Proteins from the past

Abstract

Some fragments of ancient protein are less prone to degradation because they bind strongly to the surfaces of minerals.

Keywords: Struthio camelus; biochemistry; biomineralization; eggshell; evolutionary biology; genomics; molecular dynamics; paleontology; paleoproteomics.

Figure 1.. Protein-mineral binding in the presence of water.

(A) The structure of SCA-1 (struthiocalcin-1): the domain that binds to mineral surfaces is rich in aspartic acid and is shown in color. (B) Molecular dynamics simulations performed by one of the present authors (AFW) predict that water molecules adjacent to the surface of calcite (CaCO₃; Ca = yellow, C = cyan, O = red) form ordered layers. At least three layers of ordered water can be seen in this plot, where each blue point represents the position of a water oxygen during the simulation. Darker blues indicate regions where water is most likely to be. (C) Cartoon depicting a protein (SCA) binding to a calcite surface. By disrupting the ordered layers of water molecules (dashed blue lines) near the calcite surface, it is thought that the binding process leads to an increase in entropy (∆S > 0) which, in turn, leads to a more negative binding energy (that is, stronger binding). Demarchi et al. also hypothesize that the water molecules that remain in the ordered layers adjacent to the bound protein are prevented from participating in hydrolysis reactions that would otherwise degrade the protein.