Collision-Induced Conformational Changes of Trp-cage and Ubiquitin in the Gas Phase

Abstract

Collision-induced unfolding of trp-cage and ubiquitin is studied using molecular dynamics simulations of protein ion drift in helium. We first simulate the drift of protein ions in a strong electric field, where they become activated, increasing their internal energy through collisions with gas molecules. We then simulate the drift of activated protein ions in a weak field, where they cool to a temperature close to the gas temperature. To reduce the time required for activation and cooling, the simulations are carried out at gas pressures significantly higher than the experimental ones. The internal temperature of proteins reaches steady-state values within a few nanoseconds. Their radius of gyration changes almost simultaneously with the change in temperature or even somewhat faster. For both trp-cage and ubiquitin, it increases significantly upon protein activation and returns to nearly its pre-activation value upon protein cooling. This indicates that upon activation these proteins adopt unfolded conformations and upon cooling they become compact again. The collision cross section is calculated based on the mobility determined under conditions where the protein temperature is close to the gas temperature. These calculations show that activated and then cooled proteins have collision cross sections close to those of non-activated proteins. This is in contrast to the results of ion mobility experiments, in which activated proteins have larger collision cross sections after cooling than non-activated ones. The distance between the N and C termini in activated and then cooled proteins differs from the distance between these ends in non-activated proteins. This indicates that, despite similar radii of gyration, these proteins differ significantly in conformation.