Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Cryogenic Ion Spectroscopy of a Singly Protonated Peptide DYYVVR: Locating Phosphorylation Sites of a Kinase Domain

Cryogenic ion spectroscopy (CIS) was applied to singly protonated DYYVVR, a tryptic peptide that contains the two active tyrosine residues (Y980 and Y981) of the Janus kinase 3 (JAK3) kinase domain, together with its point mutants (Y980F and Y981F) and phosphorylated peptides (pY980, pY981, and pY980pY981). The two tyrosine chromophores showed distinguishable UV absorption bands at around 35 200 and 35 450 cm^-1, respectively. By comparing with the point mutants, the lower electronic band was assigned to the absorption of Y981, and the higher one was assigned to Y980. When phosphorylated, the UV absorption of the phosphorylated chromophore shifts to higher energy above 36 500 cm^-1 but the unphosphorylated chromophore gives the absorption in the same region. Conformer-specific IR spectroscopy and density functional theory (DFT) calculations were used to tentatively assign the structure of DYYVVR. Two conformations were found, where Y981 is solvated by the protonated side chain of arginine R984, and the orientation of the carboxylic OH of D979 was different between the two. It is demonstrated that CIS can be used to distinguish the two tyrosine chromophores and to locate the phosphorylation site of a kinase domain.