Secondary Structure and Protein Deamidation

Xie, Minli; Schowen, Richard L.

doi:10.1021/js9802493

Cited by 127 publications

(85 citation statements)

References 25 publications

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“…7–9 In this degradation pathway, the side-chain carbonyl group of Asn is attacked by the deprotonated backbone NH group of the adjacent C-terminal residue to generate a cyclic succinimide intermediate. The cyclic succinimide is formed from an unstable tetrahedral intermediate and can be detected under low pH conditions.…”

Section: Introductionmentioning

confidence: 99%

“…The ratio of Asp to isoAsp varies depending on the reaction buffer and local structural environment. 9,10 …”

Section: Introductionmentioning

confidence: 99%

“…Some of these predicted “hot spots” have low or non-detectable levels of deamidation in reality because of geometric constraints imposed by secondary or tertiary structural elements in a fully folded antibody. 9,12–14 …”

Section: Introductionmentioning

confidence: 99%

“…In addition, if a backbone NH group is involved in a hydrogen bond, its ability to induce a nucleophilic attack on the Asn side chain is significantly reduced. 9 Based on Clarke’s theoretical model of Asn deamidation, Xie et al have suggested that the minimum distance for the formation of the Cγ-N bond for β-turn and loop structures ranges between 3.1 and 3.3 Å. 9 This distance is much longer than the typical C-N bond of 1.4–1.5 Å, suggesting that the deamidation rates for Asn residues within a folded protein would be much slower than the rates observed in less structured peptides.…”

Section: Introductionmentioning

confidence: 99%

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Structure Based Prediction of Asparagine Deamidation Propensity in Monoclonal Antibodies

Yan

Huang

Lewis

et al. 2018

mAbs

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Identification of asparagine (Asn) sites that are prone to deamidation is critical for the development of therapeutic monoclonal antibodies (mAbs). Despite a common chemical degradation pathway, the rates of Asn deamidation can vary dramatically among different sites, and prediction of the sensitive deamidation sites is still challenging. In this study, characterization of Asn deamidation for five IgG1 and five IgG4 mAbs under both normal and stressed conditions revealed dramatic differences in the Asn deamidation rates. A comprehensive analysis of the deamidation sites indicated that the deamidation rate differences could be explained by differences in the local structure conformation, structure flexibility and solvent accessibility. A decision tree was developed to predict the deamidation propensity for all Asn sites in IgG mAbs based on the analysis of these three structural parameters. This decision tree will allow potential Asn deamidation hot spots to be identified early in development.

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Section: Introductionmentioning

confidence: 99%

“…The ratio of Asp to isoAsp varies depending on the reaction buffer and local structural environment. 9,10 …”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structure Based Prediction of Asparagine Deamidation Propensity in Monoclonal Antibodies

Yan

Huang

Lewis

et al. 2018

mAbs

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“…Analysis of the extent of deamidation of peptides and proteins has established that secondary protein structure (8), as well as the primary sequence near the asparagine residue (9), may determine the lability toward deamidation. ␥-S protein from aged human lens should provide an ideal system to study the effects of protein structure upon deamidation, because much is known about the three-dimensional structure of this polypeptide (10).…”

Section: Discussionmentioning

confidence: 99%

Specific Glutamine and Asparagine Residues of γ-S Crystallin Are Resistant to in Vivo Deamidation

Takemoto

Boyle

2000

Journal of Biological Chemistry

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It has been hypothesized that resistance to nonenzymatic deamidation of asparagine and glutamine residues may be an important determinant of protein stability in vivo. As a test of this hypothesis, we analyzed the central region of old human lenses, which contain proteins such as ␥-S crystallin that were synthesized during the fetal-embryonic periods of development. Total protein from the fetal-embryonic region of old human lenses was digested with trypsin, followed by resolution of tryptic fragments containing amidated and deamidated forms using high pressure liquid chromatography-reverse phase chromatography together with synthetic peptide standards and mass spectral analysis. The results demonstrate no detectable deamidation of glutamine 92, glutamine 96, asparagine 143, and glutamine 170 from ␥-S crystallin from old human lenses, consistent with the hypothesis that very long-lived proteins can contain asparagine and glutamine residues that are extremely resistant to in vivo deamidation.Probably the most common post-translational modification occurring in living systems involves nonenzymatic deamidation of glutamine and asparagine residues. This process occurs during the differentiation and/or aging of cells, resulting in the accumulation of glutamate and aspartate, respectively. Because deamidation results in the introduction of negative charges, it is possible that deamidation may play a major role in protein structural changes that are known to occur in development and aging. Furthermore, it has been hypothesized that deamidation may have a major effect upon the turnover rate of proteins (1). Consistent with this hypothesis has been the observation that proteins that turn over rapidly generally have greater rates of deamidation, whereas proteins that are more stable have glutamine and/or asparagine residues that are more resistant to this process (1).Perhaps the most stable proteins in the body are ␣, ␤, and ␥ crystallins found in the lens. Because of the inability of differentiated fiber cells to synthesize appreciable amounts of new protein, lens crystallins must remain relatively intact during the entire lifetime of the individual. The central, fetal-embryonic region of an aged human lens contains crystallins that were synthesized during the prenatal period of lens growth. Characterization of these crystallins should be a good test of the hypothesis that stable proteins, which contain glutamine and asparagine residues, have very low rates of deamidation.Previous studies have shown that ␣-A crystallin, purified from total proteins of the human lens, contains some glutamine residues that are resistant to in vivo deamidation (2). Because the ␤ and ␥ crystallins belong to a different family of lens proteins, and because they comprise the majority of proteins present in the dry weight material of the lens, it is important to verify whether asparagine and glutamine residues in this class of lens proteins are also relatively resistant to in vivo deamidation.Unfortunately, it is impossible to purify any of the ...

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Effect of ‘pH’ on the rate of asparagine deamidation in polymeric formulations: ‘pH’–rate profile

Shi

Schowen

Borchardt

et al. 2001

Journal of Pharmaceutical Sciences

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Secondary Structure and Protein Deamidation

Cited by 127 publications

References 25 publications

Structure Based Prediction of Asparagine Deamidation Propensity in Monoclonal Antibodies

Structure Based Prediction of Asparagine Deamidation Propensity in Monoclonal Antibodies

Specific Glutamine and Asparagine Residues of γ-S Crystallin Are Resistant to in Vivo Deamidation

Effect of ‘pH’ on the rate of asparagine deamidation in polymeric formulations: ‘pH’–rate profile

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