Result and Discussion of Molecular Dynamic Simulation of Created Mutants

Abstract

According to prediction nine residue 67, 187 ALA, 257 ASP, 346 LYS, 321 TYR, 333 ALA, 383 THR, 399 THR, 385 GLU and 392 ALA are selected to be mutated to cysteine, as a result 5 mutant are created. The result from molecular dynamic simulation trajectory calculations shows that mutations caused considerable effect on protein stability. RMSF calculation indicates that there are four flexible regions in the structure which mostly are loops. In mutant number 1 (E385C and A392C), mutation redacted flexibility of two regions and RMSD value shows lower value than the native one which means more stability where RG calculation suggest that structure tends to become more compact than native. In mutant number 2 (Y321C and A333C), the effect was more distinctive and the mutation caused more decrease in flexibility. In mutant number 3 (T383C and T399C), both two mutated residue located in loop region and mutation caused more stability in comparison to native structure like previous mutants. Although it caused reduction in flexibility of three region in protein stability it cause growth of flexibility in other region surprisingly. In mutant number 4 (A187C), mutation caused more stability according to RMSD RMSF and RG calculations. In addition mutation caused reduction in flexibility of four region notably. In mutant number 5 (D257C and L346C), where mutations introduce in loop regions, similar to other mutants graphs analysis show that stability of mutant is increased.