Study Of The Relationship Between Structural Features And Thermostability Of Fe-SOD

Thermophilic enzymes are resistant to high temperature, physical and chemicaldenaturing agent, acid and alkaline environment and organic solvent. They are widely used inindustry. Compared to chemical catalyst, thermophilic enzymes have many advantages, suchas high catalytic efficiency and substrate specificity. Compared to mesophilic enzymes,thermophilic enzymes can accelebrate the dynamic reaction rate, reduce production cost, keepactivity for a long time and reduce bacterial contamination. 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-SODthermostability.In this paper, we studied and analysed the Fe-SOD thermostabiliy from two majoraspects: one was features and interacitons of residues, and another was protein-water andwater-water interactions. For the first aspect, we firstly wrote Perl scripts to extract andanalyse data, and then we applied principal component analysis(PCA) to find out the criticalfactors that influence thermostability of Fe-SODs.We analysed B-factor, cavity and packing density, hydrogen bond, salt bridge and solventaccesible area using perl scripts. The results show that thermophilic Fe-SODs have higherB-factor values comparing to mesophilic Fe-SODs. There are more cavities in thermophilicFe-SODs in average. The numbers of main chain-main chain hydrogen bonds andcharged-charged hygrogen bonds increase with the thermostability of Fe-SOD whileuncharged-uncharged hydrogen bonds decrease with the thermostability of Fe-SOD.Principal component analysis was used to find out the key factors that influencethermostability of Fe-SOD. We analysed the content and lenth of secondary structure,hydrogen bond, salt bridge and solvent accesible area. It’s found that the lengths of H、T、loopand G, and the contents of H、E、T and loop are inportant for the Fe-SOD thermostability.We also found that the numbers of total hydrogen bonds, main chain-main chain hydrogenbonds and charged-uncharged hydrogen bonds have an impact on the Fe-SOD thermostability.In addition, we examined the relationship between hydration waters and Fe-SODthermostability. The evaluation of hydration shells in terms of distance revealed that theaverage number of water molecules in the first hydration shell per residue increased withimproved thermostability. The Voronoi polyhedra method was also used to explore thedistribution of hydration waters around the Fe-SODs and it was interesting to find that thedistribution of hydration waters is related to the B-factor of amino acids.We also found thatthe hydrogen bond density in thermophilic Fe-SOD was higher compared to that inmesophilic Fe-SOD. In addition, larger hydrogen bond networks covered the thermophilicFe-SOD, and more waters were involved in these networks.