Merck
  • Home
  • Search Results
  • How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures?

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

Journal of the American Society for Mass Spectrometry (2015-06-28)
Shu-Hua Chen, David H Russell
ABSTRACT

Here, we critically evaluate the effects of changes in the ion internal energy (E(int)) on ion-neutral collision cross sections (CCS) of ions of two structurally diverse proteins, specifically the [M + 6H](6+) ion of ubiquitin (ubq(6+)), the [M + 5H](5+) ion of the intrinsically disordered protein (IDP) apo-metallothionein-2A (MT), and its partially- and fully-metalated isoform, the [CdiMT](5+) ion. The ion-neutral CCS for ions formed 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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Hydrochloric acid solution, ~6 M in H2O, for amino acid analysis
Supelco
Hydrochloric acid solution, volumetric, 0.1 M HCl (0.1N), endotoxin free
Sigma-Aldrich
Hydrochloric acid solution, 1.0 N, BioReagent, suitable for cell culture
Sigma-Aldrich
Hydrochloric acid, 36.5-38.0%, BioReagent, for molecular biology
Sigma-Aldrich
Tris(2-carboxyethyl)phosphine hydrochloride, powder
Sigma-Aldrich
Hydrogen chloride solution, 3 M in cyclopentyl methyl ether (CPME)
Sigma-Aldrich
Tris(2-carboxyethyl)phosphine hydrochloride, BioUltra, ≥98% (NMR)
Sigma-Aldrich
Tris(2-carboxyethyl)phosphine hydrochloride, BioUltra, suitable for electrophoresis, SDS-PAGE tested
Sigma-Aldrich
Hydrochloric acid solution, 32 wt. % in H2O, FCC
Supelco
Tris(2-carboxyethyl)phosphine hydrochloride solution, 0.5 M, pH 7.0(aqueous solution; pH was adjusted with ammonium hydroxide)