Artificial diagenesis of the intra-crystalline proteins isolated from Patella vulgata was induced by isothermal heating at 140 °C, 110 °C and 80 °C. Protein breakdown was quantified for multiple amino acids, measuring the extent of peptide bond hydrolysis, amino acid racemisation and decomposition. The patterns of diagenesis are complex; therefore the kinetic parameters of the main reactions were estimated by two different methods: 1) a well-established approach based on fitting mathematical expressions to the experimental data, e.g. first-order rate equations for hydrolysis and power-transformed first-order rate equations for racemisation; and 2) an alternative model-free approach, which was developed by estimating a “scaling” factor for the independent variable (time) which produces the best alignment of the experimental data. This method allows the calculation of the relative reaction rates for the different temperatures of isothermal heating.High-temperature data were compared with the extent of degradation detected in sub-fossil Patella specimens of known age, and we evaluated the ability of kinetic experiments to mimic diagenesis at burial temperature. The results highlighted a difference between patterns of degradation at low and high temperature and therefore we recommend caution for the extrapolation of protein breakdown rates to low burial temperatures for geochronological purposes when relying solely on kinetic data.
Over 500 Free Amino Acid (FAA) and corresponding Total Hydrolysed Amino Acid (THAA) analyses were completed from eight independently-dated, multi-century coral cores of massive Porites sp. colonies. This dataset allows us to re-evaluate the application of amino acid racemization (AAR) for dating late Holocene coral material, 20 years after Goodfriend et al. (GCA56 (1992), 3847) first showed AAR had promise for developing chronologies in coral cores. This re-assessment incorporates recent method improvements, including measurement by RP-HPLC, new quality control approaches (e.g. sampling and sub-sampling protocols, statistically-based data screening criteria), and cleaning steps to isolate the intra-crystalline skeletal protein. We show that the removal of the extra-crystalline contaminants and matrix protein is the most critical step for reproducible results and recommend a protocol of bleaching samples in NaOCl for 48 h to maximise removal of open system proteins while minimising the induced racemization. We demonstrate that AAR follows closed system behaviour in the intra-crystalline fraction of the coral skeletal proteins. Our study is the first to assess the natural variability in intra-crystalline AAR between colonies, and we use coral cores taken from the Great Barrier Reef, Australia, and Jarvis Island in the equatorial Pacific to explore variability associated with different environmental conditions and thermal histories. Chronologies were developed from THAA Asx D/L, Ala D/L, Glx D/L and FAA Asx D/L for each core and least squares Monte Carlo modelling applied in order to quantify uncertainty of AAR age determinations and assess the level of dating resolution possible over the last 5 centuries. AAR within colonies follow consistent stratigraphic aging. However, there are systematic differences in rates between the colonies, which would preclude direct comparison from one colony to another for accurate age estimation. When AAR age models are developed from a combined dataset to include this natural inter-colony variability THAA Asx D/L, Glx D/L and Ala D/L give a 2σ age uncertainty of ±19, ±38 and ±29 year, for the 20th C respectively; in comparison 2σ age uncertainties from a single colony are ±12, ±12 and ±14 year. This is the first demonstration of FAA D/L for dating coral and following strict protocols 2σ precisions of ±24 years can be achieved across different colonies in samples from the last 150 years, and can be ±10 years within a core from a single colony. Despite these relatively large error estimates, AAR would be a valuable tool in situations where a large number of samples need to be screened rapidly and cheaply (e.g. identifying material from mixed populations in beach or uplift deposits), prior to and complementing the more time-consuming geochronological tools of U/Th or seasonal isotopic timeseries.
High-temperature isothermal heating of biominerals has commonly been used to artificially accelerate protein degradation in order to extrapolate kinetic parameters to the lower temperatures experienced in vivo and in the burial environment. It is not easy to test the accuracy of these simulations due to the difficulty of finding samples of known age held at a known temperature. We compare protein degradation in the intra-crystalline organic matrix of heated (80 °C, 110 °C, and 140 °C) massive Porites sp. coral to that directly measured in the skeleton of colonies growing at ∼26 °C and deposited over the last five centuries. This provides the opportunity to critically evaluate the underlying assumption that high-temperature experiments accurately mimic degradation processes and kinetics occurring in a 'naturally aged' biomineral. In all samples the intra-crystalline protein fraction was isolated and the L-and D-concentration of multiple amino acids measured using reverse-phase high-performance liquid chromatography (RP-HPLC). There was no evidence of a failure of the closed system in the high-temperature experiments (assessed by X-ray diffraction, thermogravimetric analyses and determination of leached amino acid concentration). We compared conventional methods for estimation of kinetic parameters with a new 'model-free' approach that makes no assumptions regarding the underlying kinetics of the system and uses numerical optimisation to estimate relative rate differences. The 'model-free' approach generally produced more reliable estimates of the observed rates of racemization in 'naturally aged' coral, although rates of hydrolysis (as estimated from the release of free amino acids) were usually over-estimated. In the amino acids for which we were able to examine both racemization and hydrolysis (aspartic acid/asparagine, glutamic acid/glutamine and alanine), it was clear that hydrolysis was less temperature sensitive than racemization, which may account for the differences in degradation patterns observed between the 'naturally aged' coral and high-temperature data. It is clearly important to estimate the individual temperature dependence of each of the parallel reactions. Highlights► We compare protein degradation in heated modern, and naturally aged Porites coral. ► Heating to 140 °C does not compromise the integrity of the closed-system. ► We use a new approach that fits relative rates to estimate temperature dependence. ► Protein degradation patterns change over the temperatures investigated (26-140 °C). ► We observe different temperature sensitivities for hydrolysis and racemization.
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