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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 34, Number 5
BKCSDE 34(5)
May 20, 2013 

 
Title
Protein Structural Characterization by Hydrogen/Deuterium Exchange Mass Spectrometry with Top-down Electron Capture Dissociation
Author
Hai Dong Yu, Seonghee Ahn, Byungjoo Kim*
Keywords
FT-ICR MS, Top-down, Electron capture dissociation, Hydrogen deuterium exchange, Protein structure
Abstract
This study tested the feasibility of observing H/D exchange of intact protein by top-down electron capture dissociation (ECD) mass spectrometry for the investigation of protein structure. Ubiquitin is selected as a model system. Local structural information was obtained from the deuteration levels of c and z. ions generated from ECD. Our results showed that α-helix region has the lowest deuteration level and the C-terminal fraction containing a highly mobile tail has the highest deuteration level, which correlates well with previous X-Ray and HDX/NMR analyses. We studied site-specific H/D exchange kinetics by monitoring H/D exchange rate of several structural motives of ubiquitin. Two hydrogen bonded β-strands showed similar HDX rates. However, the outer β-strand always has higher deuteration level than the inner β-strand. The HDX rate of the turn structure (residues 8-11) is lower than that of β-strands (residues 1-7 and residues 12-17) it connects. Although isotopic distribution gets broader after H/D exchange which results in a limited number of backbone cleavage sites detected, our results demonstrate that this method can provide valuable detailed structural information of proteins. This approach should also be suitable for the structural investigation of other unknown proteins, protein conformational changes, as well as protein-protein interactions and dynamics.
Page
1401 - 1406
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