Deamidation Of Asn Residues Research Articles

Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis.

Chemical modifications of long-lived proteins, such as isomerization and epimerization, have been evoked as prime triggers for protein-damage related diseases. Deamidation of Asn residues, which results in formation of a mixture of l- and d-Asp and isoAsp via an intermediate aspartyl succinimide, can result in the disruption of cellular proteostasis and toxic protein depositions. In contrast to extensive data on the biological prevalence and functional implications of aspartyl succinimide formation, much less is known about the impact of the resulting altered backbone composition on properties of individual proteins at a molecular level. Here, we report the total chemical synthesis, biophysical characterization, and NMR structural analysis of a series of variants of the B1 domain of protein G from Streptococcal bacteria (GB1) in which all possible Asp isomers as well as an aspartyl succinimide were individually incorporated at a defined position in a solvent-exposed loop. Subtle local structural effects were observed; however, these were accompanied by notable differences in thermodynamic folded stability. Surprisingly, the noncanonical backbone connectivity of d-isoAsp led to a variant that exhibited enhanced stability relative to the natural protein.

Assessing the Structures and Interactions of γD-Crystallin Deamidation Variants

Cataracts involve the deposition of the crystallin proteins in the vertebrate eye lens, causing opacification and blindness. They are associated with either genetic mutation or protein damage that accumulates over the lifetime of the organism. Deamidation of Asn residues in several different crystallins has been observed and is frequently invoked as a cause of cataract. Here, we investigated the properties of Asp variants, deamidation products of γD-crystallin, by solution NMR, X-ray crystallography, and other biophysical techniques. No substantive structural or stability changes were noted for all seven Asn to Asp γD-crystallins. Importantly, no changes in diffusion interaction behavior could be detected. Our combined experimental results demonstrate that introduction of single Asp residues on the surface of γD-crystallin by deamidation is unlikely to be the driver of cataract formation in the eye lens.

Uncommon Modifications and Dehydration Reaction in Analysis of Lysozyme by Matrix-Assisted Laser Desorption Ionization Tandem Time of-Flight Mass Spectrometry

Abstract Tryptic digest of Lysozyme were analyzed by matrix-assisted laser desorption ionization tandem time of flight-mass spectrometry (MALDI-TOF/TOF-MS). Six unique peptides were identified with high confidence by database searching and the Mascot score is 420 with the protein coverage of 54%. Furthermore, several uncommon modifications including deamidation of Asn residue, deamidation of Asn plus oxidation of Met, deamidation of Asn plus oxidation of Met and oxidation of Trp were observed for peptide IVSDGNGMNAWVAWR (98→112). Furthermore, a dehydration reaction was observed in the process of MALDI for this peptide. All above results showed that the Asparagine at 103 rd position has a highly chemical reactivity. In addition, the modification of propionamide (Cystine) was observed for another two peptides. This study indicated that, for those of unmatched data by database searching, the data utilization and the certainty of analysis result would be increased by using manual explanation and selecting very low abundant ions in primary spectrum. This method is also helpful for finding potential post-translational modifications.

Characterization of the photodegradation of a human IgG1 monoclonal antibody formulated as a high-concentration liquid dosage form

The photodegradation of a human IgG1 monoclonal antibody has been examined in a high concentration (100 mg/mL) liquid formulation. It was observed that a yellowish color is generated when the formulation is exposed to intense and prolonged light exposure, and this discoloration occurs along with a loss in bioactivity. Extensive analytical characterization was performed to determine light induced degradation pathways that occur during exposure to intense light of ICH photodegradation conditions. It has been shown that the monoclonal antibody undergoes a combination of physical and chemical reactions under these conditions, including covalent aggregate formation, fragmentation at the hinge region, oxidation of Trp, His, and Met residues, and deamidation of Asn residues. Oxidation of Trp 94 and deamidation of Asn 93, located in the light chain CDR region, correlates with loss of bioactivity under these conditions. A series of formulation experiments were performed to elucidate the impact of the extent of light exposure, oxygen, protein concentration, and solution pH on the photostability of the formulation. Results demonstrated that photodegradation of the IgG, after intensive light exposure, can be prevented by proper secondary packaging. In addition, it is also shown that a high concentration, liquid dosage form of a human monoclonal antibody is stable upon exposure to the ambient light conditions encountered during routine manufacturing, long-term storage, and administration with proper design of formulation conditions, the primary container as well as the secondary package. © 2008 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:3117–3130, 2009

Effects of Spontaneous Deamidation on the Cytotoxic Activity of the Bacillus anthracis Protective Antigen

Protective antigen (PA) is a central virulence factor of Bacillus anthracis and a key component in anthrax vaccines. PA binds to target cell receptors, is cleaved by the furin protease, self-aggregates to heptamers, and finally internalizes as a complex with either lethal or edema factors. Under mild room temperature storage conditions, PA cytotoxicity decreased (t(1/2) approximately 7 days) concomitant with the generation of new acidic isoforms, probably through deamidation of Asn residues. Ranking all 68 Asn residues in PA based on their predicted deamidation rates revealed five residues with half-lives of <60 days, and these residues were further analyzed: Asn10 in the 20-kDa region, Asn162 at P6 vicinal to the furin cleavage site, Asn306 in the pro-pore translocation loop, and both Asn713 and Asn719 in the receptor-binding domain. We found that PA underwent spontaneous deamidation at Asn162 upon storage concomitant with decreased susceptibility to furin. A panel of model synthetic furin substrates was used to demonstrate that Asn162 deamidation led to a 20-fold decrease in the bimolecular rate constant (k(cat)/Km) of proteolysis due to the new negatively charged residue at P6 in the furin recognition sequence. Furthermore, reduced PA cytotoxicity correlated with a decrease in PA cell binding and also with deamidation of Asn713 and Asn719. On the other hand, neither deamidation of Asn10 or Asn306 nor impairment of heptamerization could be observed upon prolonged PA storage. We suggest that PA inactivation during storage is associated with susceptible deamidation sites, which are intimately involved in both mechanisms of PA cleavage by furin and PA-receptor binding.

Purification and characterization of recombinant rabbit cytosolic serine hydroxymethyltransferase.

A rabbit liver cDNA library in phage lambdagt10 was screened using the coding cDNA for human cytosolic serine hydroxymethyltransferase. A clone of 1754 bp was isolated and the nucleotide sequence showed an open reading frame of 1455 bp, which coded for rabbit cytosolic serine hydroxymethyltransferase and was flanked by 12 bp at the 5' end and 287 bp at the 3' end. The full-length cDNA was then cloned into a pET22b vector as a NdeI-EcoRI insert. HMS174(DE3) cells were transformed with this plasmid and, after induction with isopropyl beta-D-thiogalactopyranoside, expressed a catalytically active serine hydroxymethyltransferase. The enzyme was purified and shown to be the expressed rabbit enzyme lacking the first methionine residue. Spectral characteristics of the bound pyridoxal phosphate and kinetic constants for the natural substrates L-serine and tetrahydrofolate were essentially identical to the values obtained previously for the rabbit cytosolic enzyme. The pattern of bands shown by the pure recombinant enzyme on an isoelectric focusing gel containing 6 M urea showed a major band and a minor band representing about 15-20% of the protein. Upon incubation of the recombinant enzyme at pH 7.3 and 37 degreesC, three new bands were observed on isoelectric focusing with the concomitant formation of isoaspartyl residues, as determined by reactivity with protein isoaspartyl methyltransferase. These results are consistent with deamidation of Asn residues to isoaspartyl during the in vitro incubation. The enzyme purified from rabbit liver has previously been shown to contain isoaspartyl residues.

Stability of Glyceraldehyde-3-Phosphate Dehydrogenases from Hyperthermophilic Archaea at High Temperature

Summary Resistance of the primary structure towards heat-induced irreversible damages represents one of the most important prerequisites for a stable protein structure at the growth temperature of hyperthermophiles. Analyses with glyceraldehyde-3-phosphate dehydrogenases from Methothermus fervidus and Pyrococcus woesei indicate a correlation between heat resistance of the peptide chain and conformation stability. Irreversible heat injuries of the peptide chain proceed preferrently in unfolded proteins but are retarded in the folded state. Consequently, extrinsic factors stabilizing the native protein conformation also protect the peptide chain. Thus, in the case of the enzymes from M. fervidus and P. woesei high phosphate concentrations stabilize the protein conformation and accordingly the peptide chain towards deamidation of Asn residues and hydrolysis of the peptide bond, although the chemical modification reaction itself is favoured at high ionic strength.

Chemical pathways of peptide degradation. I. Deamidation of adrenocorticotropic hormone.

Deamidation of Asn residues is one of the major chemical pathways of degradation of proteins and peptides. Adrenocorticotropic hormone (ACTH), a 39-amino acid polypeptide with a single Asn residue, was shown in this study to be a useful model polypeptide for the study of the effects of pH and buffer concentration on the rate and pathway of deamidation. The disappearance of ACTH and appearance of deamidated ACTH were monitored by isoelectric focusing (IEF), and ammonia production was monitored spectrophotometrically using a coupled enzymatic assay. Using these analytical methods, the deamidation of ACTH was shown to follow pseudo-first-order kinetics and was dependent on pH and buffer concentrations. The separation of the deamidated ACTHs (Asp-ACTH and isoAsp-ACTH) from ACTH was successful, but attempts to separate Asp-ACTH from isoAsp-ACTH using cation-exchange HPLC and IEF were unsuccessful. Using bovine protein carboxymethyltransferase (PCM), which selectively methylates the carboxyl group of isoAsp residue, the isoAsp-ACTH could be detected at pH 7.0 and 9.6 but not at pH 1.9. These data support the hypothesis that under neutral and alkaline conditions, deamidation of ACTH proceeds through the formation of a cyclic imide intermediate (slow step), followed by its hydrolysis to the Asp-ACTH and isoAsp-ACTH (fast step). Under acidic conditions, the reaction appears to proceed via direct hydrolysis of the Asn residue to form Asp-ACTH without the formation of a cyclic imide intermediate.

Chemical pathways of peptide degradation. III. Effect of primary sequence on the pathways of deamidation of asparaginyl residues in hexapeptides.

Deamidation of Asn residues can occur either by direct hydrolysis of the Asn residue or via a cyclic imide intermediate. The effects of primary sequence on the pathways of deamidation of Asn residues were studied using Val-Tyr-X-Asn-Y-Ala hexapeptides with substitution on the C-terminal side (Y) and on the N-terminal side (X) of the Asn residue. In acidic media the peptides deamidate by direct hydrolysis of the Asn residue to yield only Asp peptides, whereas under neutral or alkaline conditions, the peptides deamidate by formation of the cyclic imide intermediates which hydrolyze to yield both isoAsp and Asp peptides. At neutral to alkaline pH's the rate of deamidation was significantly affected by the size of the amino acid on the C-terminal side of the Asn residue. The amino acid on the C-terminal side of the Asn residue has no effect on the rate of deamidation at acidic pH. Changes in the structure of the amino acid on the N-terminal side of the Asn residue had no significant effect on the rate of deamidation at all the pH's studied. For peptides that underwent deamidation slowly, a reaction involving the attack of the Asn side chain on the peptide carbonyl carbon resulting in peptide bond cleavage was also observed.

Chemical pathways of peptide degradation. II. Kinetics of deamidation of an asparaginyl residue in a model hexapeptide.

Deamidation of Asn residues is a major chemical pathway of degradation of peptides and proteins. To understand better the external factors that influence deamidation, we studied the degradation of the hexapeptide Val-Tyr-Pro-Asn-Gly-Ala, a fragment of adrenocorticotropic hormone, by HPLC. The deamidation of this model peptide showed marked dependence on pH, temperature, and buffer composition. In the pH range 5 to 12, the peptide deamidated exclusively via a cyclic imide intermediate with the formation of both the Asp- and the isoAsp-hexapeptides. Buffer catalysis was also observed in the pH range of 7 to 11. However, at acidic pH's, the pathway of deamidation involved direct hydrolysis of the amide side chain of Asn residue to produce only the Asp-hexapeptide.