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

Abstract

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.

A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants

“…This is consistent with previous findings that in general HPs contain more helical regions at the cost of disordered regions than MPs [28,29]. There is a strong preference for Ser, Thr, Asn and Gln to be substituted by Lys and Glu in HPs, which can be explained by the observed significant reduction of polar non-charged residues [23,26] and deamidation vulnerable residues [33,34] in HPs. Leu is preferred to be substituted by Ile to enhance thermo stability.…”

“…Notable features include: an increased level of charged residues in hyperthermophilic proteins at the cost of polar residues on surface compared to their mesophilic homologs [23,25,26]; elevated levels of proline or β-branched amino acids in loops to reduce the freedom of coil regions [1,27]; a reduced number of residues in coil regions but increases in helix runs [28,29]; increased numbers of the high helix-propensity residues such as Lys and Glu, etc. [30]; an increased compactness of hydrophobic cores resulted in enhanced apolar interactions and interior packing [30-32]; and reduced deamidation probability by replacing Gln with Glu and Asn with Asp [33,34]. …”

Extensive Computational Study on Coordination of Transition Metal Cations and Water Molecules to Glutamic Acid

“…6,7,21,28 As the size of Cu + (96 pm) is very close to that of Na + (95 pm), the results indicate that there is some similarity in the behaviors of Glu metalated with the alkali metal cation and TMC. Nevertheless, there is a difference in their bonding configurations that may be understood with the traditional hard and soft acid and base principle.…”

Deamidation reactions of protonated asparagine and glutamine investigated by ion spectroscopy

“…Table outlines the free energy differences between these four‐, five‐ and six‐membered ring structures and their different protonation sites. Earlier studies have indeed proposed such five‐membered structures, in particular the oxo‐proline structure (pyroglutamic acid). Further insights into the dissociation mechanisms may also be obtained from studies of the H 2 O loss reaction of protonated glutamic acid (GluH + ), which have often been suggested to lead to the same product ions.…”