Identification of Conformational B-cell Epitopes in Diphtheria Toxin at Varying Temperatures Using Molecular Dynamics Simulations

Document Type : Original Articles


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

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

3 Razi Vaccine and Serum Research Institute, 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, Iran


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 since its mechanism of action is similar to those of most bacterial toxins, such as botulinum, tetanus, and anthrax. The protection of conformational B-cell epitopes is critically important in the process of diphtheria vaccine production. This study aimed to evaluate the conformational changes of the DT structure at three different temperature levels (27˚C, 37˚C, and 47˚C) using molecular dynamic simulations. Secondary structures were analyzed in YASARA software. According to the results, significant decreases were observed 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. Furthermore, the tertiary structure of the DT was compared at different temperatures using the contact map.  Accordingly, the results showed that the root-mean-square deviation of the DT structure increased upon temperature rising. In addition, 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 values. The finding demonstrated that the stability of the DT structure decreased at high temperature (47˚C). The solvent-accessible surface area diagram showed that the hydrophobicity of the DT structure increased via temperature rising, and the 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 the diphtheria vaccine.


Article Title [French]

Identification des épitopes Conformationnels des Lymphocytes B dans la Toxine Diphtérique à des Températures Variables en Utilisant des Simulations de Dynamique Moléculaire

Abstract [French]

Les changements de niveaux de température peuvent potentiellement affecter les toxines en termes de stabilité et de propriétés immunologiques via l'altération de leurs structures. La toxine diphtérique (TD) est très étudiée par les scientifiques car son mécanisme d'action est similaire à ceux de la plupart des toxines bactériennes, telles que le botulisme, le tétanos et l'anthracis. La protection des épitopes conformationnels des lymphocytes B est d'une importance cruciale dans le processus de production du vaccin antidiphtérique. Cette étude visait à évaluer les changements conformationnels de la structure de la TD à trois température différentes (27˚C, 37˚C et 47˚C) à l'aide de simulations de dynamique moléculaire. Les structures secondaires ont été analysées dans le logiciel YASARA. Selon les résultats, des diminutions significatives ont été observées dans les pourcentages des feuillets β, des spires et des hélices de la structure de la TD à 47°C par rapport à ceux observés à 27°C et 37°C. De plus, la structure tertiaire de la TD a été comparée à différentes températures en utilisant la carte de contact. Les résultats de cette étude ont montré que la déviation quadratique moyenne de la structure de la TD augmentait lors de l'augmentation de la température. En outre, les acides aminés D68, G128, G171, C186 et K534-S535 à 27°C et 37°C, ainsi que les acides aminés G26, P38, S291, T267, H384, A356 et V518 à 47°C ont montré des valeurs de fluctuation quadratique moyenne plus élevées. Ces résultats ont révélé que la stabilité de la structure de la TD diminuait à haute température (47°C). Le diagramme de surface accessible aux solvants a montré que l'hydrophobicité de la structure de la TD augmentait suite à l’augmentation de température, et les résidus d'acides aminés appartenant aux épitopes de lymphocytes B se prolongeaient. Cependant, les épitopes des cellules B appartenant à la région de jonction des chaînes A et B n'étaient présents qu'à 37°C. Les résultats de cette étude devraient être applicables pour déterminer un niveau de température approprié pour le processus de production d’un vaccin contre la diphtérie.

Keywords [French]

  • Epitopes de cellules B
  • Toxine diphtérique
  • Simulation de dynamique moléculaire
  • Stabilité
  • Température
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