The effects of conformational constraints on aspartic acid racemization
Research output: Contribution to journal › Conference article › Research › peer-review
In short polypeptides, L-aspartic acid (Asp) and L-asparagine (Asn) can undergo isomerization/deamidation reactions via a succinimide (Asu) intermediate resulting in the formation of D-aspartic acid. Some experimental evidence suggests that this reaction, which has been widely used in age determinations, is severely repressed in structured regions of proteins, like for example the triple-helix of collagen, indicating that conformational constraints imposed on the local peptide geometry by the peptide superstructure may inhibit the formation of Asn-containing sequences relative to Asp- or Asn-containing sequences. To examine this, molecular mechanics and molecular dynamics calculations have been performed on constrained and unconstrained Gly-Pro-Asn-Gly-Pro and Gly-Pro-Asu-Gly-Pro pentapeptides. In the constrained calculations, the influence of the protein helix is simulated by fixing the distance between the backbone-nitrogens in the first and last residue at 11.80 Å, a distance similar to that between comparable atoms in the collagen triple-helix. The results from these simulations show that the constraint significantly destabilizes the Asn-containing pentapeptide relative to the Asn-containing sequence; the molecular dynamics simulations, in which the influence of water was specifically taken into account, predict that the constraint raises the energy difference between these two pentapeptides by 8.8 ± 3.8 kcal/mol. This shows that a protein helical structure may severely repress Asp racemization and Asn deamidation. The conservation of such structures should therefore be taken into consideration when using D/L Asp ratios for age determination.
Original language | English |
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Journal | Organic Geochemistry |
Volume | 29 |
Issue number | 5-7 |
Pages (from-to) | 1227-1232 |
Number of pages | 6 |
ISSN | 0146-6380 |
DOIs | |
Publication status | Published - 1998 |
Externally published | Yes |
Event | 18th International Meeting on Organic Geochemistry - Maastricht Exhibition and Congress Centre, Maastricht, Netherlands Duration: 22 Sep 1997 → 26 Sep 1997 |
Conference
Conference | 18th International Meeting on Organic Geochemistry |
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Location | Maastricht Exhibition and Congress Centre |
Country | Netherlands |
City | Maastricht |
Period | 22/09/1997 → 26/09/1997 |
- Age determination, Collagen, D/L Asp ratio, Molecular dynamics, Molecular mechanics
Research areas
ID: 232092735