title: Molecular dynamics and ion mobility spectrometry study of model β-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 β-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.
authors.affiliation: The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.
authors.forename: Liuxi
authors.initials: L
authors.lastname: Chen
authors.forename: Qiang
authors.initials: Q
authors.lastname: Shao
authors.forename: Yi-Qin
authors.initials: YQ
authors.lastname: Gao
authors.forename: David H
authors.initials: DH
authors.lastname: Russell
mesh_terms: D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D014364:Tryptophan / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry*
chemical_list: D007477:Ions; D014364:Tryptophan