ورود
مقالات فارسیISIکنفرانسهاژورنالها

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

محل انتشار: مجله آرشیو رازی، دوره: 75، شماره: 4
سال انتشار: 1399
نوع سند: مقاله ژورنالی
زبان: انگلیسی
مشاهده: 57

فایل این مقاله در 11 صفحه با فرمت PDF قابل دریافت می باشد

استخراج به نرم افزارهای پژوهشی:

لینک ثابت به این مقاله:
https://civilica.com/doc/1868358

شناسه ملی سند علمی:

JR_ARCHRAZI-75-4_002

تاریخ نمایه سازی: 6 دی 1402

چکیده مقاله:

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 (۲۷˚C, ۳۷˚C, and ۴۷˚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 ۴۷˚C in comparison with those at ۲۷˚C and ۳۷˚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 D۶۸, G۱۲۸, G۱۷۱, C۱۸۶, and K۵۳۴-S۵۳۵ at ۲۷˚C and ۳۷˚C, as well as amino acids G۲۶, P۳۸, S۲۹۱, T۲۶۷, H۳۸۴, A۳۵۶, and V۵۱۸ at ۴۷˚C showed higher root mean square fluctuation values. The finding demonstrated that the stability of the DT structure decreased at high temperature (۴۷˚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 ۳۷˚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.

کلیدواژه ها:

B-cell epitope ، Diphtheria toxin ، Molecular dynamics simulation ، Stability ، temperature

نویسندگان

S. Ghaderi

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

M. R. Bozorgmehr

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

M. Ahmadi

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

Sh. Tarahomjoo

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

مراجع و منابع این مقاله:

لیست زیر مراجع و منابع استفاده شده در این مقاله را نمایش می دهد. این مراجع به صورت کاملا ماشینی و بر اساس هوش مصنوعی استخراج شده اند و لذا ممکن است دارای اشکالاتی باشند که به مرور زمان دقت استخراج این محتوا افزایش می یابد. مراجعی که مقالات مربوط به آنها در سیویلیکا نمایه شده و پیدا شده اند، به خود مقاله لینک شده اند :
  • Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., ...
  • Anandakrishnan, R., Aguilar, B., Onufriev, A.V., ۲۰۱۲. H++ ۳.۰: automating ...
  • Arfken, G., ۱۹۸۵. The method of steepest descents. Math Methods ...
  • Audibert, F., Jolivet, M., Chedid, L., Alouf, J., Boquet, P., ...
  • Boquet, P., Alouf, J.E., Duflot, E., Siffert, O., Rivaille, P., ...
  • Brüschweiler, R., ۲۰۰۳. Efficient RMSD measures for the comparison of ...
  • Bussi, G., Donadio, D., Parrinello, M., ۲۰۰۷. Canonical sampling through ...
  • Chenal, A., Nizard, P., Gillet, D., ۲۰۰۲. Structure and function ...
  • Darden, T., York, D., Pedersen, L., ۱۹۹۳. Particle mesh Ewald: ...
  • Diamond, R., ۱۹۷۶. On the comparison of conformations using linear ...
  • Diamond, R., ۱۹۸۸. A note on the rotational superposition problem. ...
  • Falnes, P.O., Olsnes, S., ۱۹۹۵. Cell-mediated reduction and incomplete membrane ...
  • Ghaderi, S., Tarahomjoo, S., Bozorgmehr, M.R., ۲۰۱۶. Utilizing molecular dynamics ...
  • Gordon, V.M., Leppla, S.H., ۱۹۹۴. Proteolytic activation of bacterial toxins: ...
  • Grubmüller, H., Heller, H., Windemuth, A., Schulten, K., ۱۹۹۱. Generalized ...
  • Guerineau, F., Sorensen, A.M., Fenby, N., Scott, R.J., ۲۰۰۳. Temperature ...
  • Hess, B., Bekker, H., Berendsen, H.J., Fraaije, J.G., ۱۹۹۷. LINCS: ...
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., ...
  • Johnson, A., Johnson, T., Khan, A., ۲۰۱۲. Thermostats in Molecular ...
  • Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., ...
  • Kabsch, W., ۱۹۷۶. A solution for the best rotation to ...
  • Kabsch, W., Sander, C., ۱۹۸۳. Dictionary of protein secondary structure: ...
  • Kövér, K., Bruix, M., Santoro, J., Batta, G., Laurents, D., ...
  • Kräutler, V., Van Gunsteren, W.F., Hünenberger, P.H., ۲۰۰۱. A fast ...
  • Krieger, E., Vriend, G., ۲۰۱۵. New ways to boost molecular ...
  • Laurents, D., Pérez‐Cañadillas, J.M., Santoro, J., Rico, M., Schell, D., ...
  • Lobanov, M.Y., Bogatyreva, N., Galzitskaya, O., ۲۰۰۸. Radius of gyration ...
  • London, E., ۱۹۹۲. Diphtheria toxin: membrane interaction and membrane translocation. ...
  • Menestrina, G., Schiavo, G., Montecucco, C., ۱۹۹۴. Molecular mechanisms of ...
  • Oh, K.J., Zhan, H., Cui, C., Hideg, K., Collier, R.J., ...
  • Paliwal, R., London, E., ۱۹۹۶. Comparison of the conformation, hydrophobicity, ...
  • Pappenheimer Jr, A., ۱۹۳۷. Diphtheria Toxin. I. Isolation and Characterization ...
  • Parrinello, M., Rahman, A., Vashishta, P., ۱۹۸۳. Structural transitions in ...
  • Purohit, R., Rajendran, V., Sethumadhavan, R., ۲۰۱۱. Relationship between mutation ...
  • Purohit, R., Sethumadhavan, R., ۲۰۰۹. Structural basis for the resilience ...
  • Rajendran, V., Purohit, R., Sethumadhavan, R., ۲۰۱۲. In silico investigation ...
  • Richmond, T.J., ۱۹۸۴. Solvent accessible surface area and excluded volume ...
  • Salomon‐Ferrer, R., Case, D.A., Walker, R.C., ۲۰۱۳. An overview of ...
  • Satpathy, R., Guru, R.K., Behera, R., Priyadarshini, A., ۲۰۱۰. Homology ...
  • Steere, B., Eisenberg, D., ۲۰۰۰. Characterization of high-order diphtheria toxin ...
  • Vehlow, C., Stehr, H., Winkelmann, M., Duarte, J.M., Petzold, L., ...
  • Vendome, J., Posy, S., Jin, X., Bahna, F., Ahlsen, G., ...
  • Zhao, J.-M., London, E., ۱۹۸۶. Similarity of the conformation of ...
  • Zhao, Y., Zeng, C., Massiah, M.A., ۲۰۱۵. Molecular Dynamics Simulation ...
  • Zhou, Z., Feng, H., Ghirlando, R., Bai, Y., ۲۰۰۸. The ...
    • نمایش کامل مراجع