Comparing Structure and Conformation of Diphtheria Toxin With Its Non-toxic Mutant (E۳۴۹K) at ۳۰۰ K Using Molecular Dynamics Simulations

Background: The molecular dynamics simulations have provided detailed information on the fluctuations and conformational changes of proteins. Mutation of GLu۳۴۹ 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. Methods: 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. Results: 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 (E۳۴۹K). Moreover, residue fluctuations in the region, including Ile۳۴۴- val۳۴۷, Tyr۵۱۴-Ser۵۲۵, and Ile۵۳۳-Lys۵۳۴ of DT were greater than those of the mutant (E۳۴۹K). However, residue fluctuations in the region including Cys۱۸۶-Cys۲۰۱ and Glu۳۴۹-Val۳۵۱ of DT were lower than those of E۳۴۹K. In addition, the disulfide bridge (Cys۱۸۶–Cys۲۰۱) was formed in DT, whereas it was not observed in the mutant. The secondary structure analysis showed that the beta-sheet content of E۳۴۹K decreased compared with DT. Additionally, the conformation of DT was different from that of E۳۴۹K in the hinge loop regions (Ala۳۷۹–Thr۳۸۶ and Tyr۵۱۴-Ser۵۲۵). The radius of gyration (Rg) and the root mean square deviation (RMSD) of E۳۴۹K were greater than those of DT. The conformational stability and compactness of DT were higher than those of E۳۴۹K. Conclusions: 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.