystallographic molecular replacement using an in silico‐generated search model of SARS‐CoV‐2 ORF8
title_sort crystallographic molecular replacement using an in silico‐generated search model of sars‐cov‐2 orf8
topic Accelerated Communications
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7980513/
https://www.ncbi.nlm.nih.gov/pubmed/33625752
http://dx.doi.org/10.1002/pro.4050
work_keys_str_mv AT flowerthomasg crystallographicmolecularreplacementusinganinsilicogeneratedsearchmodelofsarscov2orf8
AT hurleyjamesh crystallographicmolecularreplacementusinganinsilicogeneratedsearchmodelofsarscov2orf8