Comparing structure and conformation of diphtheria toxin with its non-toxic mutant (E349K) at 300K using molecular dynamics simulations

Introduction and Objectives: The molecular dynamic simulations have provided detailed information on the fluctuations and conformational changes of proteins. Mutation of GLu349 of diphtheria toxin (DT) to Lys inhibits the molecular cytotoxicity in mammalian cells. In this work, we aim to evaluate the effect of the mutation on the structure and the conformation of DT using the molecular dynamic simulation. Materials and Methods: The protonation fixing process was done with the diphtheria toxin types, wild and mutant (E349K) to prepare in the natural pH (6.5) by using H++ server which was the input for molecular dynamics simulation the molecular dynamics simulations were done by GROMACS 4.5.4 package. Result: The results of our analysis indicated that amino acid residue fluctuations in catalytic domain(C) of DT are more than those its mutant (E349K). Also, residue fluctuations in the region including Ile344-val347, Tyr514-Ser525 and Ile533-Lys534 of DT were more than those of the mutant (E349K). However, residue fluctuations in the region including Cys186-Cys201 and Glu349-Val351 of DT were less than those of E349K. In addition, the disulfide bridge (Cys186–Cys201) formed in DT, whereas it was not observed in the mutant. The secondary structure analysis showed that the beta sheet content of E349K decreased compared with DT. Also, the conformation of DT was different from that of E349K in the hinge loop regions (Ala379–Thr386 and Tyr514-Ser525). The radius of gyration (Rg) and the root mean square deviation (RMSD) of E349K were more than those of DT. Conclusion: The conformational stability and compactness of DT are more than those of E349K. This method can be used to evaluation conformational change of toxins and proteins as well as vaccine candidates. Because it demonstrates structural details of the toxins that is an important aspect for predicting of activities of the receptor binding and the catalytic domains.

Keywords:

Theoretical biology , Secondary structure , Targeted mutagens