Publication Date

Fall 2013

Degree Type


Degree Name

Master of Science (MS)




Daryl K. Eggers


Hydrogen/Deuterium Exchange, Methanol, Pepsin, Protein Conformation, Ubiquitin

Subject Areas

Chemistry; Biochemistry


In aqueous solutions with high concentrations of methanol at low pH, the global conformation of ubiquitin denatures to a structure of increased helical character at 50% methanol to a highly helical denatured structure at 90% methanol. Circular dichroism analysis and hydrogen/deuterium exchange mass spectrometry experiments have been reported for the monitoring of alcohol-induced conformational transitions of ubiquitin upon exposure to increasing concentrations of methanol. A bottom-up analysis of deuterium labeled ubiquitin was used in this study to examine the local conformational transitions of ubiquitin upon exposure to solutions of varying concentrations of methanol. Analysis of ubiquitin and nine peptide fragments, produced from a ubiquitin-pepsin digest, were monitored through the use of a Varian 500-LCMS ion trap. The bottom-up approach to hydrogen/deuterium exchange mass spectrometry isolated most deuterium exchange to the β-strands of ubiquitin, suggesting the methanol-induced transitions of ubiquitin were highly characterized by the unfolding of the native-state β-sheets.