title: Enhanced digestion efficiency, peptide ionization efficiency, and sequence resolution for protein hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry.
abstract: Solution-phase hydrogen/deuterium exchange (HDX) monitored by high-resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrometry offers a rapid method to study protein conformations and protein-protein interactions. Pepsin is usually used to digest proteins in HDX and is known for lack of cleavage specificity. To improve digestion efficiency and specificity, we have optimized digestion conditions and cleavage preferences for pepsin and protease type XIII from Aspergillus saitoi. A dilution series of the proteases was used to determine the digestion efficiency for several test proteins. Protease type XIII prefers to cleave on the C-terminal end of basic amino acids and produced the highest number of fragments and the best sequence coverage compared to pepsin or protease type XVIII from Rhizhopus. Furthermore, protease type XIII exhibited much less self-digestion than pepsin and thus is superior for HDX experiments. Many highly overlapped segments from protease type XIII and pepsin digestion, combined with high-resolution FTICR mass spectrometry, provide high sequence resolution (to as few as one or two amino acids) for the assignment of amide hydrogen exchange rate. Our H/D exchange results correlate well with the secondary and tertiary structure of myoglobin. Such assignments of highly overlapped fragments promise to greatly enhance the accuracy and sequence resolution for determining conformational differences resulting from ligand binding or protein-protein interactions.
authors: Molecular Biophysics Program, Florida State University, Tallahassee, Florida 32306, USA.
authors: Hui-Min
authors: HM
authors: Zhang
authors: Sasa
authors: S
authors: Kazazic
authors: Tanner M
authors: TM
authors: Schaub
authors: Jeremiah D
authors: JD
authors: Tipton
authors: Mark R
authors: MR
authors: Emmett
authors: Alan G
authors: AG
authors: Marshall
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001230:Aspergillus / Q000201:enzymology*; D041961:Deuterium Exchange Measurement; D005583:Fourier Analysis; D005656:Fungal Proteins / Q000378:metabolism*; D006736:Horses; D013058:Mass Spectrometry / Q000379:methods*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009206:Myocardium / Q000737:chemistry; D009211:Myoglobin / Q000032:analysis* / Q000378:metabolism; D010434:Pepsin A / Q000378:metabolism*; D010447:Peptide Hydrolases / Q000378:metabolism*; D010455:Peptides / Q000032:analysis / Q000378:metabolism; D012233:Rhizopus / Q000201:enzymology*
chemical_list: D005656:Fungal Proteins; D009211:Myoglobin; D010455:Peptides; D010447:Peptide Hydrolases; D010434:Pepsin A