Thermophilic protein structure adaptation examined with Burial Depth and Travel Depth

Organisms evolved at extreme temperatures (above 80° C) have constraints on their protein structures. These constraints result in differences in residue utilization and overall structure. By studying thermophile/mesophile pairs of homologous structures, we have examined these differences.Geometric measures, specifically Burial Depth (distance from the molecular surface to each atom) and Travel Depth (distance from the convex hull to the molecular surface that avoids the protein interior), along with common metrics like packing are used to gain insight into the constraints experienced by thermophiles.Our results show that extreme thermophiles show significant trends towards becoming more “ball-like”. Their mean Travel Depth is less than their mesophilic counterparts, indicating smaller, less numerous and less deep pockets. Their mean Burial Depth is higher indicating that they bury more surface area and are more compact. This can be tracked on the individual residue level, for instance Alanine becomes more significantly buried under thermophilic conditions, and charged residues become less buried.Shown is an example pair with the thermophile at top. At left are Travel Depth surfaces, at right Burial Depth. Note the fewer, smaller pockets and the deeper core in the thermophile.View Large Image | View Hi-Res Image | Download PowerPoint Slide