Paper Info
Title
Computing H/D-exchange rates of single residues from data of proteolytic fragments.
Abstract
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.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.With our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments.
Year
DOI
Venue
2010
10.1186/1471-2105-11-424
BMC Bioinformatics
Keywords
Field
DocType
spatial resolution,proteins,high resolution,protein complex,mass spectrometry,protein protein interaction,bioinformatics,protein conformation,combinatorial optimization,wild type,microarrays,hydrolysis,algorithms
Biology,Ligand,Deuterium Exchange Measurement,Hydrogen–deuterium exchange,Deuterium,Mass spectrometry,Protease,Bioinformatics,Mutant,Protein structure
Journal
Volume
Issue
ISSN
11
1
1471-2105
Citations 
PageRank 
References 
11
0.41
3
Authors
9
Name
Order
Citations
PageRank
Ernst Althaus125726.33
Stefan Canzar211614.05
Carsten Ehrler3150.94
Mark R Emmett4443.68
Andreas Karrenbauer513320.21
Alan G Marshall6293.07
Anke Meyer-Bäse718019.36
Jeremiah D Tipton8110.41
Hui-Min Zhang9281.77