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

Bjørn Panyella Pedersen; Pontus Gourdon; Xiangyu Liu; Jesper Lykkegaard Karlsen; Poul Nissen

doi:10.1107/S2059798315022482

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

Bjørn Panyella Pedersen, Pontus Gourdon, Xiangyu Liu, Jesper Lykkegaard Karlsen, Poul Nissen

3 Citations (Scopus)

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 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.

Original language	English
Journal	Acta crystallographica Section D: Structural biology
Volume	72
Issue number	3
Pages (from-to)	440-445
Number of pages	6
ISSN	2059-7983
DOIs	https://doi.org/10.1107/S2059798315022482
Publication status	Published - 1 Mar 2016
Externally published	Yes

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title = "Initiating heavy-atom-based phasing by multi-dimensional molecular replacement",

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 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.",

author = "Pedersen, {Bj{\o}rn Panyella} and Pontus Gourdon and Xiangyu Liu and Karlsen, {Jesper Lykkegaard} and Poul Nissen",

year = "2016",

month = mar,

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doi = "10.1107/S2059798315022482",

language = "English",

volume = "72",

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T1 - Initiating heavy-atom-based phasing by multi-dimensional molecular replacement

AU - Pedersen, Bjørn Panyella

AU - Gourdon, Pontus

AU - Liu, Xiangyu

AU - Karlsen, Jesper Lykkegaard

AU - Nissen, Poul

PY - 2016/3/1

Y1 - 2016/3/1

N2 - 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.

AB - 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.

U2 - 10.1107/S2059798315022482

DO - 10.1107/S2059798315022482

M3 - Journal article

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SN - 2059-7983

VL - 72

SP - 440

EP - 445

JO - Acta Crystallographica Section D: Biological Crystallography

JF - Acta Crystallographica Section D: Biological Crystallography

IS - 3

ER -

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

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