| تعداد نشریات | 286 |
| تعداد نشریات سازمان | 84 |
| تعداد شماره‌ها | 3,020 |
| تعداد مقالات | 33,742 |
| تعداد مشاهده مقاله | 44,988,803 |
| تعداد دریافت فایل اصل مقاله | 47,429,508 |
Identification of Conformational B-cell Epitopes in Diphtheria Toxin at Varying Temperatures Using Molecular Dynamics Simulations | ||
| Archives of Razi Institute | ||
| مقاله 3، دوره 75، شماره 4، اسفند 2020، صفحه 427-437 اصل مقاله (691.22 K) | ||
| نوع مقاله: Original Articles | ||
| شناسه دیجیتال (DOI): 10.22092/ari.2019.127251.1377 | ||
| نویسندگان | ||
| S. Ghaderi1؛ M. R. Bozorgmehr2؛ M. Ahmadi* 3؛ Sh. Tarahomjoo4 | ||
| 1Division of Central Laboratory, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran | ||
| 2Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran | ||
| 3Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran | ||
| 4Division of Genomics and Genetic Engineering, Department of Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran | ||
| چکیده | ||
| 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. | ||
| کلیدواژه‌ها | ||
| B-cell epitope؛ Diphtheria toxin؛ Molecular dynamics simulation؛ Stability؛ Temperature | ||
|
سایر فایل های مرتبط با مقاله
|
||
| مراجع | ||
|
Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., et al., 2015. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19-25.
Anandakrishnan, R., Aguilar, B., Onufriev, A.V., 2012. H++ 3.0: automating p K prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res 40, 537-541.
Arfken, G., 1985. The method of steepest descents. Math Methods Phys 3, 428-436.
Audibert, F., Jolivet, M., Chedid, L., Alouf, J., Boquet, P., Rivaille, P., et al., 1981. Active antitoxic immunization by a diphtheria toxin synthetic oligopeptide. Nature 289, 593-594.
Boquet, P., Alouf, J.E., Duflot, E., Siffert, O., Rivaille, P., 1982. Characteristics of guinea-pig immune sera elicited by a synthetic diphtheria toxin oligopeptide. Mol Immunol 19, 1541-1549.
Brüschweiler, R., 2003. Efficient RMSD measures for the comparison of two molecular ensembles. Proteins 50, 26-34.
Bussi, G., Donadio, D., Parrinello, M., 2007. Canonical sampling through velocity rescaling. J Chem Phys 126, 014101.
Chenal, A., Nizard, P., Gillet, D., 2002. Structure and function of diphtheria toxin: from pathology to engineering. J Toxicol: Toxin Rev 21, 321-359.
Darden, T., York, D., Pedersen, L., 1993. Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. J Chem Phys 98, 10089-10092.
Diamond, R., 1976. On the comparison of conformations using linear and quadratic transformations. ACTA Crystall A-CRYS 32, 1-10.
Diamond, R., 1988. A note on the rotational superposition problem. Acta Crystallogr A: Found Crystallogr 44, 211-216.
Falnes, P.O., Olsnes, S., 1995. Cell-mediated reduction and incomplete membrane translocation of diphtheria toxin mutants with internal disulfides in the A fragment. J Biol Chem 270, 20787-20793.
Ghaderi, S., Tarahomjoo, S., Bozorgmehr, M.R., 2016. Utilizing molecular dynamics simulations for identification of conformational B-cell epitopes in diphtheria toxin at varying pHs. J Chem, Biol Phys Sci 7, 85-91.
Gordon, V.M., Leppla, S.H., 1994. Proteolytic activation of bacterial toxins: role of bacterial and host cell proteases. Infect Immun 62, 333-340.
Grubmüller, H., Heller, H., Windemuth, A., Schulten, K., 1991. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol Simulat 6, 121-142.
Guerineau, F., Sorensen, A.M., Fenby, N., Scott, R.J., 2003. Temperature sensitive diphtheria toxin confers conditional male‐sterility in Arabidopsis thaliana. Plant Biotechnol J 1, 33-42.
Hess, B., Bekker, H., Berendsen, H.J., Fraaije, J.G., 1997. LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18, 1463-1472.
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., Simmerling, C., 2006. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725.
Johnson, A., Johnson, T., Khan, A., 2012. Thermostats in Molecular Dynamics Simulations. UMass 1, 29.
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys 79, 926-935.
Kabsch, W., 1976. A solution for the best rotation to relate two sets of vectors. ACTA Crystall A-CRYS 32, 922-923.
Kabsch, W., Sander, C., 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
Kövér, K., Bruix, M., Santoro, J., Batta, G., Laurents, D., Rico, M., 2008. The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition. J Mol Biol 379, 953-965.
Kräutler, V., Van Gunsteren, W.F., Hünenberger, P.H., 2001. A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J Comput Chem 22, 501-508.
Krieger, E., Vriend, G., 2015. New ways to boost molecular dynamics simulations. J Comput Chem 36, 996-1007.
Laurents, D., Pérez‐Cañadillas, J.M., Santoro, J., Rico, M., Schell, D., Pace, C.N., et al., 2001. Solution structure and dynamics of ribonuclease Sa. Proteins 44, 200-211.
Lobanov, M.Y., Bogatyreva, N., Galzitskaya, O., 2008. Radius of gyration as an indicator of protein structure compactness. Mol Biol 42, 623-628.
London, E., 1992. Diphtheria toxin: membrane interaction and membrane translocation. Biochim Biophys Acta 1113, 25-51.
Menestrina, G., Schiavo, G., Montecucco, C., 1994. Molecular mechanisms of action of bacterial protein toxins. Mol Aspects Med 15, 79-193.
Oh, K.J., Zhan, H., Cui, C., Hideg, K., Collier, R.J., Hubbell, W.L., 1996. Organization of diphtheria toxin T domain in bilayers: a site-directed spin labeling study. Science 273, 810-812.
Paliwal, R., London, E., 1996. Comparison of the conformation, hydrophobicity, and model membrane interactions of diphtheria toxin to those of formaldehyde-treated toxin (diphtheria toxoid): formaldehyde stabilization of the native conformation inhibits changes that allow membrane insertion. Biochemistry 35, 2374-2379.
Pappenheimer Jr, A., 1937. Diphtheria Toxin. I. Isolation and Characterization of a Toxic Protein from Corynebacterium diphtheriae Filtrates. J Biol Chem 120, 543-553.
Parrinello, M., Rahman, A., Vashishta, P., 1983. Structural transitions in superionic conductors. Phys Rev Lett 50, 1073-1076.
Purohit, R., Rajendran, V., Sethumadhavan, R., 2011. Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: an in silico analysis. J Mol Model 17, 869-877.
Purohit, R., Sethumadhavan, R., 2009. Structural basis for the resilience of Darunavir (TMC114) resistance major flap mutations of HIV-1 protease. Interdiscip Sci 1, 320-328.
Rajendran, V., Purohit, R., Sethumadhavan, R., 2012. In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein. Amino Acids 43, 603-615.
Richmond, T.J., 1984. Solvent accessible surface area and excluded volume in proteins: Analytical equations for overlapping spheres and implications for the hydrophobic effect. J Mol Biol 178, 63-89.
Salomon‐Ferrer, R., Case, D.A., Walker, R.C., 2013. An overview of the Amber biomolecular simulation package. Wiley Interdiscip Rev Computa Mol Sci 3, 198-210.
Satpathy, R., Guru, R.K., Behera, R., Priyadarshini, A., 2010. Homology modelling of lycopene cleavage oxygenase: The key enzyme of bixin production. J Comput Sci Syst Biol 3, 059-061.
Steere, B., Eisenberg, D., 2000. Characterization of high-order diphtheria toxin oligomers. Biochemistry 39, 15901-15909.
Vehlow, C., Stehr, H., Winkelmann, M., Duarte, J.M., Petzold, L., Dinse, J., et al., 2011. CMView: interactive contact map visualization and analysis. Bioinformatics 27, 1573-1574.
Vendome, J., Posy, S., Jin, X., Bahna, F., Ahlsen, G., Shapiro, L., et al., 2011. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Nat Struct Mol Biol 18, 693-700.
Zhao, J.-M., London, E., 1986. Similarity of the conformation of diphtheria toxin at high temperature to that in the membrane-penetrating low-pH state. P Natl A Sci 83, 2002-2006.
Zhao, Y., Zeng, C., Massiah, M.A., 2015. Molecular Dynamics Simulation Reveals Insights into the Mechanism of Unfolding by the A130T/V Mutations within the MID1 Zinc-Binding Bbox1 Domain. PloS one 10, e0124377.
Zhou, Z., Feng, H., Ghirlando, R., Bai, Y., 2008. The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H. J Mol Biol 384, 531-539. | ||
|
آمار تعداد مشاهده مقاله: 15,877 تعداد دریافت فایل اصل مقاله: 26,958 |
||
