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 language | English (US) |
|---|---|
| Article number | 424 |
| Journal | BMC Bioinformatics |
| Volume | 11 |
| DOIs | |
| State | Published - Aug 11 2010 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Structural Biology
- Applied Mathematics
Cite this
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 journal › Article
}
TY - JOUR
T1 - Computing H/D-Exchange rates of single residues from data of proteolytic fragments
AU - Althaus, Ernst
AU - Canzar, Stefan
AU - Ehrler, Carsten
AU - Emmett, Mark
AU - Karrenbauer, Andreas
AU - Marshall, Alan G.
AU - Meyer-Bäse, Anke
AU - Tipton, Jeremiah D.
AU - Zhang, Hui Min
PY - 2010/8/11
Y1 - 2010/8/11
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=77955407833&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77955407833&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-11-424
DO - 10.1186/1471-2105-11-424
M3 - Article
C2 - 20701784
AN - SCOPUS:77955407833
VL - 11
JO - BMC Bioinformatics
JF - BMC Bioinformatics
SN - 1471-2105
M1 - 424
ER -