Effect of point mutation on the structure and dynamics of human superoxide dismutase ۱ using molecular dynamics simulation

SOD۱ is an important antioxidant enzyme . This enzyme contains ۱۵۳ amino acids and the occurrence of mutations in it will cause ALS disease, which can be evaluated by molecular simulation. To investigate the role of mutations in the structure and dynamic properties of the protein, the PDB file with the code ۲C۹V was first received from the protein database. Then the G۱۶S and L۱۰۶V mutations were generated on a ۲C۹V file. Gromacs software was used to create the input structure to simulate molecular dynamics for wild type and mutant enzymes. By analyzing the data during the simulation time (۵ Nano Second), the structural changes in the protein were evaluated. Using the mean square root, the accuracy of the simulation was checked and also the RMSF study showed that in the mutations of G۱۶S and L۱۰۶V in the regions of ۷۱ to ۷۹ and ۱۰۷ to ۱۱۷, a decrease in the amount of RMSF is observed compared to the wild type that indicates a decrease in flexibility and an increase in stability. Also, in regions ۱۲۷ to ۱۳۶ of the L۱۰۶V mutant, there is a significant increase in the amount of RMSF compared to the wild type. The average number of hydrogen bonds for G۱۶S and L۱۰۶V mutants is ۱۰۳ and ۱۰۱ bonds versus ۱۰۰ hydrogen bonds for wild type, respectively. These changes, albeit small, are effective in reducing the flexibility of the G۱۶S. The study of gyration radius showed partial compactness in the G۱۶S mutant and the local unfolding in the L۱۰۶V mutant compared to the wild type. molecular dynamics simulation studies support formation of aggregation and prone to ALS for mutations

کلیدواژه ها:

Point mutation ، Mean square root ، RMSF ، gyration radius ، G۱۶S mutant