Stereochemical Sequence Ion Selectivity: Proline versus Pipecolic-acid-containing Protonated Peptides

Area of Science:

• Biochemistry
• Computational Chemistry
• Mass Spectrometry

Background:

• Proline and pipecolic acid are structurally similar residues.
• Substitution of proline by pipecolic acid leads to distinct tandem mass spectra.
• The "proline effect" is absent for pipecolic acid, with C-terminal amide bond cleavage dominating.

Purpose of the Study:

• To computationally investigate the "pipecolic acid effect."
• To test hypotheses explaining the differing mass spectra of proline and pipecolic acid.
• To elucidate the underlying mechanisms through theoretical analysis.

Main Methods:

• Computational modeling and analysis of peptide fragmentation.
• Investigation of transition structures for amide bond cleavage.
• Comparison of energy barriers and stereochemical configurations.

Main Results:

• Evidence for increased flexibility in pipecolic acid-containing peptides.
• Identification of structural changes in transition states for ion formation.
• Discovery of stereochemical inversion (R to S) in transition structures for "proline effect" fragmentation.
• Prediction of stabilized amide bond cleavage barriers for pipecolic acid due to reduced steric interactions.

Conclusions:

• Computational results support increased flexibility and structural changes as key factors in the "pipecolic acid effect."
• Stereochemical inversion in transition structures is a striking finding explaining spectral differences.
• Steric interactions and experimental energy regimes are crucial for understanding peptide fragmentation spectra.