Mechanism Of Deamidation Research Articles

Breakthrough Empirical Approach to Determining Deamidation Sites and Assessing Protein Stability for an Array of Therapeutic Proteins in Solution

Proteins are complex macromolecules that require comprehensive analysis. High resolution techniques are used to determine structure of proteins, yet further understanding of protein dynamics and behavior is needed for understanding protein stability. Deamidation is a phenomenon that occurs spontaneously in proteins, while in solution when subject to heat stress, low or high pH. The mechanism of deamidation is known, involving an asparagine residue undergoing a succinimide intermediate resulting in the generation of an aspartate residue. Implications of charge in the protein of interest due to a deamidation can lead to events such as aggregation, loss of affinity towards its target, and truncation. We have developed an innovative Best-in-Class label free high throughput platform technology specifically designed for comparative characterization of an array of proteins in solution. This platform technology takes advantage of: (1) Quantum Cascade Laser (QCL) microscope with enhanced signal-to-noise ratio (SNR) within the MID IR spectral region 1780 - 1000 cm−1; (2) innovative cells, (3) Hyperspectral Images (HSI) that allow for the visual inspection of the sample to determine the size and identity of any aggregates in the 4.3 µm - 2 mm size range and (4) QCL IR spectral analysis providing amino acid level resolution that is used to define the molecular behavior of proteins in solution. Our Correlation Dynamics software with 2D IR and Co-distribution correlation algorithms are used to map glutamine and asparagine deamidation sites or assess domain stability have a direct impact on drug design and development. Furthermore, ProteinMentor is well suited to be implemented orthogonally with other well-established analytical techniques. Two case studies will be presented as proof-of-concept and validation: (1) NIST mAb standard, subject to Hurricane Maria and (2) NCI mAb fragments.

Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway

The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae, and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined KM and kcat for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.

Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides

Deamidation plays an important role in biochemical phenomena such as aging. The role of the n + 1 residue on the deamidation of asparagine (asparagine being the nth residue) in three pentapeptide chains (GGNGG, GGNMG and GGNIG) has been analysed with hybrid computational tools. Potentials of mean force at 300 K were calculated from the MD/replica exchange simulations using weighted histogram analysis (WHAM) in explicit water. The snapshots were clustered taking into account the requirements of the plausible deamidation mechanisms, as such the tautomerisation of the asparagine side chain as initial step has been confirmed, based on the proximity of water to the deamidation site. The ultimate goal being to gain an insight on the peptide backbone N-H acidity, quantum mechanical calculations have been carried out. For this purpose, the distribution of Φ/Ψ, Φ2/Ψ and end-to-end distances deduced from the WHAM diagrams have been considered and a total of 110 structures have been sampled. These neutral pentapeptides as well as their corresponding anions have been optimised (B3LYP/6-31++G(d,p)) in implicit water in order to gain an insight on the peptide backbone N-H acidity. In this study, we have shown that the open conformations of the neutrals and the anions, which display a β sheet like structure are well populated and their pKas rank in the same order as the deamidating half-lives, that is the peptides that deaminate fastest can more readily access conformations that are more acidic.

Changes in solvent accessibility of wild-type and deamidated βB2-crystallin following complex formation with αA-crystallin

Aberrant protein interactions can lead to aggregation and insolubilization, such as occurs during cataract formation. Deamidation, a prevalent age-related modification in the lens of the eye, decreases stability of the major lens proteins, crystallins. The mechanism of deamidation altering interactions between αA-crystallin and βB2-crystallin was investigated by detecting changes in solvent accessibility upon complex formation during heating. Solvent accessibility was determined by measuring hydrogen/deuterium exchange levels of backbone amides by high-resolution mass spectrometry. Deuterium levels in wild type βB2-crystallin increased 50–60% in both domains following complex formation with αA-crystallin. This increased solvent accessibility indicated a general loosening along the backbone amides. Peptides with the greatest deuterium increases were located at the buried monomer–monomer interface, suggesting that the βB2 dimer was disrupted. The only region where the deuterium levels decreased was in βB2 peptide 123–139, containing an outside loop, and may be a potential site of interaction with αA. Mimicking deamidation at the βB2 dimer interface prevented complex formation with αA. When temperatures were lowered, an αA/βB2 Q70E/Q162E complex formed with similar solvent accessibilities as αA/WT βB2. Deamidation did not disrupt specific αA/βB2 interactions but favored aggregation before complex formation with αA. We conclude that deamidation contributes to cataract formation through destabilization of crystallins before they can be rescued by α-crystallin.

Mechanism of deamidation of food proteins by cation-exchange resins of the carboxylate type

Mechanism of deamidation of food proteins by cation-exchange resins of the carboxylate type

Deamidation of Asparagine Residues: Direct Hydrolysis versus Succinimide-Mediated Deamidation Mechanisms

Quantum chemical calculations are reported to provide new insights on plausible mechanisms leading to the deamidation of asparagine residues in proteins and peptides. Direct hydrolysis to aspartic acid and several succinimide-mediated mechanisms have been described. The catalytic effect of water molecules has been explicitly analyzed. Calculations have been carried out at the density functional level (B3LYP/6-31+G**). Comparisons of free energy profiles show that the most favorable reaction mechanism goes through formation of a succinimide intermediate and involves tautomerization of the asparagine amide to the corresponding imidic acid as the initial reaction step. Another striking result is that direct water-assisted hydrolysis is competitive with the succinimide-mediated deamidation routes even in the absence of acid or base catalysis. The rate-determining step for the formation of the succinimide intermediate is cyclization, regardless of the mechanism. The rate-determining step for the complete deamidation is the hydrolysis of the succinimide intermediate. These results allow clarification of some well-known facts, such as the isolation of succinimide or the absence of iso-Asp among the reaction products observed in some experiments.

Is Asparagine Deamidation in the Porcine Odorant-Binding Protein Related to the Odor Molecules Binding?

Odorant-binding proteins are biomolecules belonging to the lipocalin family. Among all the odorant-binding proteins, the porcine odorant-binding protein has been well characterized. This protein is a monomer that is characterized by the presence of the beta-barrel structure and of the disulphide bridge. The internal cavity of the beta-barrel is the binding site. In this study we have investigated the structural properties of the porcine odorant-binding protein by mass spectrometry experiments. Our data allow us to hypothesize that specific deamidation mechanisms of specific amino acid residues can be responsible for the binding properties of this class of proteins.

Deamidation of peptides in aerobic nitric oxide solution by a nitrosative pathway

Hydrolytic deamidation of asparagine (Asn) and glutamine (Gln) residues to aspartate (Asp) and glutamate (Glu), respectively, can have significant biological consequences. We hypothesize that a wholly different mechanism of deamidation might occur in the presence of aerobic nitric oxide (NO). Accordingly, we examined the deamidating ability of aerobic NO toward three model peptides, 2,4-dinitrophenyl (DNP)-Pro-Gln-Gly, Lys-Trp-Asp-Asn-Gln, and Ser-Glu-Asn-Tyr-Pro-Ile-Val, incubating them with the NO-generating compound, Et(2)N[N(O)NO]Na (DEA/NO, 30-48 mM), in aerobic, pH 7.4, buffer at 37 degrees C. DNP-Pro-Glu-Gly was detected after 2 h, while Lys-Trp-Asp-Asp-Gln, Lys-Trp-Asp-Asn-Glu, and Ser-Glu-Asp-Tyr-Pro-Ile-Val were detected within 10 min, accumulating in apparent yields of up to approximately 10%. In the latter case, tyrosine nitration was also observed, producing the expected nitrotyrosine residue. DEA/NO solutions preincubated to exhaust the NO before the peptides were added did not induce detectable deamidation. The data demonstrate that aerobic NO exposures can lead to nitrosative deamidation of peptides, a pathway that differs from the established hydrolytic deamidation mechanism in several key respects: the by-products of the former are molecular nitrogen and an acid (HONO) while that of the latter is a base (NH(3)); the nitrosative path can in principle proceed in the absence of water molecules; Asn is much more easily deamidated than Gln in the hydrolytic pathway, while the two amino acid residues were deamidated to a similar extent by exposure to NO in the presence of oxygen.

In Vivo Deamidation Characterization of Monoclonal Antibody by LC/MS/MS

The spontaneous nonenzymatic deamidation of glutaminyl and asparaginyl residues of peptides and proteins has been observed both in vitro and in vivo. Deamidation may change the structure and function of a peptide or protein, potentially resulting in decreased bioactivity, as well as alterations in pharmacokinetics and antigenicity of the protein pharmaceutical. Therefore, it is necessary to monitor the effect of storage and formulation conditions on deamidation of a protein drug candidate. Of particular interest is the investigation of in vivo deamidation mechanisms of protein drug candidates. Several methods are available to characterize the deamidation of peptides and proteins. We present here a LC/MS/MS method used to evaluate the deamidation of an antibody after in vivo administration. A humanized monoclonal IgG1 antibody (MAb) has several "hot spots" for spontaneous deamidation. One site, amino acid residue Asn55 located in the CDR2 region of the heavy chain, is of particular interest since deamidation at this site greatly decreases the binding activity. MAb was administered to cynomolgus monkeys by intravenous and subcutaneous routes. At various times after dosing, monkey serum was prepared and MAb captured by the immobilized antigen or a goat anti-human IgG Fcgamma antibody. The captured MAb was treated with trypsin followed by endoproteinase Glu-C. The digests were separated on RP-HPLC and analyzed by MS/MS on Q-Tof Global mass spectrometer. Using this method, we were able to determine the deamidation half-life of amino acid residue Asn55 in vivo and the ratio of the deamidated derivatives, i.e., isoAsp55 and Asp55. The method is rapid and sensitive with low-nanogram quantities of protein detected in the biological matrix.

Detection of isoAspartate residues as a posttranslational modification of proteins and peptides.

During the past two decades, deamidation of Asn residues has been frequently observed as a posttranslational modification in proteins and peptides. The determination of the mechanism of deamidation has been solved by studies on small peptides. Figure 1 shows the proposed nonenzymatic mechanism where the peptide amide nitrogen, donated by the residue following asparagine, makes a nucleophilic attack on the side-chain amide of Asn to form a 5-membered succinimide ring. The ring can be hydrolyzed at either the β-carboximide group to form a peptide, with an Asp residue replacing the original Asn, or the succinimide can hydrolyze at the α-carboximide group to form an isoAsp residue where the peptide chain is connected to the β-carboxyl group of Asp. Several reviews on the mechanism and extent of deamidation have been published as late as 1995 (, , ). In accord with these earlier reviews, we will focus mostly on the information that has been observed since 1995. Open image in new window Fig. 1. Proposed mechanism for the deamidation of Asn residues in peptides and proteins. In peptides the ratio of isoAsp:Asp as products is 3:1.

Mechanism of Asparagine Deamidation During Human Senile Cataractogenesis

Previous studies have demonstrated that asparagine-143 of gammaS crystallin is preferentially deamidated in human cataractous lenses. A possible mechanism of nonenzymatic deamidation involves the initial formation of L -succinimidyl and D -succinimidyl intermediates, followed by ring cleavage and production of the respective L - and D - forms of beta-aspartate and alpha-aspartate. To determine if this mechanism occurs during cataractogenesis of the human lens, synthetic peptide standards together with reverse phase HPLC were used to purify and quantitate tryptic peptides from cataractous lenses that contained the beta-aspartate and alpha-aspartate forms of residue 143. For all lenses analysed, the ratios of beta-aspartate/alpha-aspartate produced were consistent with a mechanism of deamidation involving succinimide intermediates. Surprisingly, the D / L ratios for all beta- and alpha-aspartates produced were very low, suggesting that the mechanism of deamidation preferentially involves the L -succinimidyl intermediate, with formation of the D -succinimidyl intermediate almost completely blocked by steric hindrance. Together, the results demonstrate that deamidation of asparagine-143 from gammaS crystallin of different human cataracts undergoes the same mechanism, which due to higher ordered structure of the native protein, results in the preferential production of one of two possible succinimidyl intermediates.

Effects of amino acid sequence, buffers, and ionic strength on the rate and mechanism of deamidation of asparagine residues in small peptides.

The nonenzymatic rates of deamidation of Asn residues in a series of pentapeptides with the sequences VSNXV and VXNSV, where X is one of 10 different amino acids, were determined at neutral, alkaline, and acid pH values. The results demonstrate that in neutral and alkaline solutions the amino acid residue on the amino side of the Asn had little or no effect on the rate of deamidation regardless of its charge or size. The group on the carboxyl side of Asn affected the rate of deamidation significantly. Increasing size and branching in the side chain of this residue decreased the rate of deamidation by as much as 70-fold compared to glycine in the N-G sequence, which had the greatest rate of deamidation. In acidic solution, the rate of deamidation of the Asn residue was not affected by the amino acid sequence of the peptide. The products for each deamidation reaction were tested for the formation of isoAsp residues. In neutral and alkaline solutions, all products showed that the isoAsp:Asp peptide products were formed in about a 3:1 ratio. In acidic solution, the Asp peptide was the only deamidation product formed. All peptides in which a Ser residue follows the Asn residue were found to undergo a peptide cleavage reaction in neutral and alkaline solutions, yielding a tripeptide and a dipeptide. The rate of the cleavage reaction was about 10% of the rate of the deamidation pathway at neutral and alkaline pH values. The rates of deamidation of Asn residues in the peptides studied were not affected by ionic strength, and were not specific base catalyzed. General base catalysis was observed for small bases like ammonia. A model for the deamidation reaction is proposed to account for the observed effects.

Role of peptide conformation in the rate and mechanism of deamidation of asparaginyl residues.

The tetrapeptides Val-Asn-Gly-Ala and N-acetyl-Val-Asn-Gly-Ala undergo deamidation of the asparaginyl residue at pH 7.0 at similar rates. However, they form different products. The N-acetyl peptide gave a 3:1 ratio of N-acetyl-Val-isoAsp-Gly-Ala and N-acetyl-Val-Asp-Gly-Ala, respectively. The nonacetylated peptide gave no detectable amounts of these products but rather gave a cyclic peptide formed from the nucleophilic displacement of the asparaginyl side chain amide by the amino terminus of valine. This compound was slowly inverted at carbon 2 of the asparaginyl residue. At pH values above 7.5, the nonacetylated peptide also underwent deamidation to form Val-isoAsp-Gly-Ala and Val-Asp-Gly-Ala in the 3:1 ratio. Proton NMR spectra of the acetylated and nonacetylated tetrapeptides show that below pH 7.5 they have very different preferred conformations, and it is these different conformations which result in the different mechanisms of deamidation. Above pH 9.0, both peptides have similar conformations and deamidate by the same mechanism to give equivalent products. Neither mechanism of deamidation was subject to general base catalysis by the buffer. These results suggest that deamidation rates of the asparaginyl-glycyl sequence in proteins will vary according to the conformation of the peptide backbone of each respective protein. The results also show that asparaginyl residues which are penultimate to the amino terminus can react to form an N-terminal-blocked seven-membered ring.

Mechanism of deamidation of haemoglobin providence Asn

Some abnormal hemoglobins constitute models which allow one to evaluate the structural requirements for post-translational modifications in proteins, such as deamidation. Hb La Roche-sur-Yon [β81 (EF5) Leu → His] is an unstable hemoglobin variant displaying a moderately increased oxygen affinity. About half of the abnormal hemoglobin, in addition to the substitution at position β81, carries a deamidation of the neighboring asparagine residue, β80(EF4). The histidine at position β81 cannot fit into the small hydrophobic pocket which normally accomodates the leucine residue. This structural change opens the heme pocket and modifies the general conformation of the EF segment, thus explaining the increase in oxygen affinity and the achievement of a three-dimensional structure favoring asparagine deamidation. Histidine ß81 could also act as a catalyst in the deamidation reaction. Deamidation has already been reported for two other variants of the EF corner, Hb Providence [ß82 (EF6) Lys → Asn] and Hb J Singapore [α79 (EF8) Ala → Gly]. In all these cases it seems that a histidine may catalyze the deamidation of the asparagine residues and that disturbing the folding of the EF corner will provide an extra flexibility favoring the reaction.