Open Access Methodology article

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

Ernst Althaus1*, Stefan Canzar2, Carsten Ehrler3, Mark R Emmett45, Andreas Karrenbauer6, Alan G Marshall45, Anke Meyer-Bäse7, Jeremiah D Tipton4 and Hui-Min Zhang4

Author Affiliations

1 Institut für Informatik, Fachbereich 08, Staudingerweg 9, 55099 Mainz, Germany

2 Algorithmic Computational Biology, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands

3 Center for Bioinformatics, Computer Science Department, Saarland University, 66041 Saarbrücken, Germany

4 Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310-4005, USA

5 Department of Chemistry & Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306, USA

6 Institute of Mathematics, EPFL, Station 8, 1015 Lausanne, Switzerland

7 Department of Scientific Computing, Florida State University, Tallahassee FL 32306-4120, USA

For all author emails, please log on.

BMC Bioinformatics 2010, 11:424  doi:10.1186/1471-2105-11-424

Published: 11 August 2010

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.