Initiating Heavy-atom Based Phasing by Multi-Dimensional Molecular Replacement

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

Initiating Heavy-atom Based Phasing by Multi-Dimensional Molecular Replacement

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

Inflammation, Metabolism and Oxidation

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 concomitantly the determination of the heavy atom substructure. This is customarily done by direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available, as often the case for e.g. membrane proteins. Here we present an approach for heavy atom site identification based on a Molecular Replacement Parameter Matrix (MRPM) search. It involves an n-dimensional search to test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied in the determination of a membrane protein structure, the CopA Cu+-ATPase, when other methods had failed to resolve the heavy atom substructure. MRPM is particularly suited for proteins undergoing large conformational changes where multiple search models should be generated, and it enables the identification of weak but correct molecular replacement solutions with maximum contrast to prime experimental phasing efforts.

Originalsprog	Engelsk
Tidsskrift	arXiv
Sider (fra-til)	1-19
Antal sider	19
Status	Udgivet - 28 mar. 2014

Citationsformater

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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 concomitantly the determination of the heavy atom substructure. This is customarily done by direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available, as often the case for e.g. membrane proteins. Here we present an approach for heavy atom site identification based on a Molecular Replacement Parameter Matrix (MRPM) search. It involves an n-dimensional search to test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied in the determination of a membrane protein structure, the CopA Cu+-ATPase, when other methods had failed to resolve the heavy atom substructure. MRPM is particularly suited for proteins undergoing large conformational changes where multiple search models should be generated, 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, {Bj{\o}rn Panyella} and Gourdon, {Pontus Emanuel} and Xiangyu Liu and Karlsen, {Jesper Lykkegaard} and Poul Nissen",

year = "2014",

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T1 - Initiating Heavy-atom Based Phasing by Multi-Dimensional Molecular Replacement

AU - Pedersen, Bjørn Panyella

AU - Gourdon, Pontus Emanuel

AU - Liu, Xiangyu

AU - Karlsen, Jesper Lykkegaard

AU - Nissen, Poul

PY - 2014/3/28

Y1 - 2014/3/28

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 concomitantly the determination of the heavy atom substructure. This is customarily done by direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available, as often the case for e.g. membrane proteins. Here we present an approach for heavy atom site identification based on a Molecular Replacement Parameter Matrix (MRPM) search. It involves an n-dimensional search to test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied in the determination of a membrane protein structure, the CopA Cu+-ATPase, when other methods had failed to resolve the heavy atom substructure. MRPM is particularly suited for proteins undergoing large conformational changes where multiple search models should be generated, 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 concomitantly the determination of the heavy atom substructure. This is customarily done by direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available, as often the case for e.g. membrane proteins. Here we present an approach for heavy atom site identification based on a Molecular Replacement Parameter Matrix (MRPM) search. It involves an n-dimensional search to test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied in the determination of a membrane protein structure, the CopA Cu+-ATPase, when other methods had failed to resolve the heavy atom substructure. MRPM is particularly suited for proteins undergoing large conformational changes where multiple search models should be generated, and it enables the identification of weak but correct molecular replacement solutions with maximum contrast to prime experimental phasing efforts.

KW - q-bio.BM

M3 - Journal article

SN - 1229-2370

SP - 1

EP - 19

JO - Journal of Communications and Networks

JF - Journal of Communications and Networks

ER -

Initiating Heavy-atom Based Phasing by Multi-Dimensional Molecular Replacement

Abstract

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