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Approaches to ab initio molecular replacement of α‐helical transmembrane proteins
Author(s) -
Thomas Jens M. H.,
Simkovic Felix,
Keegan Ronan,
Mayans Olga,
Zhang Chengxin,
Zhang Yang,
Rigden Daniel J.
Publication year - 2017
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798317016436
Subject(s) - ab initio , ideal (ethics) , transmembrane protein , transmembrane domain , pipeline (software) , protein data bank , class (philosophy) , protein structure , chemistry , computer science , amino acid , artificial intelligence , biochemistry , philosophy , receptor , organic chemistry , epistemology , programming language
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.