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Initiating heavy-atom-based phasing by multi-dimensional molecular replacement

Pedersen, Bjørn Panyella ; Gourdon, Pontus LU ; Liu, Xiangyu ; Karlsen, Jesper Lykkegaard and Nissen, Poul (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
publishing date
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 and Sons Inc.
external identifiers
  • pmid:26960131
  • scopus:85008951539
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
2020-03-31 15:01:06
@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},
  language     = {eng},
  number       = {Pt 3},
  pages        = {5--440},
  publisher    = {John Wiley and 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},
}