Molecular dynamics and ion mobility spectrometry study of model ß-hairpin peptide, trpzip1.

ABSTRACT

Here, we explore the conformations of gas phase, protonated tryptophan zipper 1 (trpzip1) ions and its six derivatives by an enhanced sampling molecular dynamics, specially the integrated tempering sampling molecular dynamics simulation (ITS-MDS). The structural distributions obtained from ITS-MDS are compared with results obtained from matrix-assisted laser desorption ionization (MALDI)-ion mobility-mass spectrometry (IM-MS). The IM-MS measured collision cross-section (CCS) profiles compare well with the calculated CCS profiles obtained from ITS-MDS. Although ß-turn structures are preferred for solution phase species, the ITS-MDS and IM-MS structural analysis suggests that the γ-turn structures are preferred for gas-phase, unsolvated trpzip1 [M + H](+) ions. In addition, the data suggests that the energy landscape of the gas phase peptide ions is sensitive to the site of protonation as well as intramolecular interactions involving the lysine side chain.