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Approaches to ab initio molecular replacement of α-helical transmembrane proteins

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small lib...

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Autores principales: Thomas, Jens M. H., Simkovic, Felix, Keegan, Ronan, Mayans, Olga, Zhang, Chengxin, Zhang, Yang, Rigden, Daniel J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5713875/
https://www.ncbi.nlm.nih.gov/pubmed/29199978
http://dx.doi.org/10.1107/S2059798317016436
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author Thomas, Jens M. H.
Simkovic, Felix
Keegan, Ronan
Mayans, Olga
Zhang, Chengxin
Zhang, Yang
Rigden, Daniel J.
author_facet Thomas, Jens M. H.
Simkovic, Felix
Keegan, Ronan
Mayans, Olga
Zhang, Chengxin
Zhang, Yang
Rigden, Daniel J.
author_sort Thomas, Jens M. H.
collection PubMed
description α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.
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spelling pubmed-57138752017-12-13 Approaches to ab initio molecular replacement of α-helical transmembrane proteins Thomas, Jens M. H. Simkovic, Felix Keegan, Ronan Mayans, Olga Zhang, Chengxin Zhang, Yang Rigden, Daniel J. Acta Crystallogr D Struct Biol Research Papers α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible. International Union of Crystallography 2017-11-22 /pmc/articles/PMC5713875/ /pubmed/29199978 http://dx.doi.org/10.1107/S2059798317016436 Text en © Thomas et al. 2017 http://creativecommons.org/licenses/by/2.0/uk/ 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.http://creativecommons.org/licenses/by/2.0/uk/
spellingShingle Research Papers
Thomas, Jens M. H.
Simkovic, Felix
Keegan, Ronan
Mayans, Olga
Zhang, Chengxin
Zhang, Yang
Rigden, Daniel J.
Approaches to ab initio molecular replacement of α-helical transmembrane proteins
title Approaches to ab initio molecular replacement of α-helical transmembrane proteins
title_full Approaches to ab initio molecular replacement of α-helical transmembrane proteins
title_fullStr Approaches to ab initio molecular replacement of α-helical transmembrane proteins
title_full_unstemmed Approaches to ab initio molecular replacement of α-helical transmembrane proteins
title_short Approaches to ab initio molecular replacement of α-helical transmembrane proteins
title_sort approaches to ab initio molecular replacement of α-helical transmembrane proteins
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5713875/
https://www.ncbi.nlm.nih.gov/pubmed/29199978
http://dx.doi.org/10.1107/S2059798317016436
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