Conformation of metal ion adducts of the transmembrane peptide gramicidin A: Insight from ion mobility spectrometry and ITS-molecular dynamics

摘要

The calculated CCS peak profile can be deduced from the thermodynamics information obtained by ITS-MDS. The experimental CCS peak profile matches reasonably well the calculated ones. This free energy based-structural analysis combined with ion mobility measurement approach is capable to explore the conformation space of gas-phase peptides and make confident structural assignment of the ion mobility data. The simulation suggests that there are several beta-helix conformation found at lower energy states for gramicidin A(GA), including right-handed beta~(4,4)-helix (cluster1), left-handed beta~(4,4)-helix (cluster5), right-handed beta~(6,3)-helix (cluster7), and monomeric double-stranded beta-helix (cluster6). The simulation results indicate that the conformation of neutral GA is highly flexible in vacuo. The structural similarity between the neutral and the sodiated GA suggests that the binding of Na~(+) ions retains the inherent conformation of GA to the most extent compared to K~(+), Cs~(+), Mg~(2+). The drift time profiles of alkaline earth metal ion adducts of gramicidin A depend on the activation energy in the trap before the mobility separations in the drift cell.