Computational assessment of structural stability of E protein variants in coronaviridae
Studies on coronaviruses have received spotlight due to the CoVID-19 pandemic. These studies range from determining the structure of the protein, pathway of infection to exploring therapeutic targets within the protein. Although E protein has been proven critical for viral assembly and maturati...
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Final Year Project (FYP) |
| Language: | English |
| Published: |
Nanyang Technological University
2022
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/160699 |
| _version_ | 1826117712223404032 |
|---|---|
| author | Teo, Valerie Fang Wei |
| author2 | Konstantin Pervushin |
| author_facet | Konstantin Pervushin Teo, Valerie Fang Wei |
| author_sort | Teo, Valerie Fang Wei |
| collection | NTU |
| description | Studies on coronaviruses have received spotlight due to the CoVID-19 pandemic. These studies
range from determining the structure of the protein, pathway of infection to exploring therapeutic
targets within the protein. Although E protein has been proven critical for viral assembly and
maturation and is completely conserved in genomes of all four genera of the coronaviridae, little
is known about the function of the smallest protein encoded in SARS-CoV-2. There are many
uncertainties regarding reliability of Swiss Model predicting its 3D structure though it is the most
used homology modelling server. In this study, Molecular Dynamics simulation was performed
for 1 sequence per genus to check their stability in a lipid bilayer using GROMACS. The
primary focus is to identify the most thermostable sequence variant of E protein with the greatest
potential for structural and drug discovery studies. Results showed that the sequence from Delta
genera was the most stable, followed by Beta, Alpha then Gamma. Although conclusion derived
from Swiss Model and simulations were the same, the simulations were more informative and
reliable. Findings presented provide an alternative to traditional homology modelling and
provide a deeper understanding to E proteins stability and their amenability to structural and
relationship studies. |
| first_indexed | 2024-10-01T04:31:45Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/160699 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:31:45Z |
| publishDate | 2022 |
| publisher | Nanyang Technological University |
| record_format | dspace |
| spelling | ntu-10356/1606992023-02-28T18:09:39Z Computational assessment of structural stability of E protein variants in coronaviridae Teo, Valerie Fang Wei Konstantin Pervushin School of Biological Sciences KPervushin@ntu.edu.sg Science::Biological sciences Studies on coronaviruses have received spotlight due to the CoVID-19 pandemic. These studies range from determining the structure of the protein, pathway of infection to exploring therapeutic targets within the protein. Although E protein has been proven critical for viral assembly and maturation and is completely conserved in genomes of all four genera of the coronaviridae, little is known about the function of the smallest protein encoded in SARS-CoV-2. There are many uncertainties regarding reliability of Swiss Model predicting its 3D structure though it is the most used homology modelling server. In this study, Molecular Dynamics simulation was performed for 1 sequence per genus to check their stability in a lipid bilayer using GROMACS. The primary focus is to identify the most thermostable sequence variant of E protein with the greatest potential for structural and drug discovery studies. Results showed that the sequence from Delta genera was the most stable, followed by Beta, Alpha then Gamma. Although conclusion derived from Swiss Model and simulations were the same, the simulations were more informative and reliable. Findings presented provide an alternative to traditional homology modelling and provide a deeper understanding to E proteins stability and their amenability to structural and relationship studies. Bachelor of Science in Biomedical Sciences 2022-08-01T06:43:04Z 2022-08-01T06:43:04Z 2022 Final Year Project (FYP) Teo, V. F. W. (2022). Computational assessment of structural stability of E protein variants in coronaviridae. Final Year Project (FYP), Nanyang Technological University, Singapore. https://hdl.handle.net/10356/160699 https://hdl.handle.net/10356/160699 en application/pdf Nanyang Technological University |
| spellingShingle | Science::Biological sciences Teo, Valerie Fang Wei Computational assessment of structural stability of E protein variants in coronaviridae |
| title | Computational assessment of structural stability of E protein variants in coronaviridae |
| title_full | Computational assessment of structural stability of E protein variants in coronaviridae |
| title_fullStr | Computational assessment of structural stability of E protein variants in coronaviridae |
| title_full_unstemmed | Computational assessment of structural stability of E protein variants in coronaviridae |
| title_short | Computational assessment of structural stability of E protein variants in coronaviridae |
| title_sort | computational assessment of structural stability of e protein variants in coronaviridae |
| topic | Science::Biological sciences |
| url | https://hdl.handle.net/10356/160699 |
| work_keys_str_mv | AT teovaleriefangwei computationalassessmentofstructuralstabilityofeproteinvariantsincoronaviridae |