2 research outputs found
Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure
Ion
mobility is emerging as a rapid and sensitive tool for structural
characterization. Collision cross-section (Ω) values determined
using ion mobility are often compared to values calculated for candidate
structures generated through molecular modeling. Several methods exist
for calculating Ω values, but the trajectory method explicitly
includes contributions from long-range, ion–neutral interactions.
Recent implementations of the trajectory method have significantly
reduced its expense and have made applications to proteins far more
tractable. Here, we use ion mobility experiments and trajectory method
calculations to characterize the effects of charge state, charge distribution,
and structure on the ion mobility of proteins in nitrogen gas. These
results show that ion-induced dipole interactions contribute significantly
to the Ω values of these ions with nitrogen gas, even for the
modestly charged ions commonly observed in native mass spectrometry
experiments. Therefore, these interactions contribute significantly
to the values measured in most structural biology and biophysics applications
of ion mobility using nitrogen gas. Comparisons between the reciprocal
mobilities of protein ions in helium gas and in nitrogen gas show
that there are significant, noncorrelated differences between these
values. As a consequence, it is challenging to estimate the errors
associated with interconverting between helium- and nitrogen-based
mobilities without extensive characterization in both gases, even
for ions of proteins with similar sequences. Therefore, we recommend
reporting Ω and mobility values that are based on the predominant
gas present in the separation and applying additional caution when
comparing results from mobility experiments performed using different
gases
Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion–Molecule Complexes, and Fragment Separation
Experimental data from ion mobility
measurements and electron transfer dissociation were combined with
extensive computational analysis of ion structures and dissociation
energetics for Gly-Leu-Gly-Gly-Lys cations and cation radicals. Experimental
and computational collision cross sections of (GLGGK + 2H)<sup>2+</sup> ions pointed to a dominant folding motif that is represented in
all low free-energy structures. The local folding motifs were preserved
in several fragment ions produced by electron transfer dissociation.
Gradient optimizations of (GLGGK + 2H)<sup>+•</sup> cation-radicals
revealed local energy minima corresponding to distonic zwitterionic
structures as well as aminoketyl radicals. Both of these structural
types can isomerize to low-energy tautomers that are protonated at
the radical-containing amide group forming a new type of intermediates,
−C<sup>•</sup>O<sup>–</sup>NH<sub>2</sub><sup>+</sup>– and −C<sup>•</sup>(OH)ÂNH<sub>2</sub><sup>+</sup>–, respectively. Extensive mapping with B3LYP,
M06-2X, and MP2Â(frozen core) calculations of the potential energy
surface of the ground doublet electronic state of (GLGGK + 2H)<sup>+•</sup> provided transition-state and dissociation energies
for backbone cleavages of the N–C<sub>α</sub> and amide
C–N bonds leading to ion–molecule complexes. The complexes
can undergo facile prototropic migrations that are catalyzed by the
Lys ammonium group and isomerize enolimine <i><b>c</b></i>-type fragments to the more stable amide tautomers. In contrast,
interfragment hydrogen atom migrations in the complexes were found
to have relatively high transition energies and did not compete with
fragment separation. The extensive analysis of the intermediate and
transition-state energies led to the conclusion that the observed
dissociations cannot proceed competitively on the same potential energy
surface. The reactive intermediates for the dissociations originate
from distinct electronic states that are accessed by electron transfer