Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel

Láng, András; Jákli, Imre; Enyedi, Kata Nóra; Mező, Gábor; Menyhárd, Dóra K.; Perczel, András

doi:10.1017/s003358351900009x

Cited by 6 publications

(3 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, these methods use dihedral angles of Asn residues in crystal structures as a parameter for predicting deamidation rates. In cyclic peptides containing the Asn–Gly sequence, the deamidation rate is higher in the peptide with the shorter N N +1 –C γ distance [ 39 , 40 ]. In addition, deamidation is facilitated when the N N +1 –C γ –O γ angle is <128°.…”

Section: Introductionmentioning

confidence: 99%

Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

Kato

Nakayoshi

Kurimoto

et al. 2020

IJMS

View full text Add to dashboard Cite

Deamidation of asparagine (Asn) residues is a nonenzymatic post-translational modification of proteins. Asn deamidation is associated with pathogenesis of age-related diseases and hypofunction of monoclonal antibodies. Deamidation rate is known to be affected by the residue following Asn on the carboxyl side and by secondary structure. Information about main-chain conformation of Asn residues is necessary to accurately predict deamidation rate. In this study, the effect of main-chain conformation of Asn residues on deamidation rate was computationally investigated using molecular dynamics (MD) simulations and quantum chemical calculations. The results of MD simulations for γS-crystallin suggested that frequently deamidated Asn residues have common main-chain conformations on the N-terminal side. Based on the simulated structure, initial structures for the quantum chemical calculations were constructed and optimized geometries were obtained using the B3LYP density functional method. Structures that were frequently deamidated had a lower activation energy barrier than that of the little deamidated structure. We also showed that dihydrogen phosphate and bicarbonate ions are important catalysts for deamidation of Asn residues.

show abstract

Section: Introductionmentioning

confidence: 99%

Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

Kato

Nakayoshi

Kurimoto

et al. 2020

IJMS

View full text Add to dashboard Cite

show abstract

“…The UPLC chromatograms showed the presence of additional by-products that could not be eliminated by either protocol b or c. This suggests that the main cause of the “failure” is not the incomplete acylation with Asp but a residue-specific side reaction. In the case of Asp, this is likely to be its well-known succinimide formation, which is particularly rapid at higher temperatures. − MS analysis revealed a 30% by-product with a molecular weight of 18 Da lower than that of the expected Pep:E5D (Figure ). Considering that succinimide formation is only possible if the acylation of T(ΨPro) with Fmoc-Asp(O t Bu)-OH is successful, we can conclude that the overall acylation efficiency in this case is around 38%.…”

Section: Resultsmentioning

confidence: 96%

Improved Acylation of Pseudoproline: Masked Threonine in Flow Peptide Chemistry

Szaniszló

Ferentzi

Perczel

et al. 2023

Org. Process Res. Dev.

Self Cite

View full text Add to dashboard Cite

Pseudoproline derivatives are incorporated into polypeptides as aggregation disrupters during synthesis, from which the unmodified side chains can be recovered during the final step (resin cleavage). However, direct coupling to pseudoproline is challenging and thus dipeptides of pseudoproline, Fmoc-Xaa-Yaa(Ψ Me,Me pro)-OH, are traditionally introduced, which requires the entire library of Fmoc-Xaa-Thr(Ψ Me,Me pro)-OH in stock, making this approach expensive. Here, we show how the in situ acylation of the incorporated H-Thr(ΨPro)− can be done successful in flow peptide chemistry, with almost all proteinogenic amino acids (Xaa or X). The Xaa-Thr(ΨPro) amide bond was established with a reagent excess of three to five equivalents, with better than 75% efficiency for most Xaa and 70% in the case of Met. Only for Asp was the efficiency too low (8%) to support the direct use of pseudoproline derivatives.

show abstract

“…Throughout our work, all syntheses were performed on our continuous flow peptide synthesizer, using previously developed coupling protocols. Asi is formed most rapidly when the (i + 1) residue with respect to amino acid (i), which is Asp (or Asn), is flexible and has no side chain, making Asp-Gly the most susceptible subunit for isomerization [11][12][13][14][15][16]. Moreover, the catalytic effect of the side chain of the (i + 1) residue has also been proposed, suggesting that Ser and Thr, both residues with short side chains, -Asp-Ser-and -Asp-Thr-, are ready for isomerization within days under synthetic conditions [17].…”

Section: Introductionmentioning

confidence: 99%

Unveiling the Oxazolidine Character of Pseudoproline Derivatives by Automated Flow Peptide Chemistry

Szaniszló,

Csámpai,

Horváth

et al. 2024

IJMS

Self Cite

View full text Add to dashboard Cite

Pseudoproline derivatives such as Thr(ΨPro)-OH are commonly used in peptide synthesis to reduce the likelihood of peptide aggregation and to prevent aspartimide (Asi) formation during the synthesis process. In this study, we investigate notable by-products such as aspartimide formation and an imine derivative of the Thr(ΨPro) moiety observed in flow peptide chemistry synthesis. To gain insight into the formation of these unexpected by-products, we design a series of experiments. Furthermore, we demonstrate the oxazolidine character of the pseudoproline moiety and provide plausible mechanisms for the two-way ring opening of oxazolidine leading to these by-products. In addition, we present evidence that Asi formation appears to be catalyzed by the presence of the pseudoproline moiety. These observed side reactions are attributed to elevated temperature and pressure; therefore, caution is advised when using ΨPro derivatives under such harsh conditions. In addition, we propose a solution whereby thermodynamically controlled Asi formation can be kinetically prevented.

show abstract

Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel

Cited by 6 publications

References 55 publications

Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

Improved Acylation of Pseudoproline: Masked Threonine in Flow Peptide Chemistry

Unveiling the Oxazolidine Character of Pseudoproline Derivatives by Automated Flow Peptide Chemistry

Contact Info

Product

Resources

About