Predicting protein decomposition: the case of aspartic-acid racemization kinetics

The increase in proportion of the non-biological (D-) isomer of aspartic ac id (Asp) relative to the L-isomer has been widely used in archaeology and g eochemistry as a tool for dating. The method has proved controversial, part icularly when used for bones. The non-linear kinetics of Asp racemization h ave prompted a number of suggestions as to the underlying mechanism(s) and have led to the use of mathematical transformations which linearize the inc rease in D-Asp with respect to time. Using one example, a suggestion that t he initial rapid phase of Asp racemization is due to a contribution from as paragine (Asn), we demonstrate how a simple model of the degradation and ra cemization of Asn can be used to predict the observed kinetics. A more comp lex model of peptide bound Asx (Asn+Asp) racemization, which occurs via the formation of a cyclic succinimide (Asu), can be used to correctly predict Asx racemization kinetics in proteins at high temperatures (95-140 degrees C). The model fails to predict racemization kinetics in dentine collagen at 37 degrees C. The reason for this is that Asu formation is highly conforma tion dependent and is predicted to occur extremely slowly in triple helical collagen. As conformation strongly influences the rate of Asu formation an d hence Asx racemization, the use of extrapolation from high temperatures t o estimate racemization kinetics of Asx in proteins below their denaturatio n temperature is called into question. In the case of archaeological bone, we argue that the D:L ratio of Asx refl ects the proportion of nonhelical to helical collagen, overlain by the effe cts of leaching of more soluble land conformationally unconstrained) peptid es. Thus, racemization kinetics in bone are potentially unpredictable, and the proposed use of Asx racemization to estimate the extent of DNA depurina tion in archaeological bones is challenged.