Identification of conformational B-cell epitopes in diphtheria toxin at varying temperatures using molecular dynamics simulations

Document Type: Original Articles

Authors

1 Division of Central Laboratory, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran

2 Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran.

3 Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran

4 Division of Genomics and Genetic Engineering, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran.

Abstract

Abstract
The changes in temperature levels can potentially affect the toxins in terms of stability and immunological properties via alteration of their structures. Diphtheria Toxin (DT) is highly considered by scientists because its mechanism of action is similar to those of most bacterial toxins like botulinum, tetanus and anthrax. The protection of conformational B-cell epitopes is critically important in the process of diphtheria vaccine production. This study was therefore performed for evaluation of the conformational changes of the DT structure at three different temperature levels, including (27˚C, 37˚C and 47˚C) using molecular dynamic (MD) simulations. Secondary structures were analyzed by YASARA software. We found significant decreases in percentages of the β-sheets, turns and the helices of the DT structure at 47˚C in comparison with those at 27˚C and 37˚C. The tertiary structure of the DT compared at different temperatures using the contact map (CM). Results showed that the root mean square deviation (RMSD) of the DT structure increased upon temperature rising. Amino acids D68, G128, G171, C186 and K534-S535 at 27˚C and 37˚C as well as amino acids G26, P38, S291, T267, H384, A356 and V518 at 47˚C showed higher root mean square fluctuation (RMSF) values. Our finding demonstrated that the stability of the DT structure decreased at high temperature (47˚C). The solvent accessible surface area (SASA) diagram showed that hydrophobicity of the DT structure increased via temperature rising. Amino acid residues belonging to B-cell epitopes extended through increasing temperature. However, B-cell epitopes belonging to the junction region of chains A and B were only present at 37˚C. The results of this study are expected to be applicable for determining a suitable temperature level for the production process of diphtheria vaccine.

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