Communities in the iron superoxide dismutase amino acid network.

Amino acid networks (AANs) analysis is a new way to reveal the relationship between protein structure and function. We constructed six different types of AANs based on iron superoxide dismutase (Fe-SOD) three-dimensional structure information. These Fe-SOD AANs have clear community structures when they were modularized by different methods. Especially, detected communities are related to Fe-SOD secondary structures. Regular structures show better correlations with detected communities than irregular structures, and loops weaken these correlations, which suggest that secondary structure is the unit element in Fe-SOD folding process. In addition, a comparative analysis of mesophilic and thermophilic Fe-SOD AANs' communities revealed that thermostable Fe-SOD AANs had more highly associated community structures than mesophilic one. Thermophilic Fe-SOD AANs also had more high similarity between communities and secondary structures than mesophilic Fe-SOD AANs. The communities in Fe-SOD AANs show that dense interactions in modules can help to stabilize thermophilic Fe-SOD.

Comparison of protein-water interactions in psychrophilic, mesophilic, and thermophilic Fe-SOD.

Iron superoxide dismutase (Fe-SOD) can eliminate superoxide anion radicals and is widely used in pharmaceuticals, cosmetics and foodstuff. It's significant to determine the factors that influence Fe-SOD thermostability. Previous studies have focused on the relationship between the structural parameters and thermostability of Fe-SOD while the contribution of water molecules was overlooked. In this study, we examined the relationship between hydration waters and Fe-SOD thermostability. The Voronoi polyhedra method was used to explore the distribution of hydration waters around the Fe-SODs and it was interesting to find that the distribution of hydration waters is related to the B-factor of amino acids, i.e., the flexibility of residues can affect the distribution of waters. Protein-water and water-water hydrogen bonds were examined. We found that the hydrogen bond density in thermophilic Fe-SOD was higher than that in mesophilic Fe- SOD. In addition, larger hydrogen bond networks that involve more waters covered the thermophilic Fe-SOD.