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Computing H/D-Exchange rates of single residues from data of proteolytic fragments

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2010

Autor:innen

Althaus, Ernst
Canzar, Stefan
Ehrler, Carsten
Emmett, Mark R.
Marshall, Alan G.
Meyer-Bäse, Anke
Tipton, Jeremiah D.
Zhang, Hui-Min

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http://nbn-resolving.de/urn:nbn:de:bsz:352-172677
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https://doi.org/10.1186/1471-2105-11-424
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BMC Bioinformatics. 2010, 11(1), 424. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-11-424

Zusammenfassung

Background: Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/
Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex.
In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and
compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides
generated from the protease digest of the protein is related to the solvent accessibility of amide protons within
the original protein construct.
Results: In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on
combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data
of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue
resolution.
Conclusions: With our new method it is possible to automatically determine deuterium exchange with higher
spatial resolution than the level of digested fragments.

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ISO 690ALTHAUS, Ernst, Stefan CANZAR, Carsten EHRLER, Mark R. EMMETT, Andreas KARRENBAUER, Alan G. MARSHALL, Anke MEYER-BÄSE, Jeremiah D. TIPTON, Hui-Min ZHANG, 2010. Computing H/D-Exchange rates of single residues from data of proteolytic fragments. In: BMC Bioinformatics. 2010, 11(1), 424. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-11-424
BibTex
@article{Althaus2010Compu-17267,
  year={2010},
  doi={10.1186/1471-2105-11-424},
  title={Computing H/D-Exchange rates of single residues from data of proteolytic fragments},
  number={1},
  volume={11},
  journal={BMC Bioinformatics},
  author={Althaus, Ernst and Canzar, Stefan and Ehrler, Carsten and Emmett, Mark R. and Karrenbauer, Andreas and Marshall, Alan G. and Meyer-Bäse, Anke and Tipton, Jeremiah D. and Zhang, Hui-Min},
  note={Article Number: 424}
}
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    <dcterms:abstract xml:lang="eng">Background: Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/&lt;br /&gt;Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex.&lt;br /&gt;In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and&lt;br /&gt;compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides&lt;br /&gt;generated from the protease digest of the protein is related to the solvent accessibility of amide protons within&lt;br /&gt;the original protein construct.&lt;br /&gt;Results: In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on&lt;br /&gt;combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data&lt;br /&gt;of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue&lt;br /&gt;resolution.&lt;br /&gt;Conclusions: With our new method it is possible to automatically determine deuterium exchange with higher&lt;br /&gt;spatial resolution than the level of digested fragments.</dcterms:abstract>
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