Georgia C. Boles

Structural characterization of gas-phase cysteine and cysteine methyl ester complexes with zinc and cadmium dications by infrared multiple photon dissociation spectroscopy

Structural characterization of gas-phase ions of cysteine (Cys) and cysteine methyl ester (CysOMe) complexed to zinc and cadmium is investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy using a free electron laser in combination with density functional theory calculations. IRMPD spectra are measured for [Zn(Cys-H)](+), [Cd(Cys-H)](+), [Zn(CysOMe-H)](+), [Cd(CysOMe-H)](+) and CdCl(+)(CysOMe) and are accompanied by quantum mechanical calculations of the predicted linear absorption spectra at the B3LYP/6-311+G(d,p) (Zn(2+) complexes) and B3LYP/def2TZVP levels (Cd(2+) complexes). On the basis of these experiments and calculations, the conformation that best reproduces the IRMPD spectra for the complexes of the deprotonated amino acids, [M(Cys-H)](+) and [M(CysOMe-H)](+), is a charge-solvated (CS) tridentate structure where the metal dication binds to the amine and carbonyl groups of the amino acid backbone and the deprotonated sulfur atom of the side chain, [N,CO,S(-)]. The intact amino acid complex, CdCl(+)(CysOMe) binds in the equivalent motif [N,CO,S]. These binding motifs are in agreement with the predicted ground structures of these complexes at the B3LYP, B3LYP-GD3BJ (with empirical dispersion corrections), B3P86, and MP2(full) levels.

Experimental and theoretical investigations of infrared multiple photon dissociation spectra of glutamic acid complexes with Zn2+ and Cd2+

Complexes of glutamine (Gln) cationized with Zn(2+) and Cd(2+) were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free-electron laser. Electrospray ionization yielded complexes of deprotonated Gln with Zn(2+), [Zn(Gln-H)](+), and intact Gln with CdCl(+), CdCl(+)(Gln). For each complex, the spectra obtained were compared with those for low-energy conformers found using quantum chemical calculations to identify the structures present experimentally. Calculations were performed at the B3LYP/6-311+G(d,p) level for [Zn(Gln-H)](+) and at the B3LYP/def2-TZVP level with an SDD effective core potential on cadmium for CdCl(+)(Gln). The main binding motif observed for the Cd(2+) complex was a charge-solvated, tridentate [N,CO,COsc] structure in which the metal binds to the backbone amino group and the carbonyl oxygens of the carboxylic acid and side-chain amide groups. The Zn(2+) system similarly preferred a [N,CO(-),COsc] binding motif, where binding was observed at the carboxylate site along with the backbone amino and side-chain carbonyl groups. In both cases, the theoretically determined lowest-energy conformers explain the experimental [Zn(Gln-H)](+) and CdCl(+)(Gln) spectra well.

Thermodynamics and Mechanisms of Protonated Asparaginyl-Glycine Decomposition

Deamidation at asparagine residues, a spontaneous post-translational modification in proteins, plays a significant role in various biological processes and degenerative diseases. In the current work, we present a full description of the deamidation process as well as other key fragmentations (dehydration, peptide bond cleavage, and loss of 2 NH3) from protonated asparaginyl-glycine, H(+)(AsnGly), by studying its kinetic energy dependent collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer. These results are compared with those for sustained off-resonance irradiation (SORI)-CID of H(+)(AsnGly) with Ar in a Fourier transform ion cyclotron resonance mass spectrometer. Computationally, simulating annealing methodology and a series of relaxed potential energy scans at the B3LYP/6-31G(d) level were performed to identify all intermediate and transition state (TS) structures for each key reaction. All species were further optimized at the B3LYP and B3LYP-GD3BJ/6-311+G(d,p) levels of theory. Single point energies of all major reaction species were calculated at the B3LYP, B3P86, MP2(full), and B3LYP-GD3BJ levels of theory and using M06-2X for rate-limiting species. Relative energies of intermediates, TSs, and products allow characterization of the elementary and rate limiting steps in H(+)(AsnGly) decomposition. By combining experimental and computational results, the complete mechanistic nature of H(+)(AsnGly) deamidation and other fragmentations is explored and compared to the previously studied H(+)(Asn) complex. The influence of water solvation on key TSs is also explored. On a fundamental level, this analysis will aid in understanding the thermodynamic and kinetic characteristics of the key intramolecular interactions involved in deamidation, dehydration, and other important fragmentations of peptides.

Deamidation of Protonated Asparagine-Valine Investigated by a Combined Spectroscopic, Guided Ion Beam, and Theoretical Study

Peptide deamidation of asparaginyl residues is a spontaneous post-translational modification that is believed to play a role in aging and several diseases. It is also a well-known small-molecule loss channel in the MS/MS spectra of protonated peptides. Here we investigate the deamidation reaction, as well as other decomposition pathways, of the protonated dipeptide asparagine–valine ([AsnVal + H]+) upon low-energy activation in a mass spectrometer. Using a combination of infrared ion spectroscopy, guided ion beam tandem mass spectrometry, and theoretical calculations, we have been able to identify product ion structures and determine the energetics and mechanisms for decomposition. Deamidation proceeds via ammonia loss from the asparagine side chain, initiated by a nucleophilic attack of the peptide bond oxygen on the γ-carbon of the Asn side chain. This leads to the formation of a furanone ring containing product ion characterized by a threshold energy of 129 ± 5 kJ/mol (15 kJ/mol higher in energy than dehydration of [AsnVal + H]+, the lowest energy dissociation channel available to the system). Competing formation of a succinimide ring containing product, as has been observed for protonated asparagine–glycine ([AsnGly + H]+) and asparagine–alanine ([AsnAla + H]+), was not observed here. Quantum-chemical modeling of the reaction pathways confirms these subtle differences in dissociation behavior. Measured reaction thresholds are in agreement with predicted theoretical reaction energies computed at several levels of theory.

Structures of the dehydrogenation products of methane activation by 5d transition metal cations revisited: Deuterium labeling and rotational contours

A previous infrared multiple photon dissociation (IRMPD) action spectroscopy and density functional theory (DFT) study explored the structures of the [M,C,2H]+ products formed by dehydrogenation of methane by four, gas-phase 5d transition metal cations (M+ = Ta+, W+, Ir+, and Pt+). Complicating the analysis of these spectra for Ir and Pt was observation of an extra band in both spectra, not readily identified as a fundamental vibration. In an attempt to validate the assignment of these additional peaks, the present work examines the gas phase [M,C,2D]+ products of the same four metal ions formed by reaction with perdeuterated methane (CD4). As before, metal cations are formed in a laser ablation source and react with methane pulsed into a reaction channel downstream, and the resulting products are spectroscopically characterized through photofragmentation using the free-electron laser for intracavity experiments in the 350-1800 cm-1 range. Photofragmentation was monitored by the loss of D for [Ta,C,2D]+ and [W,C,2D]+ and of D2 in the case of [Pt,C,2D]+ and [Ir,C,2D]+. Comparison of the experimental spectra and DFT calculated spectra leads to structural assignments for all [M,C,2H/2D]+ systems that are consistent with previous identifications and allows a full description of the systematic spectroscopic shifts observed for deuterium labeling of these complexes, some of the smallest systems to be studied using IRMPD action spectroscopy. Further, full rotational contours are simulated for each vibrational band and explain several observations in the present spectra, such as doublet structures in several bands as well as the observed linewidths. The prominent extra bands in the [Pt,C,2D/2H]+ spectra appear to be most consistent with an overtone of the out-of-plane bending vibration of the metal carbene cation structure.

Protonated Asparaginyl-Alanine Decomposition: a TCID, SORI-CID, and Computational Analysis

AbstractDeamidation of asparagine residues, one of the fastest known post-translational modifications in proteins, plays a significant role in various biological functions and degenerative, aging diseases. Here, we present a full description of deamidation (as well as other key dissociation processes) from protonated asparaginyl-alanine, H+(AsnAla), by studying its kinetic energy-dependent threshold collision-induced dissociation (TCID) with Xe using a guided ion beam tandem mass spectrometer. Relative thresholds compare favorably with those acquired by sustained off-resonance irradiation-CID of H+(AsnAla) with Ar in a Fourier transform ion cyclotron resonance mass spectrometer. Absolute threshold energies from the TCID studies are compared to relative single point energies of major reaction species calculated at the B3LYP, B3LYP-GD3BJ, B3P86, MP2(full), and M06-2X levels of theory. Relative energies of key TSs and products allow for the characterization of the important rate-limiting steps involved in H+(AsnAla) decomposition. The influence of water solvation on key TSs is also explored computationally, where bridging the gap between gas-phase and solvated studies is an important aspect of the biological relevance of this analysis. The comprehensive results presented (in addition to complementary studies discussed herein) allow for an insightful comparison to previous deamidation studies such that effects of the C-terminal residue side chain can be elucidated. Graphical abstractᅟ