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

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

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number424
JournalBMC Bioinformatics
Volume11
DOIs
StatePublished - Aug 11 2010
Externally publishedYes

Fingerprint

Exchange rate
Deuterium
Fragment
Proteins
Protein
Computing
Hydrogen
Mutant Proteins
High Resolution
Data Exchange
Electronic data interchange
Mutant
Spatial Resolution
Protein Conformation
Protease
Combinatorial Optimization
Amides
Protein-protein Interaction
Accessibility
Combinatorial optimization

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

Althaus, E., Canzar, S., Ehrler, C., Emmett, M., Karrenbauer, A., Marshall, A. G., ... Zhang, H. M. (2010). Computing H/D-Exchange rates of single residues from data of proteolytic fragments. BMC Bioinformatics, 11, [424]. https://doi.org/10.1186/1471-2105-11-424

Computing H/D-Exchange rates of single residues from data of proteolytic fragments. / Althaus, Ernst; Canzar, Stefan; Ehrler, Carsten; Emmett, Mark; Karrenbauer, Andreas; Marshall, Alan G.; Meyer-Bäse, Anke; Tipton, Jeremiah D.; Zhang, Hui Min.

In: BMC Bioinformatics, Vol. 11, 424, 11.08.2010.

Research output: Contribution to journalArticle

Althaus, E, Canzar, S, Ehrler, C, Emmett, M, Karrenbauer, A, Marshall, AG, Meyer-Bäse, A, Tipton, JD & Zhang, HM 2010, 'Computing H/D-Exchange rates of single residues from data of proteolytic fragments', BMC Bioinformatics, vol. 11, 424. https://doi.org/10.1186/1471-2105-11-424
Althaus, Ernst ; Canzar, Stefan ; Ehrler, Carsten ; Emmett, Mark ; Karrenbauer, Andreas ; Marshall, Alan G. ; Meyer-Bäse, Anke ; Tipton, Jeremiah D. ; Zhang, Hui Min. / Computing H/D-Exchange rates of single residues from data of proteolytic fragments. In: BMC Bioinformatics. 2010 ; Vol. 11.
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