Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization?

Abstract

Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structure of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental “signature” has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra are observed. Despite high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y’s wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross sections of [M+4H]4+ ions yield the cis/trans “signature”, molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross section arise with equal frequency. We believe this work further underscores the importance of theoretical calculations in IM-MS structural assignments.

Combined Utilization of 1H NMR, IR, and Theoretical Calculations To Elucidate the Conformational Preferences of Some l-Histidine Derivatives

“…Thus, the study of the conformational preferences of acyclic and alicyclic compounds is of great interest for physical organic chemists, biochemists, spectroscopists, etc. In particular, extensive structural research has been conducted on the conformational equilibrium of amino acids and small peptides, − in an attempt to elucidate their dynamic role in proteins or polypeptides formation, because the spatial arrangements of the latter are intrinsically related to their corresponding biological function. − A complete understanding regarding the way these biomacromolecules fold would result in a significant impact on humanity, such as the development of more specific drugs for diseases that claim millions of lives annually.…”

Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities

“…These can be detected by molecular biology methods such as Western blot, pull-down assay, co-immunoprecipitation, etc. Recently, surface plasmon resonance combined with molecular dynamics simulations [25] and mass spectrometry [26][27][28] have been shown to hold promising results. Furthermore, although challenges remain, multiple attempts using bioinformatics and machine learning algorithms to predict cis/trans isomerization in proteins have been made [29][30][31][32][33].…”

Recent advances in mass spectrometry analysis of neuropeptides

“…While different observed conformations are attributed to the isomerization of proline using specific criteria, they do not always indicate cis/trans conformers; IM‐MS has limitations for structure elucidation. To this end, the non‐proline containing neuropeptide Y wild type and naturally occurring proline containing mutant were investigated by Lietz et al Though typical cis/trans isomerization hallmarks were present, the presence of these isomers were excluded (Lietz et al, 2016). IM‐MS and MD analyses have their limits and require other methods for validation.…”