Neighboring side chain effects on asparaginyl and aspartyl degradation: an ab initio study of the relationship between peptide conformation and backbone NH acidity.
The rate of spontaneous degradations of asparagine and aspartyl residues occurring through succinimide intermediates is dependent upon the nature of the residue on the carboxyl side in peptides. For nonglycine residues, we show here that this effect can largely be attributed to the electrostatic/inductive effect of the side chain group on the equilibrium concentration of the anionic form of the peptide bond nitrogen atom that initiates the succinimide forming reaction. However, the rate of degradation of Asn-Gly and Asp-Gly containing peptides is about an order of magnitude greater than predicted solely using this explanation. To understand the nature of the glycine effect, ab initio calculations were performed on model compounds. These calculations indicate that there is little to no change in the stability of the transition state or the tetrahedral intermediate of succinimide formation with Asn-/Asp-Gly and Asn-/Asp-Ala derivatives. However, we have found that the acidity of the backbone peptide nitrogen NH is highly dependent upon the conformation of the molecule. Since glycine residues lack the beta-carbon common to all other protein amino acids, these residues can sample additional regions of conformational space where it is possible to further stabilize the backbone amide anion and thus increase the rate of degradation. These results provide the first rationale for the particular rate enhancement of degradation in peptidyl Asn-/Asp-Gly sequences. The results also can be applied to asparagine and aspartyl residues in proteins where the 3-dimensional structure provides additional constraints on conformation that can either increase or decrease the equilibrium concentration of the backbone amide anion and thus their rate of degradation via succinimide intermediates. Understanding this chemistry will assist attempts to minimize the deleterious effect of aging at the molecular level. The relationship between these results and proton exchange experiments is discussed in the Appendix.
Radkiewicz
J L
JL
Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.
Zipse
H
H
Clarke
S
S
Houk
K N
KN
D000577:Amides / Q000737:chemistry; D001216:Asparagine / Q000737:chemistry*; D001224:Aspartic Acid / Q000737:chemistry*; D005998:Glycine / Q000031:analogs & derivatives* / Q000737:chemistry; D008956:Models, Chemical; D009584:Nitrogen / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013388:Succinimides / Q000138:chemical synthesis / Q000737:chemistry
D000577:Amides; C407066:N-formylglycinamide; D011506:Proteins; D013388:Succinimides; C032620:succinimide; D001224:Aspartic Acid; D001216:Asparagine; D009584:Nitrogen; D005998:Glycine