Investigation of tertiary structure of electrosprayed ribosomal protein L9 by Fourier transform ion cyclotron resonance mass spectrometry using low energy dissociation techniques



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Tandem mass spectrometry, using infrared multi-photon dissociation (IRMPD), sustained off-resonance irradiation (SORI), and complementary pair analysis has been applied to small proteins in the 3 kDa range. In this dissertation, these techniques are evaluated on a larger protein, Ribosomal Protein L9, which was subjected to tandem mass spectrometry on a 9.4 Tesla Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometer. This protein was selected for its large size (16.3 kDa), capacity for multiple charging, and distinctive tertiary structure. It consists of two terminal globular domains joined by a rigid α-helix. The sixteen observable charge states of L9 (+10 through +25) were individually isolated and dissociated. The resulting complementary pairs and fragments were analyzed. Utilizing the rules of gas-phase basicity, Coulombic repulsions, and the complementary pair data; the order of addition and location of the charged residues were determined. It is shown that for a molecule this size, the protons are added to preferential sites in a sequential manner. Molecular modeling was used to assist with visualizing how the structure changes when charge is added. The X-ray structure was used as a starting point and the charge was added to locations as determined in Chapter 4. Energy minimizations yielded new structures for each charge state that did not retain their secondary characteristics. Correlating the torsion angles between the original and model structures showed local areas of high correlation that ranged from 5 to 15 residues long. Threshold energy data separated the charge states into two groups based on their dissociation energies. +10 to +19 dissociated with a laser power of 10 Watts or greater, while +20 to +25 dissociated with a laser power range of 0 to 6 Watts. It was determined that the protonation of Lys109 may be responsible for a structural change that exposed the hidden His106 thereby allowing it to become charged.