Initiating heavy-atom-based phasing by multi-dimensional molecular replacement
(2016) In Acta Crystallographica Section D: Structural Biology 72(Pt 3). p.5-440- Abstract
To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different... (More)
To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts.
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- author
- Pedersen, Bjørn Panyella ; Gourdon, Pontus LU ; Liu, Xiangyu ; Karlsen, Jesper Lykkegaard and Nissen, Poul
- publishing date
- 2016-03
- type
- Contribution to journal
- publication status
- published
- keywords
- Bacterial Proteins, Crystallization, Crystallography, X-Ray, Electrons, Legionella pneumophila, Protein Conformation, Software
- in
- Acta Crystallographica Section D: Structural Biology
- volume
- 72
- issue
- Pt 3
- pages
- 6 pages
- publisher
- John Wiley & Sons Inc.
- external identifiers
-
- scopus:85008951539
- pmid:26960131
- ISSN
- 2059-7983
- DOI
- 10.1107/S2059798315022482
- language
- English
- LU publication?
- no
- id
- 3f1c9b56-b5bf-455d-afb9-f02ef55ad6f4
- date added to LUP
- 2017-04-29 15:26:25
- date last changed
- 2025-01-07 12:10:04
@article{3f1c9b56-b5bf-455d-afb9-f02ef55ad6f4,
abstract = {{<p>To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts.</p>}},
author = {{Pedersen, Bjørn Panyella and Gourdon, Pontus and Liu, Xiangyu and Karlsen, Jesper Lykkegaard and Nissen, Poul}},
issn = {{2059-7983}},
keywords = {{Bacterial Proteins; Crystallization; Crystallography, X-Ray; Electrons; Legionella pneumophila; Protein Conformation; Software}},
language = {{eng}},
number = {{Pt 3}},
pages = {{5--440}},
publisher = {{John Wiley & Sons Inc.}},
series = {{Acta Crystallographica Section D: Structural Biology}},
title = {{Initiating heavy-atom-based phasing by multi-dimensional molecular replacement}},
url = {{http://dx.doi.org/10.1107/S2059798315022482}},
doi = {{10.1107/S2059798315022482}},
volume = {{72}},
year = {{2016}},
}