Aspartate racemization

While several laboratories have shown that severe racemiza-tion of proteins can occur during treatment with sodium hydroxide (6,18,22-24,61,62) the effects of other alkalis used in food processing are documented less well. Jenkins, et al. (70) have observed substantial differences in the degree of racemization caused by lime or caustic soda treatment of zein. Lime causes only 50% to 90% of the racemization observed for several amino acyl residues compared to when caustic soda is used. Because a substantial amount of calcium ion remained bound to the protein (approx. 10,000 ppm) compared to l/20th that amount of sodium ion for the caustic soda-treated zein, it is possible that divalent calcium may stabilize the protein making it less susceptible to racemization. Tovar (14) observed increases of 40% to 50% in serine and phenylalanine racemization and a decrease of 30% aspartate racemization for caustic soda-treated fish protein concentrate compared to lime-treated protein (see Table II). These studies indicate that different alkalis have different effects on racemization of proteins specifically, lime may cause less racemization than caustic soda at a similar pH. 

The improvements in resolution achieved in each deconvolution step are shown in Figure 3-3. While the initial library could only afford a modest separation of DNB-glutamic acid, the library with proline in position 4 also separated DNP derivatives of alanine and aspartic acid, and further improvement in both resolution and the number of separable racemates was observed for peptides with hydrophobic amino acid residues in position 3. However, the most dramatic improvement and best selectivity were found for c(Arg-Lys-Tyr-Pro-Tyr-(3-Ala) (Scheme 3-2a) with the tyrosine residue at position 5 with a resolution factor as high as 28 observed for the separation of DNP-glutamic acid enantiomers. 

The noteworthy successes of a relevant model study12 provided the foundation for Merck s thienamycin syntheses. In the first approach (see Schemes 2 and 3), the journey to the natural product commences from a readily available derivative of aspartic acid this route furnishes thienamycin in its naturally occurring enantiomeric form, and is noted for its convergency. During the course of this elegant synthesis, an equally impressive path to thienamycin was under parallel development (see Schemes 4 and 5). This operationally simple route is very efficient (>10% overall yield), and is well suited for the production of racemic thienamycin on a commercial scale.. x... 

When the substrate is availabT in either the d- or 1-racemic form, it is preferable to use the appropriate isomer rather than its mixture In a case of transaminase assays for GOT and GPT activity, for example, the initial assays used the d-1 amino acid as substrate, and a marked improvement in activity and linearity was found by Henry and co-workers when they used 1-aspartate or 1-alanine, respectively (28) ... 

If the environmental temperature is constant, the racemization process takes place at a uniform rate, which is determined, at any time during the process, by the relative amounts of / and d forms of the amino acid can be measured. As the racemization proceeds and the concentration of the / form amino acid decreases, the rate of racemization gradually slows down. When there is a mixture of 50% of each of the d and / forms, the racemization process stops altogether. The half-life of the racemization of aspartic acid, for example, a common amino acid in proteins, at 20°C is about 20,000 years. This half-life makes it possible to date proteins as old as about 100,000 years. So far, however, the dates obtained with the technique have proved somewhat inconsistent, probably because of the difficulty in verifying whether the temperature of the amino acids has been constant. 

Manley, W. R, G. H. Miller, and J. Czywczynski (2000), Kinetics of aspartic acid racem-ization, in Goodfriend, G. A., M. J. Collins, M. L. Fogel, S. A. Macko, and J. F. Wehmiller (eds.), Perspectives in Amino Acid and Protein Geochemistry, Oxford Univ. Press, New York, pp. 202-218. 

Weiner, S., Z. Kustanovich, E. Gil-Av, and W. Traub (1980), Dead Sea scroll parchments Unfolding of the collagen molecules and racemization of aspartic acid, Nature 287, 820-823. 

Radkiewicz et al.184 explored the mechanism of aspartic acid racemization by means of the DFT(B3LYP)/SCRF calculations. The DFT/SCRF calculations provided quantitative rationalization of the rapid racemization observed at succinimide residues in proteins. The proposed reaction mechanism was supported by the computed increase of the acidity of the succinimide residue in aqueous solution compared to gas phase. 

Radkiewicz, J. L., H. Zipse, S. Clarke, and K. N. Houk. 1996. Acclerated Racemization of Aspartic Acid and Asparagine Residues via Succinimidine Intermediates An ab initio Theoretical Exploration of Mechanism. J. Am. Chem. Soc. 118,9148. 

E. Fernandez, J.E. Ortiz, A. Perez Perez, E. Prats, D. Turbon, T. Torres, E. Arroyo Pardo, Aspartic Acid Racemization Variability in Ancient Human Remains Implications in the Prediction of Ancient DNA Recovery, Journal of Archaeological Science, 36,965 972 (2009). 

Because at ambient temperatures the racemization rates of all amino acids are slow, it is usually found that aspartic acid is most useful archaeologically, but over much longer geological timescales aspartic acid may become racemic... 

Table 8.1 Aspartic acid racemization dates from Californian Paleoindian Skeletons. (Reprinted with Permission from Bada et al., 1974 Tables 1 and 2. Copyright 1974 American Association for the Advancement of Science.)...

Table 8.4 Revised aspartic acid racemization dates for Californian Paleoin-dians. (After Bada, 1985 Table 1, reproduced by permission of the Society for American Archaeology from American Antiquity, 50 no. 3 1985.)...

Figure 8.4 Calibration curve for racemization of aspartic acid in modern dental collagen. (From Gillard et al., 1991 Figure 1, by permission of Birkhauser Yerlag AG.)...

Bada, J.L. (1985). Aspartic acid racemization ages of California Paleoindian skeletons. American Antiquity 50 645-647. 

Bada, J.L. and Protsch, R. (1973). Racemization reaction of aspartic acid and its use in dating fossil bones. Proceedings of the National Academy of Sciences of the USA 70 1331-1334. 

Bada, J.L., Schroeder, R.A. and Carter, G.F. (1974). New evidence for the antiquity of man in North America deduced from aspartic acid racemization. Science 184 791-793. 

Masters, P.M. (1986b). Age at death determinations for the autopsied remains based on aspartic acid racemization in tooth dentin importance of postmortem conditions. Forensic Science International 32 179-184. 

Taylor, R.E., Ennis, P.J., Slota, P.J. Jr and Payen, L.A. (1989). Non-age-related variations in aspartic acid racemization in bone from a radiocarbon-dated late Holocene archaeological site. Radiocarbon 31 1048-1056. 

Van Duin, A.C.T. and Collins, MJ. (1998). The effects of conformational constraints on aspartic acid racemization. Organic Geochemistry 29 1227-1232. 

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