A. L. Heaton

Experimental and Theoretical Studies of Sodium Cation Interactions with the Acidic Amino Acids and Their Amide Derivatives

The binding of Na+ to aspartic acid (Asp), glutamic acid (Glu), asparagine (Asn), and glutamine (Gln) is examined in detail by studying the collision-induced dissociation (CID) of the four sodiated amino acid complexes with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Analysis of the energy-dependent CID cross sections provides 0 K sodium cation affinities for the complexes after accounting for unimolecular decay rates, internal energy of the reactant ions, and multiple ion-molecule collisions. Quantum chemical calculations for a number of geometric conformations of each Na+(L) complex are determined at the B3LYP/6-311+G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated examination of both experimental work and quantum chemical calculations allows the energetic contributions of individual functionalities as well as steric influences of relative chain lengths to be thoroughly explored. Na+ binding affinities for the amide complexes are systematically stronger than those for the acid complexes by 14 +/- 1 kJ/mol, which is attributed to an inductive effect of the OH group in the carboxylic acid side chain. Additionally, the Na+ binding affinity for the longer-chain amino acids (Glx) is enhanced by 4 +/- 1 kJ/mol compared to the shorter-chain Asx because steric effects are reduced.

Infrared Multiple Photon Dissociation Spectroscopy of Cationized Asparagine: Effects of Metal Cation Size on Gas-Phase Conformation

The gas phase structures of cationized histidine (His), including complexes with Li(+), Na(+), K(+), Rb(+), and Cs(+), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser, in conjunction with quantum chemical calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) (Li(+), Na(+), and K(+) complexes) and B3LYP/HW*/6-311+G(d,p) (Rb(+) and Cs(+) complexes) levels of theory, where HW* indicates that the Hay-Wadt effective core potential with additional polarization functions was used on the metals. Single point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. On the basis of these experiments and calculations, the only conformation that reproduces the IRMPD action spectra for the complexes of the smaller alkali metal cations, Li(+)(His) and Na(+)(His), is a charge-solvated, tridentate structure where the metal cation binds to the backbone carbonyl oxygen, backbone amino nitrogen, and nitrogen atom of the imidazole side chain, [CO,N(α),N(1)], in agreement with the predicted ground states of these complexes. Spectra of the larger alkali metal cation complexes, K(+)(His), Rb(+)(His), and Cs(+)(His), have very similar spectral features that are considerably more complex than the IRMPD spectra of Li(+)(His) and Na(+)(His). For these complexes, the bidentate [CO,N(1)] conformer in which the metal cation binds to the backbone carbonyl oxygen and nitrogen atom of the imidazole side chain is a dominant contributor, although features associated with the tridentate [CO,N(α),N(1)] conformer remain, and those for the [COOH] conformer are also clearly present. Theoretical results for Rb(+)(His) and Cs(+)(His) indicate that both [CO,N(1)] and [COOH] conformers are low-energy structures, with different levels of theory predicting different ground conformers.

Experimental and theoretical studies of potassium cation interactions with the acidic amino acids and their amide derivatives.

The binding of K(+) to aspartic acid (Asp), glutamic acid (Glu), asparagine (Asn), and glutamine (Gln) is examined in detail by studying the collision-induced dissociation (CID) of the four potassium cation-bound amino acid complexes with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Formed by electrospray ionization, these complexes have energy-dependent CID cross sections that are analyzed to provide 0 K bond energies after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Quantum chemical calculations for a number of geometric conformations of each K(+)(L) complex are determined at the B3LYP/6-311+G(d,p) level with single-point energies calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311+G(2d,2p) basis set. Theoretical bond dissociation energies are in good agreement with the experimental values. This coordinated examination of both experimental work and quantum chemical calculations allows for a comprehensive understanding of the molecular interactions of K(+) with the Asx and Glx amino acids. K(+) binding affinities for the amide complexes are systematically stronger than those for the acid complexes by 9+/-1 kJ/mol, which is attributed to an inductive effect of the OH group in the carboxylic acid side chain. Additionally, the K(+) binding affinity for the longer-chain amino acids (Glx) is enhanced by 5+/-1 kJ/mol compared to the shorter-chain Asx because steric effects are reduced. Further, a detailed comparison between experimental and theoretical results reveals interesting differences in the binding of K(+) and Na(+) to these amino acids.

Experimental and Theoretical Studies of Sodium Cation Interactions with d-Arabinose, Xylose, Glucose, and Galactose

The binding of Na (+) to arabinose (Ara), xylose (Xyl), glucose (Glc), and galactose (Gal) is examined in detail by studying the collision-induced dissociation (CID) of the four sodiated monosaccharide complexes with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Analysis of the energy-dependent CID cross-sections provides 0 K sodium cation affinities for experimental complexes after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations for a number of geometric conformations of each Na (+)(L) complex with a comprehensive analysis of the alpha and beta anomeric forms are determined at the B3LYP/6-311+G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated examination of both experimental work and quantum chemical calculations allows for determination of the bond energy for both the alpha and beta forms of each monosaccharide studied here. An understanding of the energetic contributions of individual structural characteristics as well as the energetic trends in binding among the monosaccharides is developed. Structural characteristics that affect the energetics of binding involve multidentate sodium cation coordination, ring sterics, and hydrogen bonding schemes. The overall trend in sodium binding affinities for the eight ligands follows beta-Ara < alpha-Ara < beta-Xyl < beta-Glc < alpha-Glc < alpha;-Xyl < alpha-Gal < beta-Gal.

Thermodynamics and mechanism of protonated asparagine decomposition

Deamidation of the amino acid asparagine (Asn) is a primary route for spontaneous post-translational protein modification biologically and is a pH dependent process. Here we present a full molecular description of the deamidation and (H2O + CO) loss reactions of protonated asparagine, H+(Asn), by studying its collision-induced dissociation (CID) with Xe using a guided ion beam (GIB) tandem mass spectrometer. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for the deamidation and (H2O + CO) loss reactions after accounting for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition among the decay channels. Relaxed potential energy surface scans performed at the B3LYP/6-31G(d) level identify the transition-state (TS) and intermediate reaction species for these processes, structures that are further optimized at the B3LYP/6-311+G(d,p) level. Intrinsic reaction coordinate (IRC) calculations are also performed at this level on the rate-limiting reaction TSs to validate the molecular details and energy dependence of these species. Single point energies of the key optimized TSs and intermediates are calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311+G(2d,2p) basis set. A number of alternative high-energy mechanisms for (H2O + CO) loss from H+(Asn) are also investigated. Combining both experimental work and quantum chemical calculations allows for a complete characterization of the elementary steps of these reactions as well as a comprehensive evaluation of the complex behavior of the deamidation reaction.

Metal cation dependence of interactions with amino acids: bond energies of Rb+ to Gly, Ser, Thr, and Pro.

The interactions of rubidium cations with the four amino acids (AA), glycine (Gly), serine (Ser), threonine (Thr), and proline (Pro), are examined in detail. Experimentally, the bond energies are determined using threshold collision-induced dissociation of the Rb(+)(AA) complexes with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy dependent cross sections include consideration of unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. 0 K bond energies of 108.9 +/- 7.0, 115.7 +/- 4.9, 122.1 +/- 4.6, and 125.2 +/- 4.5 kJ/mol are determined for complexes of Rb(+) with Gly, Ser, Thr, and Pro, respectively. Quantum chemical calculations are conducted at the B3LYP, B3P86, and MP2(full) levels of theory with geometries and zero point energies calculated at the B3LYP level using both HW*/6-311+G(2d,2p) and Def2TZVP basis sets. Results obtained using the former basis sets are systematically low compared to the experimental bond energies, whereas the latter basis sets show good agreement. For Rb(+)(Gly), the ground state conformer has the rubidium ion binding to the carbonyl group of the carboxylic acid, and a similar geometry is found for Rb(+)(Pro) except the secondary nitrogen accepts the carboxylic acid hydrogen to form the zwitterionic structure. Both Rb(+)(Ser) and Rb(+)(Thr) are found to have tridentate binding at the B3LYP and MP2(full) levels, whereas the B3P86 slightly prefers binding Rb(+) at the carboxylic acid. Comparison of these results to those for the lighter alkali ions provides insight into the trends in binding affinities and structures associated with metal cation variations.

Experimental and Theoretical Studies of Sodium Cation Complexes of the Deamidation and Dehydration Products of Asparagine, Glutamine, Aspartic Acid, and Glutamic Acid

The deamidation and dehydration products of Na+(L), where L = asparagine (Asn), glutamine (Gln), aspartic acid (Asp), and glutamic acid (Glu), are examined in detail utilizing collision-induced dissociation (CID) with Xe in a guided ion beam tandem mass spectrometer (GIBMS). Results establish that the Na+(L) complexes decompose upon formation in our dc discharge/flow tube ion source to form a bis-ligand complex, Na+(L-HX)(HX), composed of a sodium cation, the (L-HX) decomposition product, and HX, where HX = NH3 for the amides and H2O for the acids. Analysis of the energy-dependent CID cross sections for the Na+(L-HX)(HX) complexes provides unambiguous identification of the (L-HX) fragmentation products as 3-amino succinic anhydride (a-SA) for Asx and oxo-proline (O-Pro) for Glx. Furthermore, these experiments establish the 0 K sodium cation affinities for these five-membered ring decomposition products and the H2O and NH3 binding affinities of the Na+(a-SA) and Na+(O-Pro) complexes after accounting for unimolecular decay rates, the internal energy of reactant ions, and multiple ion-molecule collisions. Quantum chemical calculations are determined for a number of geometric conformations of all reaction species as well as a number of candidate species for (L-HX) at the B3LYP/6-311+G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated examination of both the experimental work and quantum chemical calculations allows for a complete characterization of the products of deamidation and dehydration of Asx and Glx, as well as the details of Na+, H2O, and NH3 binding to the decomposition species.

Thermodynamics and Mechanism of the Deamidation of Sodium-Bound Asparagine

The deamidation of asparagine (Asn) residues is the most common type of spontaneous post-translational protein modification and plays a vital role in inflammation, protein transformation, apoptosis, aging, and a number of degenerative diseases. Here we present a full molecular description of asparagine deamidation in the Na(+)(Asn) complex by studying its collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Advanced methods for analysis of the energy-dependent CID cross section, considering both competing and sequential processes, provide the 0 K barrier for deamidation after accounting for unimolecular decay rates, internal energy of reactant ions, and multiple ion-neutral collisions. Relaxed potential energy surface scans performed at the B3LYP/6-31G(d) level identify the transition state (TS) and intermediate reaction species for Na(+)(Asn) deamidation, structures that are further optimized at the B3LYP/6-311+G(d,p) level. Single-point energies of the key optimized structures are calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. This coordinated application of both experimental work and quantum chemical calculations allows for a complete characterization of the elementary steps of this reaction and identification of the rate-limiting elementary step of Asn deamidation. The latter is measured to require 1.61 +/- 0.08 eV and involves formation of a cyclic succinic ring structure.