Cargando…
ARCIMBOLDO on coiled coils
ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, t...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947760/ https://www.ncbi.nlm.nih.gov/pubmed/29533227 http://dx.doi.org/10.1107/S2059798317017582 |
_version_ | 1783322434810675200 |
---|---|
author | Caballero, Iracema Sammito, Massimo Millán, Claudia Lebedev, Andrey Soler, Nicolas Usón, Isabel |
author_facet | Caballero, Iracema Sammito, Massimo Millán, Claudia Lebedev, Andrey Soler, Nicolas Usón, Isabel |
author_sort | Caballero, Iracema |
collection | PubMed |
description | ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i. |
format | Online Article Text |
id | pubmed-5947760 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-59477602018-05-30 ARCIMBOLDO on coiled coils Caballero, Iracema Sammito, Massimo Millán, Claudia Lebedev, Andrey Soler, Nicolas Usón, Isabel Acta Crystallogr D Struct Biol Research Papers ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers. ARCIMBOLDO_LITE has been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures using ARCIMBOLDO. Features from Phaser v.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification and SHELXE autotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode within ARCIMBOLDO for the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) or ARCIMBOLDO_LITE task interface in CCP4i. International Union of Crystallography 2018-03-02 /pmc/articles/PMC5947760/ /pubmed/29533227 http://dx.doi.org/10.1107/S2059798317017582 Text en © Caballero et al. 2018 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 Caballero, Iracema Sammito, Massimo Millán, Claudia Lebedev, Andrey Soler, Nicolas Usón, Isabel ARCIMBOLDO on coiled coils |
title |
ARCIMBOLDO on coiled coils |
title_full |
ARCIMBOLDO on coiled coils |
title_fullStr |
ARCIMBOLDO on coiled coils |
title_full_unstemmed |
ARCIMBOLDO on coiled coils |
title_short |
ARCIMBOLDO on coiled coils |
title_sort | arcimboldo on coiled coils |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947760/ https://www.ncbi.nlm.nih.gov/pubmed/29533227 http://dx.doi.org/10.1107/S2059798317017582 |
work_keys_str_mv | AT caballeroiracema arcimboldooncoiledcoils AT sammitomassimo arcimboldooncoiledcoils AT millanclaudia arcimboldooncoiledcoils AT lebedevandrey arcimboldooncoiledcoils AT solernicolas arcimboldooncoiledcoils AT usonisabel arcimboldooncoiledcoils |