Development of crystallographic methods for phasing highly modulated macromolecular structures

[eng] Pathologies that result in highly modulated intensities in macromolecular crystal structures pose a challenge for structure solution. To address this issue two studies have been performed: a theoretical study of one of these pathologies, translational non- crystallographic symmetry (tNCS), and...

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Author: Caballero Muñoz, Iracema
Format: doctoral thesis
Status:Published version
Publication Date:2021
Country:España
Institution:Universidad de Barcelona
Repository:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/183636
Online Access:https://hdl.handle.net/2445/183636
http://hdl.handle.net/10803/673601
Access Level:Open access
Keyword:Biologia molecular
Proteòmica
Macromolècules
Cristal·lografia
Estructura cristal·lina (Sòlids)
Molecular biology
Proteomics
Macromolecules
Crystallography
Layer structure (Solids)
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oai_identifier_str oai:diposit.ub.edu:2445/183636
network_acronym_str ES
network_name_str España
repository_id_str
spelling Development of crystallographic methods for phasing highly modulated macromolecular structuresCaballero Muñoz, IracemaBiologia molecularProteòmicaMacromolèculesCristal·lografiaEstructura cristal·lina (Sòlids)Molecular biologyProteomicsMacromoleculesCrystallographyLayer structure (Solids)[eng] Pathologies that result in highly modulated intensities in macromolecular crystal structures pose a challenge for structure solution. To address this issue two studies have been performed: a theoretical study of one of these pathologies, translational non- crystallographic symmetry (tNCS), and a practical study of paradigms of highly modulated macromolecular structures, coiled-coils. tNCS is a structural situation in which multiple, independent copies of a molecular assembly are found in similar orientations in the crystallographic asymmetric unit. Structure solution is problematic because the intensity modulations caused by tNCS cause the intensity distribution to differ from a Wilson distribution. If the tNCS is properly detected and characterized, expected intensity factors for each reflection that model the modulations observed in the data can be refined against a likelihood function to account for the statistical effects of tNCS. In this study, a curated database of 80482 protein structures from the PDB was analysed to investigate how tNCS manifests in the Patterson function. These studies informed the algorithm for detection of tNCS, which includes a method for detecting the tNCS order in any commensurate modulation. In the context of automated structure solution pipelines, the algorithm generates a ranked list of possible tNCS associations in the asymmetric unit, which can be explored to efficiently maximize the probability of structure solution. Coiled-coils are ubiquitous protein folding motifs present in a wide range of proteins that consist of two or more α-helices wrapped around each other to form a supercoil. Despite the apparent simplicity of their architecture, solution by molecular replacement is challenging due to the helical irregularities found in these domains, tendency to form fibers, large dimensions in their typically anisometric asymmetric units, low-resolution and anisotropic diffraction. In addition, the internal symmetry of the helices and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors, a Patterson map that indicates tNCS is present, and intensity modulations similar to those in true tNCS. In this study, we have explored fragment phasing on a pool of 150 coiled-coils with ARCIMBOLDO_LITE, an ab initio phasing approach that combines fragment location with Phaser and density modification and autotracing with SHELXE. The results have been used to identify limits and bottlenecks in coiled-coil phasing that have been addressed in a specific mode for solving coiled-coils, allowing the solution of 95% of the test set and four previously unknown structures, and extending the resolution limit from 2.5 Å to 3.0 Å.Universitat de BarcelonaUsón Finkenzeller, IsabelMcCoy, Airlie J.Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació2021info:eu-repo/semantics/doctoralThesisinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/183636http://hdl.handle.net/10803/673601Tesis Doctorals - Facultat - Farmàcia i Ciències de l'Alimentacióreponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaIngléscc by-nc-sa (c) Caballero Muñoz, Iracema, 2022http://creativecommons.org/licenses/by-nc-sa/3.0/es/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1836362026-05-27T06:46:51Z
dc.title.none.fl_str_mv Development of crystallographic methods for phasing highly modulated macromolecular structures
title Development of crystallographic methods for phasing highly modulated macromolecular structures
spellingShingle Development of crystallographic methods for phasing highly modulated macromolecular structures
Caballero Muñoz, Iracema
Biologia molecular
Proteòmica
Macromolècules
Cristal·lografia
Estructura cristal·lina (Sòlids)
Molecular biology
Proteomics
Macromolecules
Crystallography
Layer structure (Solids)
title_short Development of crystallographic methods for phasing highly modulated macromolecular structures
title_full Development of crystallographic methods for phasing highly modulated macromolecular structures
title_fullStr Development of crystallographic methods for phasing highly modulated macromolecular structures
title_full_unstemmed Development of crystallographic methods for phasing highly modulated macromolecular structures
title_sort Development of crystallographic methods for phasing highly modulated macromolecular structures
dc.creator.none.fl_str_mv Caballero Muñoz, Iracema
author Caballero Muñoz, Iracema
author_facet Caballero Muñoz, Iracema
author_role author
dc.contributor.none.fl_str_mv Usón Finkenzeller, Isabel
McCoy, Airlie J.
Universitat de Barcelona. Facultat de Farmàcia i Ciències de l'Alimentació
dc.subject.none.fl_str_mv Biologia molecular
Proteòmica
Macromolècules
Cristal·lografia
Estructura cristal·lina (Sòlids)
Molecular biology
Proteomics
Macromolecules
Crystallography
Layer structure (Solids)
topic Biologia molecular
Proteòmica
Macromolècules
Cristal·lografia
Estructura cristal·lina (Sòlids)
Molecular biology
Proteomics
Macromolecules
Crystallography
Layer structure (Solids)
description [eng] Pathologies that result in highly modulated intensities in macromolecular crystal structures pose a challenge for structure solution. To address this issue two studies have been performed: a theoretical study of one of these pathologies, translational non- crystallographic symmetry (tNCS), and a practical study of paradigms of highly modulated macromolecular structures, coiled-coils. tNCS is a structural situation in which multiple, independent copies of a molecular assembly are found in similar orientations in the crystallographic asymmetric unit. Structure solution is problematic because the intensity modulations caused by tNCS cause the intensity distribution to differ from a Wilson distribution. If the tNCS is properly detected and characterized, expected intensity factors for each reflection that model the modulations observed in the data can be refined against a likelihood function to account for the statistical effects of tNCS. In this study, a curated database of 80482 protein structures from the PDB was analysed to investigate how tNCS manifests in the Patterson function. These studies informed the algorithm for detection of tNCS, which includes a method for detecting the tNCS order in any commensurate modulation. In the context of automated structure solution pipelines, the algorithm generates a ranked list of possible tNCS associations in the asymmetric unit, which can be explored to efficiently maximize the probability of structure solution. Coiled-coils are ubiquitous protein folding motifs present in a wide range of proteins that consist of two or more α-helices wrapped around each other to form a supercoil. Despite the apparent simplicity of their architecture, solution by molecular replacement is challenging due to the helical irregularities found in these domains, tendency to form fibers, large dimensions in their typically anisometric asymmetric units, low-resolution and anisotropic diffraction. In addition, the internal symmetry of the helices and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors, a Patterson map that indicates tNCS is present, and intensity modulations similar to those in true tNCS. In this study, we have explored fragment phasing on a pool of 150 coiled-coils with ARCIMBOLDO_LITE, an ab initio phasing approach that combines fragment location with Phaser and density modification and autotracing with SHELXE. The results have been used to identify limits and bottlenecks in coiled-coil phasing that have been addressed in a specific mode for solving coiled-coils, allowing the solution of 95% of the test set and four previously unknown structures, and extending the resolution limit from 2.5 Å to 3.0 Å.
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/doctoralThesis
info:eu-repo/semantics/publishedVersion
format doctoralThesis
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/183636
http://hdl.handle.net/10803/673601
url https://hdl.handle.net/2445/183636
http://hdl.handle.net/10803/673601
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv cc by-nc-sa (c) Caballero Muñoz, Iracema, 2022
http://creativecommons.org/licenses/by-nc-sa/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc by-nc-sa (c) Caballero Muñoz, Iracema, 2022
http://creativecommons.org/licenses/by-nc-sa/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universitat de Barcelona
publisher.none.fl_str_mv Universitat de Barcelona
dc.source.none.fl_str_mv Tesis Doctorals - Facultat - Farmàcia i Ciències de l'Alimentació
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.300724

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