How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?

Abstract

by "native-state" ESI show a strong dependence on E int . Collisional activation is used to increase E int prior to the ions entering and within the traveling wave (TW) ion mobility analyzer. Comparisons of experimental CCSs with those generated by molecular dynamics (MD) simulation for solution-phase ions and solvent-free ions as a function of temperature provide new insights about conformational preferences and retention of solution conformations. The E int -dependent CCSs, which reveal increased conformational diversity of the ion population, are discussed in terms of folding/unfolding of solvent-free ions. For example, ubiquitin ions that have low internal energies retain native-like conformations, whereas ions that are heated by collisional activation possess higher internal energies and yield a broader range of CCS owing to increased conformational diversity due to losses of secondary and tertiary structures. In contrast, the CCS profile for the IDP apoMT is consistent with kinetic trapping of an ion population composed of a wide range of conformers, and as the E int is increased, these structurally labile conformers unfold to an elongated conformation.

Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin

“…Efforts to combine this approach with ion mobility have mostly focused on large, noncovalent complexes, and in these cases, little or no conformational change has generally been observed [5,[29][30][31]. Our CCS values are larger than reported in a recent study [24]; however, that study used an IM calibration protocol [16] which relies on reference values measured in helium by the Clemmer group [14]. A reasonably good correlation is known to exist between CCS values measured in He and N 2 , particularly for peptides of the same charge state [16,17,32].…”

“…Ubiquitin is known to adopt various conformations in the gas phase, particularly at intermediate charge states [14,22,23]. It was recently shown that the relative abundances of these conformations result at least in part from gas-phase activation [24]. Thus, we decided to systematically vary the sampling cone (activating the 8+ ESI-generated ion) and trap DC bias (activating the 6+ charge-reduced product) voltages under ETD conditions, whilst isolating the Assuming as we will later show to be true that gas-phase unfolding and collapse lead to a small number of quite well-defined conformations, the CCS distribution of the 6+ charge-reduced ion can be meaningfully represented as a (weighted) average of these states.…”

“…1400 Ų), and E(xtended)-1 (ca. 1500 Ų) states in [24]. At the bottom of each panel in Figure 3, the lowest-energy (blue) CCS distribution is represented by a linear combination of these three (Gaussian) components.…”

“…Crucially, relatively low (< 7+) charge states were typically selected, occurring (according to our IM data as well as that of others [14,16,24]) in compact and intermediate conformations and resulting in a lack of observed fragmentation in certain regions mostly those spanned by salt bridges. Conversely, in our work, both the 8+ precursor isolated in the quadrupole, as well as the first (7+) charge-reduced state, occur fully in the extended state (Supplementary Figure S-2).…”

Effects of Multidentate Metal Interactions on the Structure of Collisionally Activated Proteins: Insights from Ion Mobility Spectrometry and Molecular Dynamics Simulations

“…60 The present study examines how nonspecific metal adducts influence the CIU behavior of proteins electrosprayed from non-denaturing solutions. We focus on Na + and Ca 2+ binding to ubiquitin (Ubq), cytochrome c (Cyt), and holo-myoglobin (hMb).…”