Interaction of peptide backbones and transition metal ions: 1. an IM-MS and DFT study of the binding pattern, structure and fragmentation of Pd(II)/Ni(II)-Polyalanine complexes

Abstract

The interaction between metal ions and peptides have attracted interests because of the important roles of metal ions in many biological processes and the potential application in different fields. The binding patterns of Pd(II)/Ni(II) with polyalanine and the consequent conformational changes as well as the effects on fragmentation have been studied by electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) experiments and density functional theory (DFT). The collision cross section (CCS) values that were measured showed that such complexes tend to adopt compact globular conformations in the case of polyalanines with more than 6 residues, while conformational change was detected in shorter polyalanines with 4 or 5 residues. Collision induced dissociation (CID) experiments revealed a characteristic fragmentation pattern for Pd(II)/Ni(II)-polyalanine complexes of length n in which neutral part Ala4–H2O + M–2H (M = Pd or Ni) and fragment ions [b4+M–2 H]+, [a4+M–2 H]+ were formed in much higher abundance than any other product ions. Density functional theory (DFT) calculations indicated that Pd(II) and Ni(II) preferred to coordinating to the N atoms of the four residues at the N-terminus. Such a binding pattern accelerates fragmentation involving a structure moiety containing four residues and a metal. This analysis suggested a strong structural correlation between Pd(II) and Ni(II) and the four residues located at the N-terminus of polyalanines.