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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2017
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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. |
format | Online Article Text |
id | pubmed-5713875 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
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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