Thermal and ionic effect on Euplotes focardii superoxide dismutase structure

Superoxide dismutases (SODs) are ubiquitous enzymes, which catalyse the dismutation of superoxide to molecular oxygen and peroxide. Generally, cold adapted enzymes are characterized by an increased flexibility related to a low stability at higher temperature and an improved catalytic efficiency in the cold; these modifications involve the structural stability of psychrophilic enzymes. Euplotes focardii is an Antarctic marine ciliate. The optimal temperature for growth and reproduction is 4°C. It has two Cu/Zn - SODs isoforms which display about 40% of sequence identity. MD simulations were performed with the GPU implementation of the pmemd code, from AMBER14. The calculations employed the ff99SSBildn forcefield. Results are interpreted in comparison with E. crassus SODs, a congeneric mesophilic marine species. At the respective phisiological living temperatures SOD1 displays greater difference between rmsd values of simulations with and without ions -> more evident ionic effect SOD2 is more flexible than SOD1, it displays a reduced difference between rmsd values of simulations with and without ions -> lower influence of temperature and ionic presence Both ions presence and temperature changes mainly influence the loops forming the ions binding site.