| dc.description.abstract | Dengue is caused by one of four related viruses. Even though few vaccines are
already available and more are in the stage of the clinical trial, all of them have their
drawbacks. Therefore, developing a vaccine against the dengue virus is among the
top priorities in the field. The main objective of this research is to study the
dynamics of the pre-fusion conformation of the dengue virus envelope protein to
design a vaccine candidate using computational methods. For that, the changes in
the dengue virus pre-fusion envelope protein were investigated using Molecular
Dynamics simulations. The present study focused on the dengue virus envelope
protein, serotype 2 (PDB ID: 10KE), and serotype 3 (PDB ID: 1UZG). RMSF, RMSD,
experimental B-factor, and secondary structure profile analyses were carried out
using NAMD and VMD software packages to investigate the dynamics of the prefusion
conformation. Mean RMSD, mean RMSF, and B-factor were higher in
serotype 3 when compared to serotype 2. Domain Ⅲ displayed higher fluctuations
in RMSD when compared to other domains. RMSF of the side chain displayed higher
values in the positions where glycans are present. The secondary structure profile
revealed that both serotypes contain a higher percentage of β sheets. Our
preliminary data indicated that the structural stability of serotype 2 is relatively
higher compared to serotype 3. Additionally, the lowest structural deviation was
observed within domain Ⅱ of the dengue virus. The observations obtained from
this study lays the foundation for the development of a vaccine against the dengue
virus. | en_US |
