Nonenzymatic Deamidation Mechanism on a Glutamine Residue with a C-Terminal Adjacent Glycine Residue: A Computational Mechanistic Study
Abstract
:1. Introduction
2. Computational Methods
3. Results and Discussion
3.1. Comparison of the Optimized Geometries in the Cyclization Step
3.2. Comparison of the Optimized Geometries in the Deammoniation Step
3.3. Energy Profiles
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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φ | ψ | χ1 | χ2 | |
---|---|---|---|---|
RC-A | −150 | 145 | −173 | −79.6 |
TS1-A | −157 | −178 | 179 | −66.4 |
INT1-A | −155 | −157 | 176 | −63.8 |
RC-B | −150 | 136 | −167 | −70.2 |
TS1-B | −157 | −177 | −178 | −68.2 |
INT1-B | −155 | −154 | 172 | −61.0 |
RC-C | −147 | 141 | −177 | −75.4 |
TS1-C | −155 | 169 | 172 | −57.1 |
INT1-C | −106 | −148 | 177 | −64.0 |
Chain A | Chain B | |||||||
---|---|---|---|---|---|---|---|---|
φ | ψ | χ1 | χ2 | φ | ψ | χ1 | χ2 | |
Gln16 | −118 | 158 | −58.4 | −70.2 | −79.3 | 168 | −57.9 | −48.2 |
Gln63 | −52.5 | 128 | −174 | 166 | −47.9 | 135 | 165 | 173 |
Gln92 | −101 | 135 | −103 | 51.4 | −87.9 | 138 | −130 | 60.2 |
Gln120 | −93.7 | −31 | −174 | 180 | −87.4 | −27.2 | −171 | 177 |
φ | ψ | χ1 | χ2 | |
---|---|---|---|---|
INT2 | −107 | −152 | 173 | −60.4 |
TS2 | −107 | −153 | 174 | −58.8 |
PC | −99.6 | −163 | −179 | −48.8 |
HF | B3LYP | CAM-B3LYP | ωB97XD | MP2 | |
---|---|---|---|---|---|
RC | 0 | 0.0 | 0 | 0 | 0.0 |
TS1 | 161 | 115 | 115 | 113 | 96.9 |
INT1 | 90.1 | 91.3 | 78.9 | 74.1 | 53.9 |
INT2 | 81.7 | 71.1 | 61.9 | 63.9 | 49.2 |
TS2 | 139 | 89.2 | 85.1 | 89.3 | 74.2 |
PC | 18.7 | 31.8 | 35.9 | 49.1 | 37.9 |
HF | B3LYP | CAM-B3LYP | ωB97XD | MP2 | |
---|---|---|---|---|---|
RC | 0 | 0 | 0 | 0 | 0 |
TS1 | 156 | 111 | 111 | 106 | 85.4 |
INT1 | 89.6 | 89.0 | 78.6 | 77.9 | 55.8 |
INT2 | 91.2 | 76.5 | 65.8 | 63.0 | 46.5 |
TS2 | 148 | 94.3 | 89.0 | 89.1 | 71.7 |
PC | 19.8 | 38.5 | 41.0 | 46.5 | 29.8 |
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Asai, H.; Kato, K.; Nakayoshi, T.; Ishikawa, Y.; Kurimoto, E.; Oda, A.; Fukuishi, N. Nonenzymatic Deamidation Mechanism on a Glutamine Residue with a C-Terminal Adjacent Glycine Residue: A Computational Mechanistic Study. AppliedChem 2021, 1, 142-155. https://doi.org/10.3390/appliedchem1020011
Asai H, Kato K, Nakayoshi T, Ishikawa Y, Kurimoto E, Oda A, Fukuishi N. Nonenzymatic Deamidation Mechanism on a Glutamine Residue with a C-Terminal Adjacent Glycine Residue: A Computational Mechanistic Study. AppliedChem. 2021; 1(2):142-155. https://doi.org/10.3390/appliedchem1020011
Chicago/Turabian StyleAsai, Haruka, Koichi Kato, Tomoki Nakayoshi, Yoshinobu Ishikawa, Eiji Kurimoto, Akifumi Oda, and Nobuyuki Fukuishi. 2021. "Nonenzymatic Deamidation Mechanism on a Glutamine Residue with a C-Terminal Adjacent Glycine Residue: A Computational Mechanistic Study" AppliedChem 1, no. 2: 142-155. https://doi.org/10.3390/appliedchem1020011