Mechanistic Study of the Deamidation Reaction of Glutamine: A Computational Approach

Computational Insights into Protein Aging: Spontaneous Deamidation of Glutamine

Spontaneous deamidation of amino acids is a physiologically important process, particularly for protein aging and diseases. Despite its widespread occurrence, the mechanism of glutamine deamidation particularly within proteins remains poorly understood. We have used a multiscale computational approach to investigate glutamine deamidation in the tripeptide Glycine-Glutamine-Glycine (Gly-Gln-Gly) and γS-Crystallin protein. Specifically, both the 5- and 6-membered water-assisted deamidation pathways in the tripeptide have been elucidated and compared. Both are found to occur in three stages: iminol formation, cyclization, and deamination. The rate-limiting step in each mechanism is nucleophilic attack of the backbone iminol nitrogen, formed in the first stage, at the glutamine's side-chain carbonyl carbon. For the 6- and 5-membered mechanisms, this occurs with a free energy cost of 136.4 and 179.5 kJ mol-1, respectively. Thus, overall, in the Gly-Gln-Gly tripeptide, the 6-membered pathway is preferred. Furthermore, the free energies for forming cyclic intermediates and products at selected Gln residues (based on experimentally reported % deamidation) in γS-Crystallin have been obtained. It is found that the 5-membered product complex is exergonic at -25.3 kJ mol-1, while the 6-membered product complex is calculated to be endergonic at 90.7 kJ mol-1. Thus, the deamidation pathway in folded and constrained proteins may not exclusively follow the 6-membered route. Molecular dynamics (MD) simulations of γS-Crystallin indicate that deamidation is more likely to occur when two or more water molecules are in the proximity of the glutamine residue. Consequently, significant conformational changes are found to accompany Gln120 deamidation in γS-Crystallin. This in turn can influence water availability at the other Gln residues considered and hence potentially their deamidation. Collectively, these results provide comprehensive insights into spontaneous water-assisted deamidation of glutamine residues in peptides and into the role and impact of Gln deamidation in proteins.

Computing the Differences between Asn-X and Gln-X Deamidation and Their Impact on Pharmaceutical and Physiological Proteins: A Theoretical Investigation Using Model Dipeptides

Protein deamidation is a degradation mechanism that significantly impacts both pharmaceutical and physiological proteins. Deamidation impacts two amino acids, Asn and Gln, where the net neutral residues are converted into their acidic forms. While there are multiple similarities between the reaction mechanisms of the two residues, the impact of Gln deamidation has been noted to be most significant on physiological proteins while Asn deamidation has been linked to both pharmaceutical and physiological proteins. For this purpose, we sought to analyze the thermochemical and kinetic properties of the different reactions of Gln deamidation relative to Asn deamidation. In this study, we mapped the deamidation of Gln-X dipeptides into Glu-X dipeptides using density functional theory (DFT). Full network mapping facilitated the prediction of reaction selectivity between the two primary pathways, as well as between the two products of Gln-X deamidation as a function of solvent dielectric. To achieve this analysis, we studied a total of 77 dipeptide reactions per solvent dielectric (308 total reactions). Modeled at a neutral pH and using quantum chemical and statistical thermodynamic methods, we computed the following values: enthalpy of reaction (ΔH_RXN), entropy (ΔS_RXN), Gibbs free energy of reaction (ΔG_RXN), activation energy (E_A), and the Arrhenius preexponential factor (log(A)) for each dipeptide. Additionally, using chemical reaction principles, we generated a database of computed rate coefficients for all possible N-terminus Gln-X deamidation reactions at a neutral pH, predicted the most likely deamidation reaction mechanism for each dipeptide reaction, analyzed our results against our prior study on Asn-X deamidation, and matched our results against qualitative trends previously noted by experimental literature.

Computational Insights in DNA Methylation: Catalytic and Mechanistic Elucidations for Forming 3-Methyl Cytosine

Methylation at C5 position of cytosine (5 mC) is the most abundantly occurring methylation process at CpG island, which has been well known as an epigenetic modification linked to many human diseases. Recently, another methylation approach has been discovered to show that DNA methyltransferases (DNMTs) promote the addition of the methyl group at position 3 to yield 3 mC. The existence of 3 mC can cause severe damages to the DNA strand, such as blocking its replication, repair, and transcription, affecting its stability, and initiating a double-strand DNA break. To gain a deeper insight into the formation of 3 mC, we have performed density functional theory (DFT) modeling studies at different levels of theory to clearly map out the mechanistic details for this new methylation approach. Our computed results are in harmony with pertinent experimental observations and shed light on a crucial off-target activity of DNMTs.

Deamidation reaction network mapping of pharmacologic and related proteins: impact of solvation dielectric on the degradation energetics of asparagine dipeptides

Asn-X deamidation pathways in the FV region of the monoclonal antibody (mAb).

Computational Studies on the Nonenzymatic Deamidation Mechanisms of Glutamine Residues

The nonenzymatic deamidation reactions of asparagine (Asn) and glutamine (Gln) residues in proteins are associated with protein turnover and age-related diseases. The reactions are also believed to provide a molecular clock for biological processes. Although Gln deamidation is assumed to occur through the glutarimide intermediate, the mechanisms for this are unclear because under normal physiological conditions, Gln deamidation occurs relatively less frequently and at a lower rate than Asn deamidation. We investigate the mechanisms underlying glutarimide formation from Gln residues, which proceeds in two steps (cyclization and deammoniation) catalyzed by phosphate and carbonate. We also compare these reactions with noncatalytic mechanisms and water-catalyzed mechanisms. The calculations were performed on the model compound Ace-Gln-Nme (Ace = acetyl, Nme = methylamino) using the density functional theory with the B3LYP/6-31+G(d,p) level of theory. Our results suggest that all the catalysts used in our study can mediate the proton relays required for glutarimide formation. We further determined that the calculated activation barriers of the reactions catalyzed by phosphate ions (115 kJ mol^-1) and carbonate ions (112 kJ mol^-1) are sufficiently low for the reactions to occur under normal physiological conditions. We also show that nucleophilic enhancement of Nme nitrogen is essential for the cyclization of Gln residues.

Freezing of Aqueous Solutions and Chemical Stability of Amorphous Pharmaceuticals: Water Clusters Hypothesis

Molecular mobility has been traditionally invoked to explain physical and chemical stability of diverse pharmaceutical systems. Although the molecular mobility concept has been credited with creating a scientific basis for stabilization of amorphous pharmaceuticals and biopharmaceuticals, it has become increasingly clear that this approach represents only a partial description of the underlying fundamental principles. An additional mechanism is proposed herein to address 2 key questions: (1) the existence of unfrozen water (i.e., partial or complete freezing inhibition) in aqueous solutions at subzero temperatures and (2) the role of water in the chemical stability of amorphous pharmaceuticals. These apparently distant phenomena are linked via the concept of water clusters. In particular, freezing inhibition is associated with the confinement of water clusters in a solidified matrix of an amorphous solute, with nanoscaled water clusters being observed in aqueous glasses using wide-angle neutron scattering. The chemical instability is suggested to be directly related to the catalysis of proton transfer by water clusters, considering that proton transfer is the key elementary reaction in many chemical processes, including such common reactions as hydrolysis and deamidation.

Hydration and Secondary Ozonide of the Criegee Intermediate of Sabinene

A computational study of the formation of secondary ozonide (SOZ) from the Criegee intermediates (CIs) of sabinene, including hydration reactions with H₂O and 2H₂O, was performed. All of the geometries were optimized at the B3LYP and M06-2X with several basis sets. Further single-point energy calculation at the CCSD(T) was performed. Two major pathways of SOZ formation suggest that it is mainly formed from the sabinene CI and formaldehyde rather than sabina ketone and formaldehyde-oxide. However, in both pathways, the activation energies are within a range of ±5 kJ mol^-1. Furthermore, the hydration reactions of the anti-CI with H₂O and 2H₂O showed that the role of the second water molecule is a mediator (catalyst) in this reaction. The dimer hydration reaction has lower activation energies than the monomer by 60 and 69 kJ mol^-1, at the M06-2X/6-31G(d) and CCSD(T)+CF levels of the theory, respectively. A novel water-mediated vinyl hydroperoxide (VHP) channel from both the monomer and dimer has been investigated. The results indicate that the direct nonmediated VHP formation and dissociation is interestingly more possible than the water-mediated VHP. The density functional theory calculations show that the monomer is faster than the dimer by roughly 22 kJ mol^-1. Further, the infrared spectrum of sabina ketone was calculated at B3LYP/6-311+G(2d,p); the calculated carbonyl stretching of 1727 cm^-1 is in agreement with the experimental range of 1700-1800 cm^-1.

A Computational Study of the Mechanism of Succinimide Formation in the Asn-His Sequence: Intramolecular Catalysis by the His Side Chain

The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide intermediate are known to be strongly dependent on the nature of the following residue on the carboxyl side (Xxx). The formation of the succinimide intermediate is by far the fastest when Xxx is glycine (Gly), the smallest amino acid residue, while extremely slow when Xxx is bulky such as isoleucine (Ile) and valine (Val). In this respect, it is very interesting to note that the succinimide formation is definitely accelerated when Xxx is histidine (His) despite its large size. In this paper, we computationally show that, in an Asn-His sequence, the His side-chain imidazole group (in the neutral Nε-protonated form) can specifically catalyze the formation of the tetrahedral intermediate in the succinimide formation by mediating a proton transfer. The calculations were performed for Ace-Asn-His-Nme (Ace = acetyl, Nme = methylamino) as a model compound by the density functional theory with the B3LYP functional and the 6-31+G(d,p) basis set. We also show that the tetrahedral intermediate, once protonated at the NH₂ group, easily releases an ammonia molecule to give the succinimide species.