Periodic Reporting for period 1 - ProArc (The protein archive: preservation potential of ancient human diets and diseases.)
Periodo di rendicontazione: 2021-04-01 al 2023-03-31
Milk proteins are widely reported in the archaeological record, and are dominated by two classes, both widely studied in the food industry: acid-insoluble caseins (the main component of curds) and acid-soluble lactoglobulins (whey proteins). Dental calculus is regarded by many as the most informative ancient remains and is in high demand, being used to explore: ancient diets and human-environment interaction. One surprising find is that whey protein (β-lactoglobulin; BLG) is typically the only protein preserved in ancient dental calculus (apatite?), whereas lime-scale (calcite) from ceramics shows the survival of both the milk proteins curd (caseins) and whey (lactoglobulins). For both the calculus and the ceramic scale, the proteins are extracted in a similar manner, and their burial environment is not distinct enough to play a role for the different survival. The paucity of milk proteins on calculus contrasted with their comparative abundance on ceramics implies selective differences in incorporation or preservation. Understanding the protein-mineral interaction is key both for accessing the mechanisms controlling the protein-mineral interactions and understanding the longevity of minerals preserved different (milk) protein record in deep time.
Therefore, ProArc aims to address 4 research objectives (RO):
RO1: assess different ancient protein-mineral associations and preservation states in potsherds from different archaeological sites to map the differences in physical and chemical storage conditions over time.
RO2: investigate the in vitro organic-molecules-mineral interactions of mineral at the single bond level (bond breaking and reforming) in different relevant solution compositions to quantify the energy and kinetic parameters associated with the interacting bonds.
RO3. examine the organic-mineral interactions at the bulk level (nature, fraction and stability of interacting bonds) and link those to the single bond level energetics to quantify the longevity of the biomolecule-mineral in different environmentally relevant solution compositions.
RO4. link the archaeological biomolecules data to the in vitro single bond and bulk data then make a conceptual model for addressing the characteristics and longevity of biomolecule-mineral system(s), and improve our understanding of cultural heritage of milk protein.
Overall, our Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses of archeological remains, AFM (nano-imaging, rupture forces), FTIR data, and ultraviolet data (adsorption isotherms) suggest that the milk protein-mineral association is strongly influenced by the interfacial geochemistry and it is sensitive to mineral surface charge, mineral charge density, pH, solution composition and solution salinity.
Therefore, ProArc aims to address 4 research objectives (RO):
RO1: assess different ancient protein-mineral associations and preservation states in potsherds from different archaeological sites to map the differences in physical and chemical storage conditions over time.
RO2: investigate the in vitro organic-molecules-mineral interactions of mineral at the single bond level (bond breaking and reforming) in different relevant solution compositions to quantify the energy and kinetic parameters associated with the interacting bonds.
RO3. examine the organic-mineral interactions at the bulk level (nature, fraction and stability of interacting bonds) and link those to the single bond level energetics to quantify the longevity of the biomolecule-mineral in different environmentally relevant solution compositions.
RO4. link the archaeological biomolecules data to the in vitro single bond and bulk data then make a conceptual model for addressing the characteristics and longevity of biomolecule-mineral system(s), and improve our understanding of cultural heritage of milk protein.
Overall, our Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses of archeological remains, AFM (nano-imaging, rupture forces), FTIR data, and ultraviolet data (adsorption isotherms) suggest that the milk protein-mineral association is strongly influenced by the interfacial geochemistry and it is sensitive to mineral surface charge, mineral charge density, pH, solution composition and solution salinity.
Work Performed for RO1 and Results: I have carried out protein and DNA extraction on archeological samples and fossil samples with different mineralogical characteristics. Also, milk protein was heated at neutral pH conditions (pH 7) to discover the effect of heat on the ancient proteins. By mass spectrometry, almost all of the protein sequence is identifiable and recoverable, but there is a variation in the depth of coverage of these sequences after four days and zero four zero written in numbers the pattern is broadly similar although the structures around the N-terminus open up a bit more and we have greater sequence coverage however by 128 days and N1280. In addition, we re-analyzed the coverage of these milk proteins in published data sets. We noted that only a very small fraction of the mass spectrometry (MS2) queries were identified to find that the regions that persist are linked to the mineral surface.
Work Performed under RO2 and Results: Calcite and mica crystals, whey protein β-lactoglobulin (BLG) based on the WP1, and different environmentally relevant solution compositions at pH 7 were used to conduct the AFM experiments (tapping, contact force and dynamic force modes). The present data indicate that ionic solutions (MgCl2; NaCl) and calcite surfaces influenced the adsorption of BLG (Figure 1). BLG only adsorbs to the mica surface when ionic solution MgCl2 was used (Figure 2). The adsorption of BLG onto calcite surface in air (Figure 3) is possible and was affected by the surface topography and concentration of ionic solutions. Rupture forces are also significantly different between calcite and mica surfaces, and are also affected by the ionic solutions and their concentration in the solution. For mica, the adhesion forces were larger when adding 10 mM MgCl2 than the 100 mM NaCl. This could be due to the effect of the double charge on the Mg. A higher ionic strength causes a smaller electrical double layer enabling a higher adsorption strength. I coauthor a paper that was recently accepted by Environmental DNA journal (Wiley), where our experimental data show that DNA damage can be induced by mineral binding if there is a strong driving force for adsorption.
Work Performed under RO3 and Results: I used vibrational Fourier Transform Infrared Spectroscopy in attenuated total reflectance (ATR-FTIR) to measure BLG adsorption to five different minerals—calcite, hydroxyapatite, goethite, kaolinite and mica, and activated charcoal. The results show that the BLG binds to minerals mainly through cationic bridging with the carbonyl (C=O) amide I and amide amide II vN-H. BLG adsorption was affected by the background electrolytes (type and concentration) and minerals.
Work Performed under RO4 and Results: From RO2-RO3, it is clear that the biomolecules-mineral association is strongly influenced by interfacial geochemistry and is sensitive to mineral surface charge, mineral charge density, pH, solution composition and salinity. The AFM images reveal the protein/DNA adsorption behavior (conformation and sites for adsorption) changes with the background cations. The FTIR experiments showed that a cation with a high ionic potential is able to immobilise the protein on a negatively charged surface (carbonyl and amide groups). Since AFM cannot provide a quantitative measure of adsorption capacity, I used UV-visible to determine adsorbed BLG to carbonate (calcite) and clay (mica) to supplement bulk adsorption experiments data so we can quantify how salinity and ionic composition influence the adsorption capacity. Further, the sensitivity of the biomolecule-mineral bond to solution composition (background electrolytes, pH) also kinetics, and hence longevity of the biomolecules-mineral association through time and space. Besides, I worked on subfossil and modern bivalve Methuselah (Arctica islandica shells). The results show that biomolecules, i.e. proteins, DNA and polysaccharide, that are associated with mineral surfaces persist for longer periods. No website has been developed for the project
Work Performed under RO2 and Results: Calcite and mica crystals, whey protein β-lactoglobulin (BLG) based on the WP1, and different environmentally relevant solution compositions at pH 7 were used to conduct the AFM experiments (tapping, contact force and dynamic force modes). The present data indicate that ionic solutions (MgCl2; NaCl) and calcite surfaces influenced the adsorption of BLG (Figure 1). BLG only adsorbs to the mica surface when ionic solution MgCl2 was used (Figure 2). The adsorption of BLG onto calcite surface in air (Figure 3) is possible and was affected by the surface topography and concentration of ionic solutions. Rupture forces are also significantly different between calcite and mica surfaces, and are also affected by the ionic solutions and their concentration in the solution. For mica, the adhesion forces were larger when adding 10 mM MgCl2 than the 100 mM NaCl. This could be due to the effect of the double charge on the Mg. A higher ionic strength causes a smaller electrical double layer enabling a higher adsorption strength. I coauthor a paper that was recently accepted by Environmental DNA journal (Wiley), where our experimental data show that DNA damage can be induced by mineral binding if there is a strong driving force for adsorption.
Work Performed under RO3 and Results: I used vibrational Fourier Transform Infrared Spectroscopy in attenuated total reflectance (ATR-FTIR) to measure BLG adsorption to five different minerals—calcite, hydroxyapatite, goethite, kaolinite and mica, and activated charcoal. The results show that the BLG binds to minerals mainly through cationic bridging with the carbonyl (C=O) amide I and amide amide II vN-H. BLG adsorption was affected by the background electrolytes (type and concentration) and minerals.
Work Performed under RO4 and Results: From RO2-RO3, it is clear that the biomolecules-mineral association is strongly influenced by interfacial geochemistry and is sensitive to mineral surface charge, mineral charge density, pH, solution composition and salinity. The AFM images reveal the protein/DNA adsorption behavior (conformation and sites for adsorption) changes with the background cations. The FTIR experiments showed that a cation with a high ionic potential is able to immobilise the protein on a negatively charged surface (carbonyl and amide groups). Since AFM cannot provide a quantitative measure of adsorption capacity, I used UV-visible to determine adsorbed BLG to carbonate (calcite) and clay (mica) to supplement bulk adsorption experiments data so we can quantify how salinity and ionic composition influence the adsorption capacity. Further, the sensitivity of the biomolecule-mineral bond to solution composition (background electrolytes, pH) also kinetics, and hence longevity of the biomolecules-mineral association through time and space. Besides, I worked on subfossil and modern bivalve Methuselah (Arctica islandica shells). The results show that biomolecules, i.e. proteins, DNA and polysaccharide, that are associated with mineral surfaces persist for longer periods. No website has been developed for the project
Data generated by ProArc can advance existing (milk) protein extraction, conformational structures, and advance analysis protocols. Also, present work could be exploited by various organizations for the identification of the presence of endangered or invasive species that is very difficult to detect visually. Researchers working in the fields of biodiversity, environmental and biomedical science or relevant fields will also benefit from such an advancement of extraction and analysis techniques.