Structural Elucidation of Gas-Phase Peptide Ions by Tandem Mass Spectrometry and Molecular Dynamics Simulations
Nguyen, Huong Thi Huynh
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The invention of the mass spectrometer has enabled scientists to discover numerous fascinating reactive gas-phase chemical species such as peptide cation radicals. The generation of these radicals can be accomplished via several methods including electron-based methods such as electron transfer dissociation or electron capture dissociation, collision-induced dissociation of transition metal-peptide complexes, photodissociation of iodinated peptide ions, etc. The basic mechanism of electron-based methods relies on the electron transfer from an anion radical donor (fluoranthene) to multiply-charged peptide cations. Electron transfer dissociation (ETD) of peptides results in energetic cation radical species, which oftentimes undergo non-specific N-Cα bond dissociation to form N-terminal c-fragment ions and C-terminal z-fragment ions. ETD has been used widely in the field of proteomics for peptide and protein sequence analysis. One of the advantages that ETD offers is its ability to preserve labile post translational modifications within the biological system of study, which enhances its accuracy for diagnosing abnormalities in proteoforms. The fragmentation mechanism of ETD is considered to be affected tremendously by the conformation of the parent ions; and thus the structures of the generated peptide cation radicals is a fascinating topic of study to many analytical chemists. There are several methods available for probing the conformational structures of gas-phase ions such as collision-induced dissociation (CID), ion mobility (IM), infrared multiphoton dissociation (IRMPD), and UV-Vis photodissociation (UVPD). CID is a slow-heating process in which the ion of study is excited vibrationally via collisions with neutral gas atoms or molecules in the mass spectrometer. IRMPD is also considered as a slow-heating process where the peptide ion must have a chromophore present to absorb multiple IR photons to cause fragmentation. Due to the nature of CID and IRMPD, cation radicals generated from the ETD method oftentimes suffer radical-induced isomerization, which compromises the integrity of their conformational structures. IM relies on the measurement of conformers’ collisional cross sections to distinguish one conformer from the others. However, in some cases, IM cannot provide sufficient selectivity due to very similar collisional cross section measurements between ions. UVPD is the only method that enables investigation of the electronic structure of the ion of interest, although it requires the presence of a chromophore. Herein, we present a new method which combines ETD and UVPD at 355 nm to probe the structures of gas-phase ions. In addition, we have also applied computational methods with different density functionals and basis sets in conjunction with molecular dynamics simulations to gain further insights regarding the structures of ETD-formed peptide cation radicals. In the first part of this work, which includes Chapters 2-5, the electronic structures of ETD-formed z-fragment ions were studied in detail using tandem mass spectrometry and molecular dynamics simulations. Chapter 2 investigates the photoreactivity of z-fragment ions originating from model peptide sequences AAXAR and AAXK, where X is a residue of interest analyzed by both UV-Vis photodissociation at 355 nm and computational methods. UVPD results in dissociations of backbone CO – NH bonds followed by hydrogen transfer to produce fragment ions [yn]+. Chapter 3 details the near UV-photoreactivity of the intact peptide reduced cation radicals from the effect of electrontransfer no dissociation, whereas Chapters 4 and 5 focus on elucidating radical-induced reactions that occur in the system of study using UV action spectroscopy and theoretical modeling. In a further attempt to investigate the 3D structures of peptide ions in the gas phase, we also explored the chemistry of diazirine as a way to freeze the conformations of the ion before subjecting it to structural analysis. Diazirine has been used widely in numerous studies regarding peptide or protein interactions in both solution and gas phase. Diazirine is known for its photoreactivity in the long-wavelength region of 330-370 nm, which is absent in natural peptide or protein chromophores. The photochemistry of diazirine can be summarized as follows: under the exposure to light at 355 nm, the diazirine is photodissociated to form a highly reactive carbene intermediate, which can form a covalent bond (X-H insertion) with a neighboring atom that has a hydrogen available. The X-H insertion competes with a fast carbene intramolecular isomerization by 1,2-hydrogen shift, which forms a nonreactive olefin. This competitive side reaction can take place within 10-7 s, which provides an internal clock for the timescale of the covalent bond formation. The carbene insertion can potentially be located by using collision-induced dissociation in combination with molecular dynamics simulations. In part II of this work, which includes Chapter 6, the chemistry of diazirines was implemented to study non-covalent interactions of peptide complexes generated in the gas phase. Specifically, we incorporated diazirine-tagged amino acids (photoleucine, L*) into the target peptide of study. The non-covalent complex ion was formed via electrospray ionization before being subjected to UVPD at 355 nm to establish a covalent bond between the two moieties. The covalently-bonded complex ion was then subjected to collision-induced dissociation for structural analysis. In addition, we also combined UVPD/CID tandem mass spectrometry technique and molecular dynamics simulations to pinpoint the location of carbene insertion.
- Chemistry