Comparing Structure and Conformation of Diphtheria Toxin With Its Non-toxic Mutant (E349K) at 300 K Using Molecular Dynamics Simulations

The molecular dynamics 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 thus aimed to evaluate the effects of the mutation on the structure and the conformation of DT using molecular dynamic simulations.

PYMOL system was used for introducing the mutant amino acid to DT. Three dimensional structures were visualized using YASARA. The protonation fixing process was done using H++ server. SPD viewer was then applied to retrieve missing hydrogen atoms. Molecular dynamic simulations were also carried out using GROMACS software. Finally, RMSF, Rg, and RMSD graphs were drawn by Sigma Plot using GROMACS outputs.

The results of our analysis indicated that amino acid residue fluctuations in the catalytic domain (C) of DT were greater than those of its mutant (E349K). Moreover, residue fluctuations in the region, including Ile344- val347, Tyr514-Ser525, and Ile533-Lys534 of DT were greater than those of the mutant (E349K). However, residue fluctuations in the region including Cys186-Cys201 and Glu349-Val351 of DT were lower than those of E349K. In addition, the disulfide bridge (Cys186–Cys201) was 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. Additionally, 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 greater than those of DT. The conformational stability and compactness of DT were higher than those of E349K.

The method used in this study can demonstrate the structural details of toxins as important aspects to predict activities of the receptor binding and the catalytic domains. Therefore, it can be used to evaluate conformational changes of toxins as well as other vaccine candidates.