Glutamine deamidation: an indicator of antiquity, or preservational quality?

Abstract

RATIONALE:Much credence has been given in the paleoproteomic community to glutamine deamidation as a proxy for the age of proteins derived from fossil and subfossil material, and this modification has been invoked as a means for determining the endogeneity of molecules recovered from very old fossil specimens. METHODS: We re-evaluated the relationship between glutamine deamidation and geologic time by examining previously published data from five recent mass spectrometry studies of archeaological fossils. Deamidation values recovered for fossils were graphed against their reported chronologic age using WebPlotDigitizer. RESULTS: The experimental data that has been produced from fossil material to date show that the extent of glutamine deamidation does not correspond to the absolute age of the specimens being examined, but rather show extreme variation between specimens of similar age and taxonomic affinity. CONCLUSIONS: Because deamidation rates and levels can be greatly affected by numerous chemical and environmental factors, we propose that glutamine deamidation is better suited as an indicator of preservational quality and/or environmental conditions than a mark of the endogeneity or authenticity of ancient proteins.

Proteomic profiling of archaeological human bone

“…To address the issue of endogenous molecule quality, proteomic data from the samples were assessed using two indices: the rate of deamidation and the proportion of type I collagen. Deamidation is an indicator of the preservational quality, and the rate of deamidation of glutamine range is 0–20% in bones of 0–2000 years ago [54]. In this study, the rate of deamidation was 10% on average (range 4–13%; table 1), which is compatible with bones dating ca 500 years before present.…”

Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

“…The rates of deamidation of asparagine (N) and glutamine (Q) residues to aspartic acid (D) and glutamic acid (E), respectively, have been used as in vivo molecular clocks (Robinson & Robinson, 2001; Robinson & Robinson, 2004) as well to estimate the level of degradation in ancient proteins (Wilson, et al, 2012; Schroeter & Cleland, 2016). While asparagine tends to deamidate relatively rapidly, at least in denatured proteins and in flexible regions of native proteins (van Duin & Collins, 1998; Robinson & Robinson, 2001; Robinson & Robinson, 2004), glutamine deamidation is markedly slower and thus can be used to assess protein degradation in archaeological contexts (van Doorn, et al, 2012; Wilson, et al, 2012).…”

Bone protein “extractomics”: comparing the efficiency of bone protein extractions ofGallus gallusin tandem mass spectrometry, with an eye towards paleoproteomics

“…Primary among these challenges is the inherent uncertainty surrounding the nature of the fossils themselves, which have undergone processes that are impossible to directly measure or observe, but which profoundly affect the chemistry of organic matter remaining within them. These include, but are not limited to, uncertainty in the rates at which proteins may degrade over geologic time, and the role that any given environmental factor plays in protein preservation and/or degradation (Hedges, 2002; Nielsen-Marsh et al, 2000; Nielsen-Marsh & Hedges, 2000), uncertainty regarding diagenetic modifications that might alter the chemical structure of ancient molecules (e.g., AGEs) (Cleland, Schroeter & Schweitzer, 2015; Nielsen-Marsh et al, 2005; Van Klinken & Hedges, 1995), and finally, uncertainty over what fluctuations in the biological, thermal, and hydrological conditions a fossil may have been subjected to over thousands to millions of years, and how these may affect their molecular composition (Schroeter & Cleland, 2016; Smith et al, 2003). However, although molecular studies on fossil remains will always be laden with unknown (and unknowable) variables that must be studied indirectly, the nascent field of molecular paleontology is also affected by unexplored gaps in our knowledge which must be addressed and resolved for the field to continue to progress.…”