Hydrogen scrambling in non-covalent complexes of peptides

RATIONALE Mass spectrometry analysis combined with hydrogen-deuterium exchange (HDX-MS) is arising as a tool for quick analysis of native protein conformation. However, during collision-induced dissociation (CID) the spatial distribution of deuterium is not always conserved. It is therefore important to find out how hydrogen scrambling occurs this study concentrates on the possibility of scrambling between amino acid residues spatially close together, but not connected by covalent bonds. METHODS Peptides used in this study were synthesized by Fmoc strategy. Deuteration occurred in ammonia formate solution in D2O. Non-covalent complexes consisting of a deuterated and a non-deuterated peptide were analyzed by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR-MS) with quadrupole mass filter. Low-energy CID was used for complex dissociation. RESULTS The complexes were isolated on a quadrupole and subjected to CID to cause dissociation. The deuterium distribution before and after the dissociation of a non-covalent complex to its components was measured. The study revealed that no significant scrambling occurred between the constituents of the complexes the degree of scrambling did not exceed 10%. CONCLUSIONS The results obtained for the complexes should be similar to those for protein parts spatially close together hydrogen scrambling between them should be negligible. The knowledge that almost all the scrambling occurs along peptide chains gives a better insight into the mechanism of HDX inside a protein. Copyright (C) 2012 John Wiley & Sons, Ltd.