Fact-checked by Grok 2 weeks ago

Deamidation

Deamidation is a post-translational modification in which the amide side chains of asparagine (Asn) and glutamine (Gln) residues in proteins are converted to carboxylic acid groups, yielding aspartic acid (Asp) or its isomer isoaspartic acid (isoAsp) from Asn, and glutamic acid (Glu) or isoGlu from Gln, respectively. This process occurs spontaneously under physiological conditions as a non-enzymatic reaction or can be catalyzed by specific enzymes called deamidases.^[1]^[2]^[3] The mechanism of non-enzymatic deamidation primarily involves the formation of a cyclic imide intermediate—succinimide for Asn and glutarimide for Gln—facilitated by nucleophilic attack from the backbone nitrogen of the adjacent residue, followed by hydrolysis that releases ammonia and generates the acidic product. Reaction rates are highly dependent on factors such as pH (optimal at neutral to alkaline for imide formation), temperature, the primary sequence context (e.g., Asn-Gly motifs accelerate deamidation), and tertiary structure, which can modulate accessibility and local conformation to influence activation energy. Asn residues deamidate more rapidly than Gln, with half-lives ranging from days to years under physiological conditions (e.g., ~1 day for some Asn sites versus ~500 days for Gln at pH 7.4 and 37°C).^[2]^[3]^[4] Biologically, deamidation alters protein charge, backbone geometry (particularly with isoAsp formation, which introduces a kink), and stability, often leading to functional impairment, aggregation, or enhanced proteasomal degradation. It accumulates in long-lived proteins like crystallins and histones, serving as a molecular clock for cellular aging and contributing to age-related pathologies, including cataracts, Alzheimer's disease (via tau protein modification), and cancer progression. In biopharmaceuticals, such as monoclonal antibodies, deamidation reduces efficacy by diminishing antigen-binding affinity and immunogenicity. Enzymatic deamidation, mediated by transglutaminases or specific deamidases (e.g., in bacterial virulence factors), enables precise regulation of signaling pathways.^[1]^[2]^[3] Detection of deamidation typically relies on mass spectrometry, which identifies a +0.984 Da mass shift, and has applications in forensics (as a protein age marker) and food science (e.g., assessing dairy protein stability). Research on deamidation dates back to the 1960s, with foundational studies elucidating its role in protein turnover, and continues to inform strategies for enhancing therapeutic protein shelf-life.^[1]^[4]

Fundamentals

Definition and Reaction

Deamidation refers to the chemical hydrolysis of an amide functional group (-CONH₂) present in the side chains of the amino acids asparagine (Asn) or glutamine (Gln), resulting in the formation of a carboxylic acid (-COOH) and the release of ammonia (NH₃). This post-translational modification alters the protein's charge and structure by converting Asn to aspartic acid (Asp) and Gln to glutamic acid (Glu).^[5]^[6] The general reaction equation for deamidation is:

\ce{R-CONH2 + H2O -> R-COOH + NH3}

where R represents the protein backbone or residue context. This process is a form of protein degradation observed across various contexts, including synthetic peptides and biological samples.^[7]^[8] Deamidation proceeds either spontaneously via non-enzymatic hydrolysis, which is pH- and temperature-dependent, or enzymatically through specific deamidases that accelerate the reaction in targeted substrates. Non-enzymatic deamidation is ubiquitous in aging proteins, while enzymatic variants enable regulated modifications in cellular processes.^[8]^[9] Early studies on deamidation emerged in the 1930s, with initial observations of glutamine degradation rates in peptides, laying the foundation for understanding its role in protein stability.^[10] Deamidation commonly occurs in biological systems, contributing to protein turnover.^[11]

Types of Deamidation

Deamidation is primarily classified by the substrate involved, with the most common forms occurring at the amide groups of asparagine (Asn) and glutamine (Gln) residues in proteins and peptides. In asparagine deamidation, the side-chain amide is hydrolyzed to aspartic acid (Asp), while glutamine deamidation yields glutamic acid (Glu). The side chain of Asn is shorter, consisting of a single methylene group (-CH₂-CONH₂), compared to the two-carbon chain of Gln (-CH₂-CH₂-CONH₂), which influences reactivity; Asn deamidation proceeds more rapidly due to the geometric favorability of forming a five-membered succinimide intermediate, whereas Gln requires a six-membered glutarimide intermediate, resulting in rates approximately 580 times slower for nonenzymatic processes in model peptides.^[12] Deamidation can occur through non-enzymatic or enzymatic pathways. Non-enzymatic deamidation is a spontaneous hydrolytic reaction driven by environmental factors such as pH and temperature, affecting both Asn and Gln residues without catalytic assistance. In contrast, enzymatic deamidation is mediated by specific hydrolases; L-asparaginase catalyzes the conversion of Asn to Asp and ammonia, primarily sourced from bacterial species like Escherichia coli and used therapeutically against acute lymphoblastic leukemia. Similarly, glutaminases, including protein-glutaminase (EC 3.5.1.44), selectively deamidate Gln residues to Glu and ammonia, with applications in food processing to modify protein solubility.^[13]^[14] A distinctive feature of Asn deamidation, particularly in non-enzymatic contexts, involves the formation of a succinimide intermediate when the backbone nitrogen attacks the side-chain carbonyl, leading to subsequent hydrolysis that produces either normal Asp (α-linked) or isoaspartic acid (isoAsp, β-linked) in a ratio often favoring isoAsp (up to 3:1 depending on sequence context). This isomerization can alter protein backbone geometry and function. Gln deamidation via glutarimide yields Glu or isoGlu isomers, though direct hydrolysis to Glu predominates more than in Asn cases.^[7]^[3] Beyond proteins, deamidation occurs in non-protein contexts, such as the chemical hydrolysis of synthetic amides under acidic or basic conditions, which converts the amide to a carboxylic acid and ammonia (NH₃), often studied in peptide synthesis to assess stability.

Mechanism

Reaction Pathway

Deamidation of asparagine residues proceeds non-enzymatically through a succinimide-mediated pathway under physiological conditions. The initial step involves the nucleophilic attack by the backbone amide nitrogen (from the subsequent residue) on the side-chain carbonyl carbon of asparagine, forming a tetrahedral intermediate. This intermediate undergoes proton transfers, often facilitated by phosphate or bicarbonate ions, leading to the closure of a five-membered succinimide ring and the release of ammonia.^[2]^[7] The succinimide intermediate is highly reactive and serves as a key branch point in the pathway. It spontaneously hydrolyzes via water addition to the imide carbonyl, resulting in a second tetrahedral intermediate that collapses to yield a mixture of aspartic acid (Asp) and isoaspartic acid (isoAsp, or β-aspartyl) residues in approximately a 1:3 ratio. During this process, the succinimide can also racemize, producing D-enantiomers of Asp and isoAsp, which introduces stereochemical diversity and potential structural disruptions in proteins.^[15]^[2] For glutamine residues, non-enzymatic deamidation follows an analogous but slower direct hydrolysis pathway or, less commonly, via a six-membered glutarimide intermediate, ultimately producing a mixture of glutamic acid (Glu) and isoGlu, with potential racemization similar to the Asn pathway. Enzymatic deamidation of glutamine, however, is catalyzed by enzymes such as tissue transglutaminase 2 (TG2), which operates in a calcium-dependent manner. In this pathway, the active-site cysteine (Cys277) performs a nucleophilic attack on the glutamine γ-carbonyl, forming a thioester intermediate and releasing ammonia; subsequent hydrolysis by water yields glutamate. This enzymatic route enhances specificity and efficiency compared to the non-enzymatic process, particularly at neutral pH.^[16]^[8]^[3] The energy barriers for succinimide formation in asparagine deamidation vary with molecular conformation and catalysis, typically ranging from 82.7 kJ/mol (syn conformation, carbonate-catalyzed) to 111 kJ/mol (anti conformation, phosphate-catalyzed), with cyclization being the rate-limiting step. The pathway exhibits pH dependence, with the succinimide formation favored at neutral to basic pH, while direct hydrolysis predominates at acidic pH (<5). The overall deamidation rate shows a minimum near pH 6–7, increasing at both lower and higher pH values due to specific catalytic mechanisms.^[2]^[8]^[17]

Influencing Factors

The rate of deamidation in proteins is significantly influenced by structural factors, particularly the primary sequence context surrounding the asparagine residue. For instance, the presence of glycine as the adjacent residue (Asn-Gly motif) accelerates deamidation due to increased backbone flexibility, which facilitates the formation of the succinimide intermediate.^[5] This effect arises from reduced steric constraints, allowing easier nucleophilic attack by the peptide backbone nitrogen. In contrast, bulkier residues adjacent to asparagine, such as histidine or phenylalanine, can slow the reaction by imposing steric hindrance.^[18] Protein folding and higher-order structures further modulate deamidation; residues in flexible loops or unstructured regions deamidate more readily than those buried in rigid alpha-helices or beta-sheets, where conformational constraints limit access to the reactive site.^[19] Environmental conditions play a critical role in modulating deamidation kinetics. Temperature exerts a pronounced effect, with rates increasing exponentially as temperature rises, often following Arrhenius behavior due to the activation energy barrier of the reaction.^[20] The pH dependence is complex and pathway-specific; for asparagine deamidation via the succinimide intermediate, rates are typically higher in mildly acidic conditions (pH 4-5) compared to neutral or basic pH, where the reaction exhibits a minimum near pH 6-7 before rising again at higher pH values.^[7] Solvent effects, particularly water activity, are also influential; higher water content or activity enhances deamidation by promoting molecular mobility and facilitating hydrolysis steps, whereas low-water environments in solid formulations can suppress the reaction.^[21] Steric and electronic effects from side-chain substitutions and local microenvironment further fine-tune deamidation propensity. Bulky hydrophobic side chains near the asparagine can sterically impede the cyclization to the succinimide, reducing rates, while electron-withdrawing groups on adjacent residues may stabilize the transition state and accelerate the process.^[7] Protein folding-induced steric occlusion often protects buried asparagines, but unfolding under stress can expose them, promoting deamidation.^[22] Oxidative conditions can promote deamidation through reactive oxygen species (ROS), which induce structural changes that expose susceptible residues or alter local electrostatics. For example, ROS-mediated oxidation can unfold proteins, increasing accessibility to asparagine sites and accelerating deamidation, as observed in ceruloplasmin under aging-related oxidative stress.^[23] Similarly, metal-ion catalyzed ROS generation elevates both oxidation and deamidation levels in plasma proteins.^[24]

Biological Significance

In Proteins and Peptides

Deamidation predominantly targets asparagine (Asn) residues in proteins, with site-specific hotspots often occurring in sequences like Asn-Gly, where the glycine facilitates nucleophilic attack due to its small side chain and structural flexibility.^[25] In monoclonal antibodies, such motifs are common in complementarity-determining regions (CDRs), such as CDRH2 (e.g., Asn-Gly at position H54 in evolocumab, exhibiting 65.1% deamidation liability) and CDRL1 (e.g., Asn-Ser or Asn-Gly sequences contributing to 81.8% of light chain events across 131 clinical-stage antibodies).^[26] Similarly, in lens crystallins, Asn151 in human αA-crystallin serves as a hotspot, undergoing rapid deamidation in vitro at rates of 2.3% per day at 50°C, leading to accumulation of up to 60% L-β-Asp isomer.^[27] The conversion of neutral Asn to negatively charged aspartate (Asp) or isoaspartate (isoAsp) introduces electrostatic repulsion and alters local hydrogen bonding, thereby disrupting protein folding and stability.^[9] This modification can destabilize secondary and tertiary structures, as observed in lens crystallins where deamidation reduces thermal stability and promotes unfolding.^[28] In monoclonal antibodies, deamidation at CDR hotspots enhances aggregation propensity, particularly at low pH, by increasing surface hydrophobicity and self-association, which compromises colloidal stability. In peptide hormones, deamidation contributes to degradation and loss of signaling efficacy. For instance, salmon calcitonin, a 32-amino-acid peptide, undergoes deamidation at glutamine residues such as Gln14 and Gln20, contributing to its instability in aqueous solutions.^[29] Glucagon, a 29-amino-acid hormone, experiences deamidation primarily at Gln3, Gln20, and Asn28 in acidic conditions, representing major pathways that hydrolyze the amide side chain and diminish its glucose-mobilizing function.^[30] Asn deamidation serves as a molecular clock for estimating protein age in vivo, with half-lives typically ranging from 1 to 500 days under physiological conditions (pH 7.4, 37°C), depending on sequence context and local structure.^[31] This time-dependent accumulation allows tracking of long-lived proteins, such as lens crystallins, where deamidation levels correlate with tissue age and provide insights into protein turnover.^[32]

Physiological and Pathological Roles

Deamidation serves physiological roles in regulating protein turnover and functioning as a molecular timer in biological processes. In proteins such as cytochrome c, non-enzymatic deamidation of asparagine residues controls in vivo degradation rates, thereby influencing the lifespan and stability of proteins under physiological conditions.^[33] This process acts as a programmable chronoregulator, where the half-life of asparagine deamidation—ranging from less than a day to centuries depending on sequence context and structure—helps time protein function and turnover, potentially contributing to rhythmic biological events like circadian regulation through alterations in clock protein stability.^[34] In pathological contexts, deamidation contributes to several diseases by disrupting protein structure and function. In cataracts, deamidation of β-crystallin proteins in the eye lens increases their aggregation propensity and light scattering, leading to opacification and vision loss, with modified residues enhancing precipitation in vivo.^[35] Similarly, in Alzheimer's disease, deamidation of tau protein results in isoaspartate formation within paired helical filaments, altering the microtubule-binding domain and promoting neurofibrillary tangles that correlate with neuronal loss.^[36] Autoimmune disorders like celiac disease involve enzymatic deamidation of gluten peptides by tissue transglutaminase 2, which converts glutamine to glutamic acid, enhancing T-cell stimulatory activity and triggering intestinal inflammation upon gluten exposure.^[37] Deamidation accumulates with age, serving as a biomarker for protein aging and tissue longevity. Post-translational deamidation rates increase over time in long-lived proteins, such as those in the human lens, where site-specific modifications correlate with chronological age and contribute to age-related dysfunction like cataract formation.^[32] Elevated levels of deamidated products and isoaspartate in blood proteins, such as human serum albumin, have been linked to neurodegenerative diseases and proposed as early diagnostic biomarkers for conditions involving protein damage.^[38] This accumulation reflects a gradual loss of protein integrity, with deamidation serving as a molecular clock for cellular aging.^[39] Evolutionarily, deamidation sites are conserved in protein domains, suggesting selective pressure to maintain these unstable residues for functional timing. Asparagine and glutamine positions prone to deamidation are preserved across species in structurally critical regions, indicating that the resulting charge changes and instability provide adaptive benefits, such as regulating protein half-life in conserved pathways despite the risk of dysfunction.^[40] This conservation underscores deamidation's role as an ancient mechanism balancing protein utility and degradation.

Kinetics

Rate Equations

Non-enzymatic deamidation of asparagine and glutamine residues in proteins typically follows first-order kinetics, where the reaction rate is proportional to the concentration of the amide-containing substrate. The rate equation is given by:

\text{Rate} = k [\text{amide}]

Here, k represents the first-order rate constant, and [\text{amide}] is the concentration of the deamidation-prone residue. This model assumes unimolecular decomposition via nucleophilic attack, leading to succinimide formation followed by hydrolysis, and is widely observed in model peptides and proteins under physiological conditions.^[27]^[41] The temperature dependence of the rate constant k is described by the Arrhenius equation:

k = A e^{-E_a / RT}

where A is the pre-exponential factor, E_a is the activation energy, R is the gas constant, and T is the absolute temperature. For asparagine deamidation, typical activation energies range from 20 to 25 kcal/mol, reflecting the energy barrier for succinimide ring formation in aqueous environments. These values enable prediction of deamidation rates across physiological temperatures, such as 37°C.^[42]^[43]^[44] Enzymatic deamidation, mediated by enzymes such as transglutaminases or asparaginases, adheres to Michaelis-Menten kinetics, accounting for enzyme-substrate binding. The initial velocity v is expressed as:

v = \frac{V_{\max} [S]}{K_m + [S]}

where V_{\max} is the maximum rate, [S] is the substrate concentration, and K_m is the Michaelis constant indicating substrate affinity. This hyperbolic relationship describes saturation at high substrate levels and is applicable to processes like protein deamidation in food processing or therapeutic interventions.^[45] Deamidation rates exhibit pH dependence, with non-enzymatic processes accelerating at higher pH due to increased nucleophilicity of the backbone amide, while sequence context modulates the rate constant significantly; for instance, the Asn-Gly motif displays a rapid deamidation rate constant of approximately 0.5 day^{-1} at pH 7.4 and 37°C, far exceeding slower sequences like Asn-Leu. These variations underscore the role of local environment in kinetic profiles.^[46]^[42]^[47]

Experimental Measurement

Experimental measurement of deamidation rates typically involves in vitro assays where peptides or proteins are incubated under controlled conditions of pH and temperature to induce and monitor the reaction, followed by analysis of the deamidated products using techniques such as mass spectrometry or chromatography.^[48] For instance, solutions of target proteins are maintained at specific pH values (e.g., 8.0) and elevated temperatures (e.g., 40°C) for defined periods, allowing the accumulation of deamidated species to be quantified over time.^[48] These assays enable the determination of rate constants by fitting experimental data to first-order kinetic models.^[11] Isotope labeling techniques enhance the precision of rate measurements by tracking specific atoms involved in the deamidation process. Incorporation of ¹⁸O from labeled water during hydrolysis allows monitoring of oxygen exchange in the aspartate product via mass spectrometry, providing direct evidence of reaction progress in peptides from proteins like calmodulin or ribonuclease A.^[49] Similarly, ¹⁵N labeling of asparagine residues facilitates the detection of ammonia release, offering a complementary approach to quantify deamidation extent in controlled incubations.^[49] Long-term studies often employ accelerated aging protocols at elevated temperatures to extrapolate deamidation rates under physiological conditions, as higher temperatures increase reaction velocity while mimicking aging processes. For example, proteins incubated at temperatures above 37°C, such as in stability assessments for therapeutic candidates, allow prediction of in vivo deamidation over extended periods by applying Arrhenius-based extrapolation.^[33] This method has been used to evaluate asparagine deamidation in enzymes, revealing structure-dependent rate accelerations under thermal stress.^[19] Integration of computational modeling, particularly molecular dynamics (MD) simulations, supports experimental rate measurements by estimating site-specific deamidation susceptibilities based on local protein dynamics and solvent exposure. MD simulations of asparagine residues in folded proteins predict relative deamidation liabilities by analyzing conformational flexibility and hydrogen bonding patterns, which are then validated against in vitro data.^[43] These approaches have been applied to therapeutic proteins, aiding the interpretation of experimentally observed site-specific rates.^[50]

Analytical Methods

Detection Techniques

Mass spectrometry (MS) is a primary technique for detecting deamidation in proteins, leveraging the characteristic +1 Da mass shift resulting from the conversion of asparagine (Asn) or glutamine (Gln) to aspartic acid (Asp) or glutamic acid (Glu), respectively.^[51] Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, often combined with enzymatic digestion using endoproteinase Asp-N, enables the identification of deamidation sites by observing shifts in peptide mass spectra, particularly useful for distinguishing deamidated from non-deamidated species.^[52] Liquid chromatography coupled with MS (LC-MS), including top-down, middle-down, and bottom-up approaches, provides higher resolution for site-specific detection; fragmentation techniques such as electron capture dissociation (ECD) or electron transfer dissociation (ETD) further differentiate isoAsp from Asp isomers by revealing distinct backbone cleavage patterns.^[51]^[53] Electrophoretic methods, particularly isoelectric focusing (IEF), detect deamidation through shifts in the isoelectric point (pI) caused by the introduction of a negatively charged carboxyl group from Asp or Glu formation.^[54] In traditional gel-based IEF or capillary IEF (cIEF), deamidated protein variants migrate to different positions on the pH gradient, allowing qualitative separation and visualization of charge heterogeneity; this is especially effective for monitoring deamidation in recombinant proteins where multiple isoforms may arise.^[54] Imaged cIEF enhances sensitivity by combining fluorescence detection with whole-column imaging, facilitating rapid identification of pI variants in complex samples without the need for prior purification.^[55] Antibody-based detection targets isoAsp residues specifically, offering a targeted approach for qualitative assessment in biological contexts such as serum proteins. Monoclonal antibodies (mAbs) engineered for high specificity to isoAsp, such as mAb 1A3 against isoAsp in human serum albumin, enable immunoassays like enzyme-linked immunosorbent assay (ELISA) to confirm the presence of deamidation products without mass alterations.^[56] These antibodies bind preferentially to the altered backbone conformation of isoAsp, distinguishing it from normal Asp, and have been validated for detecting low levels of modification in therapeutic proteins and aging-related samples.^[56] Nuclear magnetic resonance (NMR) spectroscopy provides structural insights into deamidation by observing chemical shift perturbations in protein spectra. In proteins and peptides, deamidation induces changes in backbone amide (HN) and side-chain signals, particularly for residues adjacent to the modified Asn or Gln; triple-resonance experiments like HNCACB detect the formation of isoAsp through distinct carbon chemical shifts in the succinimide intermediate or final products.^[57] Two-dimensional 1H NMR techniques identify and quantify deamidation isoforms by resolving peak duplications arising from the altered peptide geometry, as demonstrated in early studies on ribonuclease A.^[58] This method is particularly valuable for solution-state analysis of small proteins or peptides where site-specific structural effects need confirmation.^[57]

Quantification Approaches

Quantification of deamidation in proteins and peptides typically involves determining the extent of modification at specific sites or overall abundance, often building on the detection of a +1 Da mass shift observed in mass spectrometry.^[54] These approaches provide numerical outputs such as percentage occupancy or molar ratios, enabling assessment of deamidation levels in complex samples like biopharmaceuticals. Peptide mapping using liquid chromatography tandem mass spectrometry (LC-MS/MS) is a primary method for site-specific quantification. Proteins are enzymatically digested into peptides, separated by reversed-phase LC, and analyzed by MS/MS to identify deamidated species based on their mass shift. The extent of deamidation is calculated by integrating peak areas of deamidated versus native peptides, often expressed as percentage occupancy using the formula: % deamidation = (area of deamidated peptide / total area of native + deamidated peptides) × 100. This approach achieves high sensitivity and accuracy, with limits of detection around 0.1-1% for monoclonal antibodies.^[59] A modified strategy incorporating low-pH digestion minimizes artificial deamidation artifacts, improving reliability for site-specific measurements.^[60] Amino acid analysis offers a global quantification of total deamidation by measuring the ammonia (NH₃) released during complete acid hydrolysis of the protein. The extent of deamidation is determined by the decrease in NH₃ relative to a non-deamidated control, as only intact Asn and Gln residues contribute to NH₃ release upon hydrolysis. Hydrolyzed samples are analyzed for NH₃ using ion-exchange chromatography or colorimetric assays. This method quantifies overall deamidation extent but lacks site specificity, as hydrolysis converts both Asn to Asp and Gln to Glu.^[51] It was historically used for pentapeptide studies before MS dominance and remains valuable for bulk protein assessments. Stable isotope dilution mass spectrometry enhances precision for molar quantification of deamidated species in complex mixtures. Synthetic peptides with heavy isotope labels (e.g., ¹³C/¹⁵N) serve as internal standards, added prior to digestion and LC-MS analysis; ratios of light to heavy ions in MS spectra yield absolute concentrations via calibration curves, correcting for ionization efficiencies and matrix effects. This technique achieves sub-picomolar sensitivity and is particularly useful for therapeutic proteins, reducing variability to <5% relative standard deviation.^[61] Software tools facilitate deconvolution of mass spectra to compute site-specific deamidation percentages from overlapping isotopic distributions. Algorithms in platforms like Agilent MassHunter BioConfirm model charge states and integrate peaks for native and +1 Da species, automating % calculations with error estimates based on signal-to-noise ratios.^[62] Similarly, Byos software handles co-eluting deamidated peptides through PTM-specific scoring and quantification, supporting high-throughput analysis of biotherapeutics.^[63] These tools integrate with LC-MS workflows to streamline data processing and ensure reproducible results.

Applications

In Biotechnology and Pharmaceuticals

Deamidation poses significant stability challenges in biopharmaceuticals, particularly for biologics such as monoclonal antibodies (mAbs), where it can alter protein structure, function, and pharmacokinetics. In mAbs, deamidation frequently occurs at asparagine residues in the complementarity-determining regions (CDRs) or the Fc region, leading to charge variants that may reduce binding affinity, effector functions like antibody-dependent cellular cytotoxicity (ADCC), and overall efficacy. For instance, in the Fc region, modifications at or near Asn297—the canonical N-glycosylation site—can arise in aglycosylated or partially glycosylated variants, converting Asn to Asp and introducing negative charge, which subtly impacts physical stability across pH ranges 4.0–6.0 and may compromise interactions with Fc receptors, potentially affecting therapeutic potency. Such changes also heighten immunogenicity risks by generating neo-epitopes that elicit anti-drug antibodies, thereby reducing drug half-life and safety profiles in vivo.^[64]^[65]^[64] To mitigate deamidation during manufacturing, storage, and administration, formulation strategies emphasize buffer selection, excipient incorporation, and pH optimization tailored to the protein's stability profile. Deamidation rates are highly pH-dependent, generally accelerating at neutral to alkaline conditions due to nucleophilic attack on the Asn side chain, while acidic environments slow the process but risk other degradations like aggregation or isomerization; thus, formulations often target mildly acidic pH (5.0–6.5) to balance chemical stability. Common buffers include histidine or acetate, which maintain this pH range without catalyzing hydrolysis, while excipients such as sucrose or polysorbate 80 stabilize against thermal stress and interfacial degradation, reducing deamidation-induced aggregation by up to 50% in stressed conditions. Avoiding prolonged low pH storage (below 4.5) prevents excessive exposure that could exacerbate alternative pathways, ensuring product shelf-life exceeds 24 months at 2–8°C for many mAb therapeutics.^[64] Protein engineering offers proactive solutions by redesigning sequences to eliminate deamidation-prone Asn residues without impairing biological activity. Site-directed mutagenesis commonly replaces vulnerable Asn with serine, alanine, or glutamine, particularly in CDRs or Fc domains where deamidation impacts function; for example, mutating the downstream glycine residue adjacent to Asn (e.g., NG motifs) enhances resistance by altering the local conformation that facilitates succinimide intermediate formation. In one engineered anti-CD52 mAb, such modifications reduced deamidation liability by over 90% under accelerated stress while preserving antigen binding affinity (KD ~1 nM). These approaches are integrated early in discovery to improve developability, minimizing downstream purification burdens and ensuring consistent quality attributes. Regulatory frameworks, particularly from the FDA and ICH, underscore the need for rigorous monitoring of deamidation as a critical quality attribute (CQA) in biopharmaceutical quality control, with heightened emphasis since the early 2000s following ICH Q6B adoption in 1999. Specifications must include tests for degradation products like deamidation variants, using methods such as peptide mapping or ion-exchange chromatography to quantify levels below 5–10% thresholds, ensuring batch-to-batch consistency and product safety. FDA guidances on process validation (e.g., 2011 updates) require stability-indicating assays to track deamidation throughout the product lifecycle, from cell culture to final formulation, to mitigate risks to efficacy and immunogenicity in clinical use. Non-compliance can lead to holds or recalls, as seen in post-approval assessments emphasizing real-time release testing.

In Food Science and Industry

In food science, deamidation serves as a key protein modification technique to enhance the functional properties of ingredients derived from plant and animal sources, improving solubility, emulsification, and foaming capacities essential for product formulation.^[66] Enzymatic deamidation, particularly using protein-glutaminase (PG), has been applied to wheat gluten to increase its dispersibility in ethanol-water systems, facilitating better incorporation into baked goods and extruded products by altering glutamine residues to glutamic acid, thereby boosting negative charge and hydration. This method offers advantages over chemical approaches due to its specificity and milder conditions, with microbial transglutaminase also contributing to deamidation under certain processing parameters, enhancing gluten's solubility for improved baking functionality.^[67] Deamidation positively impacts the nutritional profile of proteins by enhancing digestibility, which is particularly beneficial for developing hypoallergenic foods. For instance, PG-mediated deamidation of soy protein isolates improves solubility across a broad pH range (3-10) and increases in vitro digestibility, reducing potential antigenic responses and supporting applications in infant formulas or allergy-friendly products. Similarly, glutaminase treatment of rice protein enhances its structural and functional properties while maintaining its inherently low allergenicity, promoting better amino acid bioavailability and suitability for hypoallergenic beverages and supplements. Processing-induced deamidation occurs during thermal treatments in dairy and brewing, influencing product quality. In dairy processing, heat applied to caseinate solutions (110-145°C) triggers deamidation of asparagine and glutamine residues, leading to structural breakdown and altered micelle stability that affects texture in products like cheese and yogurt.^[68] Industrial deamidation methods have evolved since the 1970s, with acid and heat treatments initially dominating for their simplicity and cost-effectiveness in modifying proteins like soy and wheat isolates under harsh conditions (e.g., pH 2-4, 80-120°C).^[67] Enzymatic approaches, commercialized from the 1980s onward using PG or transglutaminase, provide controlled deamidation (up to 50-70% degree) under neutral pH and moderate temperatures (37-50°C), minimizing off-flavors and preserving nutritional integrity compared to chemical methods.^[66] These enzymatic processes, optimized for scalability, have become preferred in modern food manufacturing for targeted functionality enhancements.^[69]

References

[1]
Advances in the Study of Protein Deamidation: Unveiling Its ...
Protein deamidation, a nonenzymatic post-translational modification that converts asparagine and glutamine residues into their acidic forms, such as aspartic ...Missing: definition | Show results with:definition
[2]
Mechanisms of Deamidation of Asparagine Residues and Effects of ...
Sep 24, 2020 · Deamidation of asparagine (Asn) residues is a nonenzymatic post-translational modification of proteins. Asn deamidation is associated with ...
[3]
Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics
Asparagine and Gln are uniquely unstable amino acids that can spontaneously deamidate under physiological conditions. Deamidation can modulate protein function, ...
[4]
Tertiary Structure Is a Principal Determinant to Protein Deamidation
The protein deamidation process involves the conversion of the amide side-chain moieties of asparagine and glutamine residues to carboxyl groups.
[5]
Deamidation - an overview | ScienceDirect Topics
Deamidation is a chemical reaction in which an amide functional group is removed from a protein leading to the degradation of the protein.
[6]
Deamidation Definition - BioPharmaSpec
A chemical reaction in which an amide functional group on the side chain of the amino acids asparagine or glutamine is removed, typically converting asparagine ...Missing: hydrolysis | Show results with:hydrolysis
[7]
Deamidation of Asparagine Residues: Direct Hydrolysis versus ...
Deamidation is completed when the succinimide intermediate undergoes hydrolysis and an Asp residue forms. It is noteworthy to indicate that the hydrolysis may ...Missing: definition | Show results with:definition
[8]
Deamidation - an overview | ScienceDirect Topics
Deamidation is a spontaneous non-enzymatic reaction during which the covalent amide functional group is converted to a carboxylic acid. In proteins and peptides ...
[9]
Protein deamidation in biopharmaceutical manufacture ...
Nov 17, 2015 · In proteins and peptides a deamidation reaction occurs when an amide group is lost via a chemical reaction from the side-chain residue of either ...
[10]
[PDF] Introducing protein deamidation: Landmark discoveries ... - HAL
Jul 22, 2024 · ABSTRACT. Our current knowledge on protein deamidation results from a journey that started almost 100 years.
[11]
Protein deamidation - PMC - NIH
Protein deamidation is the spontaneous, nonenzymatic change in protein structure through the deamidation of glutaminyl and asparaginyl residues.
[12]
Computational Studies on the Nonenzymatic Deamidation ...
Feb 18, 2019 · The nonenzymatic deamidation reactions of asparagine (Asn) and glutamine (Gln) residues in proteins are associated with protein turnover and ...
[13]
A Comprehensive Review on L-Asparaginase and Its Applications
Nov 7, 2015 · L-asparaginase (LA) catalyzes the degradation of asparagine, an essential amino acid for leukemic cells, into ammonia and aspartate.
[14]
Application Prospect of Protein-Glutaminase in the Development of ...
Feb 2, 2022 · Protein-glutaminase (EC 3.5.1.44) is a new type of protein-deamidating enzyme that catalyzes the deamidation of glutamine residues in substrate ...
[15]
Deamidation as a consequence of beta-elimination ... - PubMed - NIH
The effects of deamidation are investigated for five different amide-containing synthetic peptides exposed to beta-elimination conditions.
[16]
Cytidine deaminases catalyze the conversion of N ( S , O ) 4 - Science
Feb 3, 2023 · Cytidine deaminases (CDAs) catalyze the hydrolytic deamination of cytidine and 2′-deoxycytidine to uridine and 2′-deoxyuridine.
[17]
https://pubmed.ncbi.nlm.nih.gov/16618128/
[18]
The propensity for deamidation and transamidation of peptides by ...
Transglutaminase 2 (TG2) catalyzes cross-linking or deamidation of glutamine residues in peptides and proteins. The in vivo deamidation of gliadin peptides ...
[19]
Sequence and Solution Effects on the Prevalence of d-Isomers ...
Deamidation of asparagine is a spontaneous and irreversible post-translational modification associated with a growing list of human diseases.
[20]
Engineering deamidation-susceptible asparagines leads to ... - NIH
Deamidation rate in a protein is influenced by a many factors such as the primary sequence, tertiary structure, and also various parameters including ionic ...
[21]
Protein Deamidation Analysis - Creative Proteomics
Deamidation of proteins can occur spontaneously under physiological conditions, but it can also be accelerated by factors such as temperature, pH, and the ...
[22]
Chemical stability of peptides in polymers. 1. Effect of water on ...
Jun 12, 2000 · The rate of Asn-hexapeptide deamidation increases with increasing water content or water activity and, hence, decreasing Tg. The rate of ...
[23]
Does deamidation cause protein unfolding? A top-down tandem ...
Incomplete deamidation of some Asparagine residues was expected because of steric hindrance effects of the 3D protein structure. It has also been noted ...
[24]
Oxidation-induced Structural Changes of Ceruloplasmin Foster NGR ...
In conclusion, both Cp NGR sites can deamidate during aging under oxidative conditions, likely as a consequence of oxidative-induced structural changes, thereby ...
[25]
Metal-induced oxidative stress and human plasma protein ... - Nature
Feb 10, 2023 · Out of 53 proteins identified with oxidative modifications or deamidation, 38 proteins showed an increased level of oxidation and deamidation ...
[26]
Mechanism-Driven Features Enable Asn Deamidation Reactivity ...
Sep 19, 2025 · The spontaneous deamidation of Asparagine (Asn) residues is a common post-translational modification of proteins that can occur on disparate ...
[27]
Deamidation and isomerization liability analysis of 131 clinical-stage ...
Dec 10, 2018 · The dominant deamidation pathway at pH 8.5 is Asu-mediated (Asn → Asu ⇌ [IsoAsp ⇌ Asp]). The alternative direct hydrolysis pathway (Asn → Asp) ...
[28]
Site‐specific rapid deamidation and isomerization in human lens αA ...
Deamidation of Asn to Asp in proteins occurs more rapidly than isomerization/racemization of Asp, although the reaction passes through the same intermediate in ...Missing: monoclonal antibodies
[29]
Deamidation destabilizes and triggers aggregation of a lens protein ...
Deamidation decreased protein stability and may decrease stability in vivo. A potential mechanism for deamidation-induced aggregation may be destabilization.Missing: impact | Show results with:impact
[30]
Scientific Considerations for Generic Synthetic Salmon Calcitonin ...
Peptides appear to be more susceptible to deamidation than larger proteins whose conformations appear to protect sites from potential deamidation. Indeed, a ...
[31]
The degradation pathways of glucagon in acidic solutions
The major pathways of glucagon degradation were glutaminyl deamidation and aspartyl peptide cleavage. The former was demonstrated to occur at residues 3, 20 ...
[32]
Advances in the Study of Protein Deamidation: Unveiling Its ...
Apr 27, 2025 · This review explores the recent advances in understanding protein deamidation, its impact on cellular homeostasis, protein misfolding, and age-related and ...<|separator|>
[33]
Age-Dependent Deamidation of Lifelong Proteins in the Human Lens
Deamidation was highly localized. No deamidation was detected in the first 22 residues, containing five possible sites, and indeed little deamidation was ...
[34]
Protein deamidation - PNAS
Gln deamidation, like Asn deamidation, depends strongly upon the residue on the carboxyl side of the amide, with Gln-Gly being the fastest to deamidate.
[35]
Chronoregulation by Asparagine Deamidation - PubMed
Under physiologic conditions, the deamidation half-life of individual asparagines in proteins is proposed to range from less than a day to several centuries.
[36]
Lens β-crystallins: The role of deamidation and related modifications ...
Therefore, deamidation of β-crystallins may enhance their precipitation and light scattering in vivo contributing to cataract formation. Future experiments are ...
[37]
Deamidation and isoaspartate formation in smeared tau in paired ...
Mar 12, 1999 · Deamidation and isoaspartate formation in smeared tau in paired helical filaments. Unusual properties of the microtubule-binding domain of tau.
[38]
Selective deamidation by tissue transglutaminase strongly ... - PubMed
Here we demonstrate that tTG selectively deamidates gluten peptides, which results in strongly enhanced T cell-stimulatory activity.
[39]
Deamidation-related blood biomarkers show promise for early ...
Dec 27, 2022 · Testing the link between isoaspartate and Alzheimer's disease etiology. Alzheimers Dement. 2022:1–12. Wang J, et al. First immunoassay for ...
[40]
Deamidation of human proteins - PNAS
Deamidation of asparaginyl and glutaminyl residues causes time-dependent changes in charge and conformation of peptides and proteins.
[41]
Introducing protein deamidation: Landmark discoveries, societal ...
They indicate that the first works began around 1935, where the degradation rates of glutamine alone or included as the carboxy-terminal residue in dipeptides ...
[42]
Deamidation as a ticking bomb in proteins: An evolutionarily ...
Feb 14, 2025 · But the deamidation clock starts ticking as soon as a protein is produced, even if in a bioreactor. Hence, in the pharmaceutical industry ...
[43]
Structure Based Prediction of Asparagine Deamidation Propensity in ...
As shown in. Figure 2C , the deamidation rates increased significantly under heat stress at pH 8.5, with half-times ranging between 4 and 10 days for all three ...
[44]
Deamidation, isomerization, and racemization at asparaginyl and ...
Deamidation hydrolyzes the amide linkage, isomerization transfers the peptide backbone, and racemization inverts the amino acid's configuration.Missing: non- | Show results with:non-
[45]
Molecular Modeling of the Deamidation Reaction in Solution
Oct 30, 2023 · The amino acid on the C-terminal side of Asn has no effect on the rate of deamidation at acidic pH. Changes in the structure of the amino acid ...
[46]
A Computational Study of the Mechanism of Succinimide Formation ...
The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide ...Missing: enzymatic | Show results with:enzymatic
[47]
Membrane Reactor for Enzymic Deamidation of Food Proteins - 1991
Time course, predicted by a Michaelis-Menten equation integrated for mixed zero- and first-order kinetics with the corrections for the ultrafiltration (UF) ...Missing: enzymatic | Show results with:enzymatic
[48]
Molecular clocks - PNAS
Amides may serve as molecular indicators that the integrity of each protein molecule has been maintained. Because deamidation rates are suppressed by three- ...Missing: circadian rhythm
[49]
Deamidation, isomerization, and racemization at asparaginyl and ...
From these data, it was possible to calculate an activation energy of 21.2 kcal/mol. This large value indicates that the rate of deamidation is temperature ...
[50]
Machine Learning Enables Accurate Prediction of Asparagine ... - NIH
In particular, the spontaneous non-enzymatic conversion of asparagine to aspartic acid or iso-aspartic acid via deamidation is a major pathway of protein ...Missing: seminal | Show results with:seminal
[51]
Use of 18O labels to monitor deamidation during protein and ... - NIH
Methods for detection of deamidation are usually based on the charge sensitive techniques or mass spectrometry analysis. Deamidation introduces negative charges ...Experimental Section · Calmodulin Tryptic Peptide... · Rnase A And Lysozyme Tryptic...
[52]
Deciphering deamidation and isomerization in therapeutic proteins
Some of these PTMs are spontaneous chemical reactions that lead to degradation, such as deamidation of asparagine (Asn→Asp/iso-Asp), isomerization of aspartic ...Missing: seminal enzymatic
[53]
Mass spectrometric analysis of protein deamidation – A focus on top ...
Deamidation is a spontaneous non-enzymatic reaction during which the covalent amide functional group is converted to a carboxylic acid. In proteins and peptides ...
[54]
A method for the detection of asparagine deamidation and aspartate ...
A method for the detection of asparagine deamidation and aspartate isomerization of proteins by MALDI/TOF-mass spectrometry using endoproteinase Asp-N · Abstract.
[55]
Detecting Deamidation Products in Proteins by Electron Capture ...
The isoaspartyl residue is generally difficult to detect particularly using mass spectrometry because isoaspartic acid is isomeric with aspartic acid so that ...
[56]
Analytical tools for the characterization of deamidation in ...
This review focuses on the deamidation of asparagine in monoclonal antibodies, one of the well-known degradation pathways.
[57]
Direct deamidation analysis of intact adeno-associated virus ...
May 1, 2023 · ... isoelectric focusing (icIEF) is used for monitoring purity and charge variants. ... The direct deamidation analysis of intact capsid proteins can ...
[58]
First Immunoassay for Measuring Isoaspartate in Human Serum ...
Here we report on a novel monoclonal antibody (mAb) 1A3 with excellent specificity to isoAsp in the functionally important domain of HSA.
[59]
Asparagine Deamidation Reduces DNA-binding Affinity of ... - PubMed
Oct 24, 2015 · Formation of iso-aspartate, the major deamidation product, is detected by HNCACB triple-resonance NMR spectroscopy. The rate of deamidation is ...
[60]
Identification of an isoaspartyl linkage formed upon ... - PubMed
These studies demonstrate that 2D 1H NMR techniques can be used to identify and quantitate the two isoforms produced upon deamidation of a protein and to assess ...Missing: detection | Show results with:detection
[61]
https://www.researchgate.net/publication/338405474_Assessment_method_for_deamidation_in_proteins_using_carboxylic_acid_derivatization-liquid_chromatography-tandem_mass_spectrometry
[62]
https://www.agilent.com/cs/library/applications/an_peptide_mapping_deamidation_oxidation_mab-5994-7519en-agilent.pdf
[63]
https://support.proteinmetrics.com/hc/en-us/articles/11916099472788-Asparagine-Deamidation-Quantified
[64]
Deamidation of food proteins to improve functionality
Several chemical and enzymatic methods are described for food protein deamidation to improve solubility, emulsification, foaming, and other functional ...
[65]
A Novel Protein-Deamidating Enzyme from Chryseobacterium ... - NIH
An enzyme catalyzing deamidation of proteins has a great potential for industrial applications. Deamidation of proteins can improve protein functionalities such ...