Structural investigation of naturally occurring peptides by electron capture dissociation and AMBER force field modelling

Abstract

We present a detailed analysis of the relative yields in dissociation products of doubly protonated polypeptide cations obtained via electron capture dissociation (ECD). These experimental studies are complemented by molecular dynamics force field modelling, using the AMBER force field, to correlate with putative gas-phase conformations for these peptides. It is shown that the highest gas-phase basicity amino acid residue (i.e. arginine) is included in all the charged fragments. This is of particular use in determining the primary structure tryptic digest peptides, which will ordinarily posses a high basicity C-terminal residue (i.e. arginine or lysine). Further, these results suggest that the relative ECD dissociation pattern is related to the secondary structure of the peptide. In particular, the ECD fragmentation pattern in gonadatropin releasing hormone (GnRH) variants appears to depend on whether a β-turn or an extended α-helical structure is formed. In the peptide bradykinin, modelling suggests that the C-terminal arginine engages in much more extended solvation of the backbone than the N-terminal arginine. This strongly correlates with the observed dominance of c over z fragments. This work forms the first attempt at a systematic qualitative correlation of the low-energy structures of modelled gas-phase polypeptides, and their corresponding ECD dissociation pattern.

Keywords:

• Naturally occurring peptides
• Structural investigation
• Electron capture dissociation
• AMBER force field modelling

Acknowledgements

We would like to thank the Scottish Higher Education Funding Council (SHEFC), Scottish Enterprise (SE), the Engineering and Physical Sciences Research Council (EPSRC), and Bruker Daltonics for funding. The Scottish Instrumentation and Research Centre for Advanced Mass Spectrometry (SIRCAMS) is kindly acknowledged for providing world-class facilities. The Edinburgh Protein Interaction Center (EPIC) is thanked for use of its computational facilities. PB would especially like to thank the EPSRC for funding her Advanced Research Fellowship. Further, NP thanks the University of Edinburgh for receiving the Dewar–Ritchie studentship for his post-graduate studies.

Notes

Present address: FOM Institute for Plasma Physics ‘Rijnhuizen’, Edisonbaan 14, 3430 BE Nieuwegein, The Netherlands.

Additional information

Notes on contributors

Perdita E. Barran *

Present address: FOM Institute for Plasma Physics ‘Rijnhuizen’, Edisonbaan 14, 3430 BE Nieuwegein, The Netherlands.