Photodissociative Cross-Linking of Non-covalent Peptide-Peptide Ion Complexes in the Gas Phase

  • Huong T. H. Nguyen
  • Prokopis C. Andrikopoulos
  • Lubomír Rulíšek
  • Christopher J. Shaffer
  • František Tureček
Research Article


We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H–X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS3) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H)+ complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H–X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data.

Graphical Abstract


Peptide-peptide complexes Diazirine tags Photodissociation Cross-linking Born-Oppenheimer molecular dynamics 


Funding Information

Research at University of Washington has received support from the Chemistry Division of the National Science Foundation (Grants CHE-1543805, CHE-1661815, and CHE-1624430). F.T. thanks the Klaus and Mary Ann Saegebarth Endowment for general support. Research at the IOCB Prague was supported by the Grant Agency of the Czech Republic (grant 17-24155S).

Supplementary material

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ESM 1 (PDF 2576 kb)


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Copyright information

© American Society for Mass Spectrometry 2018

Authors and Affiliations

  1. 1.Department of Chemistry, Bagley HallUniversity of WashingtonSeattleUSA
  2. 2.Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesPragueCzech Republic
  3. 3.Laboratory of Biomolecular Recognition, Institute of BiotechnologyCzech Academy of SciencesVestecCzech Republic
  4. 4.Valspar CorporationMinneapolisUSA

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