Proton affinity of dipeptides containing alanine and diaminobutyric acid

Batoon, Patrick; Ren, Jianhua

doi:10.1016/j.ijms.2014.07.025

Cited by 4 publications

(8 citation statements)

References 52 publications

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“…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.…”

Section: Experimental and Computational Methodsmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

2018

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Oligopeptides containing 2,3-diaminopropionic acid (Dap) serve as a unique model to study conformational effects on the ionizability of a side-chain group. In this study, conformations of acetylated isomeric dipeptide ions containing alanine (Ala) and Dap, AlaDapH and DapAlaH, are studied by infrared multiple photon dissociation (IRMPD) spectroscopy and computation. The IRMPD spectra are characterized in detail by comparing them with theoretical IR spectra of a set of low-energy conformations calculated at the ωB97X-D/6-311+G(d) level of theory. The averaged IR spectra according to the Boltzmann distribution of the set of conformations have a good match to the IRMPD spectra. The characteristic amide I band of AlaDapH appears to be downshifted compared to that of DapAlaH. The relative positions of the amide band suggest a stronger hydrogen-bonding interaction between the charged side-chain amino group and the amide carbonyl groups in AlaDapH than in DapAlaH. The stronger hydrogen bonding in the former is likely due to a better alignment of the N-H and O═C bonds, which enables an effective sequestering of the positive charge at the amino group. The effect results in a higher proton affinity of acetylated dipeptides with the Dap residue at the C-terminus.

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Section: Experimental and Computational Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

2018

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“…We have determined and reported the proton affinities of ADab and DabA previously . For comparison purpose, the bracketing results for the two peptides are shown in Figure c.…”

Section: Resultsmentioning

confidence: 99%

“…The final results of proton affinity, protonation entropy, and gas-phase basicity values for all of the dipeptides studied, including ADab and DabA, are summarized in Table . The results show that ALys, AOrn, ADab, and ADap have experimentally determined proton affinities of 246.3 ± 2.2, 244.0 ± 2.4, 244.7 ± 1.9, and 237.0 ± 2.9 kcal mol –1 , respectively, while LysA, OrnA, DabA, and DapA have proton affinities of 241.5 ± 2.3, 243.0 ± 2.3, 242.0 ± 1.8, and 234.5 ± 2.9 kcal mol –1 , respectively.…”

Section: Resultsmentioning

confidence: 99%

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

Batoon

Ren

2016

J. Phys. Chem. B

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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.

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Characterization of protonated AcAlaDab and AcDabAla by IRMPD spectroscopy and molecular modeling

Batoon

Zhang

Berden

et al. 2019

International Journal of Mass Spectrometry

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Proton affinity of dipeptides containing alanine and diaminobutyric acid

Cited by 4 publications

References 52 publications

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

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

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

Characterization of protonated AcAlaDab and AcDabAla by IRMPD spectroscopy and molecular modeling

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