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

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

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ALTHAUS, 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. 11(1), 424. eISSN 1471-2105. Available under: doi: 10.1186/1471-2105-11-424

@article{Althaus2010Compu-17267, title={Computing H/D-Exchange rates of single residues from data of proteolytic fragments}, year={2010}, doi={10.1186/1471-2105-11-424}, 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} }

Zhang, Hui-Min 2011-12-01T12:54:23Z Ehrler, Carsten Tipton, Jeremiah D. Computing H/D-Exchange rates of single residues from data of proteolytic fragments Marshall, Alan G. Canzar, Stefan terms-of-use Background: Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/<br />Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex.<br />In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and<br />compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides<br />generated from the protease digest of the protein is related to the solvent accessibility of amide protons within<br />the original protein construct.<br />Results: In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on<br />combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data<br />of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue<br />resolution.<br />Conclusions: With our new method it is possible to automatically determine deuterium exchange with higher<br />spatial resolution than the level of digested fragments. Karrenbauer, Andreas Meyer-Bäse, Anke Ehrler, Carsten Emmett, Mark R. Marshall, Alan G. Zhang, Hui-Min 2010 First publ. in: BMC Bioinformatics ; 11 (2010). - 424 Althaus, Ernst Canzar, Stefan Meyer-Bäse, Anke 2011-12-01T12:54:23Z Althaus, Ernst Emmett, Mark R. Tipton, Jeremiah D. Karrenbauer, Andreas eng

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