ArticleInternational journal of molecular sciences2020
Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Expanding the Chemoproteomic Toolkit to Asparagine and Glutamine.ACS chemical biology · 2026Article
- Improvement of Analysis and Transferability in Peptide Purification: From HPLC to FPLC and Back Again.Journal of peptide science : an official publication of the European Peptide Society · 2026Article
- Extensive Backbone Cleavage Coverage of Intact Proteoforms in a Mass Range of 10-70 kDa by Integrating Electron, Collision, and Photon-Based Fragmentation Techniques during an Electrophoretic Time Scale.Journal of the American Society for Mass Spectrometry · 2026Article
- Review
- Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA.Nature communications · 2025Article
- Investigation of the Effect of C-Terminal Adjacent Phenylalanine Residues on Asparagine Deamidation by Quantum Chemical Calculations.International journal of molecular sciences · 2025Article
- The Unified Theory of Neurodegeneration Pathogenesis Based on Axon Deamidation.International journal of molecular sciences · 2025Review
- Revisiting the Effect of Trypsin Digestion Buffers on Artificial Deamidation.Journal of the American Society for Mass Spectrometry · 2025Article
- Genesis and regulation of C-terminal cyclic imides from protein damage.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dynamic energy conversion in protein catalysis: From brownian motion to enzymatic function.Computational and structural biotechnology journal · 2025Review
- General instability of dipeptides in concentrated sulfuric acid as relevant for the Venus cloud habitability.Scientific reports · 2024Article
- HLA-DQB1*05 subtypes and not DRB1*10:01 mediates risk in anti-IgLON5 disease.Brain : a journal of neurology · 2024Article
- Stability of Protein Pharmaceuticals: Recent Advances.Pharmaceutical research · 2024Review
- Heat-induced structural and chemical changes to a computationally designed miniprotein.Protein science : a publication of the Protein Society · 2024Article
- Understanding the Specific Implications of Amino Acids in the Antibody Development.The protein journal · 2024Review
- Streamlined Multi-Attribute Assessment of an Array of Clinical-Stage Antibodies: Relationship Between Degradation and Stability.Applied spectroscopy · 2024Article
- Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity.bioRxiv : the preprint server for biology · 2023Article
- Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers.Journal of the American Society for Mass Spectrometry · 2023Article
- Designing Formulation Strategies for Enhanced Stability of Therapeutic Peptides in Aqueous Solutions: A Review.Pharmaceutics · 2023Review
- Circular Dichroism Study of Orexin B under Oxidative Stress Conditions.Molecules (Basel, Switzerland) · 2023Article
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4 authors.
Funding
Abstract
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.
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