Master of Science
Mass Spectrometry (MS) has been revolutionized by the ability to produce intact gaseous protein ions by electrospray ionization (ESI). The question to what extent these ions retain solution-like conformations under “native” ESI conditions remains a matter of debate. Traditional high-resolution structure determination techniques only report on proteins in the condensed phase. For this reason, MD simulations play an important role in exploring the behavior of gas phase proteins. In this research, mobile and non-mobile proton MD simulations along with mass spectrometry data at 300 K in both positive and negative ion mode indicated that native-like conformations were largely retained. Surface titratable side chains were found to adopt orientations that were less extended than in crystals and in solution (with the radius of gyration [Rg] values 3-5% lower than for the X-ray coordinates), causing the gaseous protein to be somewhat more compact than in the condensed phase. Calculated collision cross sections of these MD structures were in good agreement with experimental data.
Bakhtiari, Maryam, "Protein Conformations in the Gas Phase Probed by Mass Spectrometry and Molecular Dynamics Simulations" (2019). Electronic Thesis and Dissertation Repository. 5992.