Proton Affinity of Isomeric Dipeptides Containing Lysine and Non-Proteinogenic Lysine Homologues

Abstract

Conformational effects on the proton affinity of oligopeptides have been studied using six alanine (A)-based acetylated dipeptides containing a basic probe that is placed closest to either the C- or the N-terminus. The basic probe includes Lysine (Lys) and two nonproteinogenic Lys-homologues, ornithine (Orn) and 2,3-diaminopropionic acid (Dap). The proton affinities of the peptides have been determined using the extended Cooks kinetic method in a triple quadrupole mass spectrometer. Computational studies have been carried out to search for the lowest energy conformers and to calculate theoretical proton affinities as well as various molecular properties using the density functional theory. The dipeptides containing a C-terminal probe, ALys, AOrn, and ADap, were determined to have a higher proton affinity by 1-4 kcal/mol than the corresponding dipeptides containing an N-terminal probe, LysA, OrnA, and DapA. For either the C-probe peptides or the N-probe peptides, the proton affinity reduces systematically as the side-chain of the probe residue is shortened. The difference in the proton affinities between isomeric peptides is largely associated with the variation of the conformations. The peptides with higher values of the proton affinity adopt a relatively compact conformation such that the protonated peptides can be stabilized through more efficient internal solvation.

Conformations of Protonated AlaDap and DapAla Characterized by IRMPD Spectroscopy and Molecular Modeling

“…As mentioned in Introduction, among the two sets of the acetylated dipeptides containing an ionizable residue (X), the set with the ionizable residue at the C-terminus (AlaX) has a higher proton affinity than their counterparts with the ionizable residue at the N-terminus (XAla). Specifically, AlaDap has a proton affinity higher than that of DapAla by 2.5 kcal mol –1 . It is clear that the higher proton affinity of AlaDap and of other peptides with the sequence AlaX is likely due to a single strong hydrogen-bonding interaction that effectively stabilizes the charge upon protonation of the peptides.…”

“…Specifically, AlaDap has a proton affinity higher than that of DapAla by 2.5 kcal mol −1 . 24 It is clear that the higher proton affinity of AlaDap and of other peptides with the sequence AlaX is likely due to a single strong hydrogen-bonding interaction that effectively stabilizes the charge upon protonation of the peptides.…”

“…The peptides were synthesized via solid-phase peptide synthesis using a protocol described in our previous publications. , Infrared multiple photon dissociation (IRMPD) experiments were carried out at FELIX Laboratory (Radboud University Nijmegen, The Netherlands) using a 4.7 T Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer coupled to the FELIX infrared free-electron laser. The principles and the procedure of the IRMPD experiments have been described previously by Eyler, Oomens, Polfer, and their co-workers. ,,− To perform the IRMPD experiment, peptide solutions were prepared by dissolving the solid form of the peptide into a 1:1 (v/v) mixture of acetonitrile/water to achieve a concentration of about 0.5 mM.…”

“…Therefore, Dap-containing peptides are expected to have reduced conformational flexibility. We have recently studied a series of N-terminal acetylated dipeptides containing alanine (Ala) and a basic residue containing a side-chain amino group, such as Lys and Lys homologues, including Dap. , The peptides are divided into two sets, one with the basic residue (X) at the C-terminus (AlaX) and the other at the N-terminus (XAla) (Scheme ). The two sets display a notable difference in terms of proton affinity.…”

Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids

“…The details of the computational procedure are described in our previously published work. 48,49 Briefly, the initial pool of conformations (~10,000) were generated by using the Merck molecular force field (MMFF) in the Spartan'14 suite (Wavefunction, Irvine, CA). 50 From these, the 100 low energy conformations were kept for geometry refinement using the PM6 semiempirical method.…”