3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules
A fast way to reconstruct and validate the three-dimensional molecular conformation of SARS-CoV-2 virus proteins is addressed in this article, involving the most worrying variant discovered in patients from Brazil so far in late 2021, the lineage B.1.1.28/P.1. The proposed methodology is based on t...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Centro Latinoamericano de Estudios en Informática
2022-05-01
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| Series: | CLEI Electronic Journal |
| Subjects: | |
| Online Access: | https://clei.org/cleiej/index.php/cleiej/article/view/540 |
| _version_ | 1818553420670304256 |
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| author | Clarice de Souza Micael Oliveira João Alfredo Bessa Kelson Mota Rosiane de Freitas |
| author_facet | Clarice de Souza Micael Oliveira João Alfredo Bessa Kelson Mota Rosiane de Freitas |
| author_sort | Clarice de Souza |
| collection | DOAJ |
| description |
A fast way to reconstruct and validate the three-dimensional molecular conformation of SARS-CoV-2 virus proteins is addressed in this article, involving the most worrying variant discovered in patients from Brazil so far in late 2021, the lineage B.1.1.28/P.1. The proposed methodology is based on the sequencing of virus proteins and that, through the incorporation of mutations in silico, which are then computationally reconstructed using an enumerative feasibility algorithm validated by the Ramachandran diagram and structural alignment, in addition to the subsequent study of structural stability through classical molecular dynamics. From the resulting structure to the ACE2-RBD complex, the valid solution presented 97.06\% of the residues in the most favorable region while the reference crystallographic structure presented 95.0\%, a difference therefore very small and revealing the great consistency of the developed algorithm. Another important result was the low RMSD alignment between the best solution by the BP algorithm and the reference structure, where we obtained 0.483 A. Finally, the molecular dynamics indicated greater structural stability in the ACE2-RBD interaction with the P.1 strain, which could be a plausible explanation for convergent evolution that provides an increase in the interaction affinity with the ACE2 receptor.
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| first_indexed | 2024-12-12T09:25:36Z |
| format | Article |
| id | doaj.art-2c90c58d9ef943cba1befd75234794f1 |
| institution | Directory Open Access Journal |
| issn | 0717-5000 |
| language | English |
| last_indexed | 2024-12-12T09:25:36Z |
| publishDate | 2022-05-01 |
| publisher | Centro Latinoamericano de Estudios en Informática |
| record_format | Article |
| series | CLEI Electronic Journal |
| spelling | doaj.art-2c90c58d9ef943cba1befd75234794f12022-12-22T00:29:02ZengCentro Latinoamericano de Estudios en InformáticaCLEI Electronic Journal0717-50002022-05-0125210.19153/cleiej.25.2.93D structural prediction, analysis and validation of Sars-Cov-2 protein moleculesClarice de Souza0Micael Oliveira1João Alfredo Bessa2Kelson Mota3Rosiane de Freitas4Universidade Federal do Amazonas Federal University of AmazonasFederal University of AmazonasFederal University of AmazonasFederal University of Amazonas A fast way to reconstruct and validate the three-dimensional molecular conformation of SARS-CoV-2 virus proteins is addressed in this article, involving the most worrying variant discovered in patients from Brazil so far in late 2021, the lineage B.1.1.28/P.1. The proposed methodology is based on the sequencing of virus proteins and that, through the incorporation of mutations in silico, which are then computationally reconstructed using an enumerative feasibility algorithm validated by the Ramachandran diagram and structural alignment, in addition to the subsequent study of structural stability through classical molecular dynamics. From the resulting structure to the ACE2-RBD complex, the valid solution presented 97.06\% of the residues in the most favorable region while the reference crystallographic structure presented 95.0\%, a difference therefore very small and revealing the great consistency of the developed algorithm. Another important result was the low RMSD alignment between the best solution by the BP algorithm and the reference structure, where we obtained 0.483 A. Finally, the molecular dynamics indicated greater structural stability in the ACE2-RBD interaction with the P.1 strain, which could be a plausible explanation for convergent evolution that provides an increase in the interaction affinity with the ACE2 receptor. https://clei.org/cleiej/index.php/cleiej/article/view/540algorithmsBranch-and-Prune methodCOVID-19 pandemicNuclear Magnetic Resonanceprotein foldingSARS-CoV-2 |
| spellingShingle | Clarice de Souza Micael Oliveira João Alfredo Bessa Kelson Mota Rosiane de Freitas 3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules CLEI Electronic Journal algorithms Branch-and-Prune method COVID-19 pandemic Nuclear Magnetic Resonance protein folding SARS-CoV-2 |
| title | 3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules |
| title_full | 3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules |
| title_fullStr | 3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules |
| title_full_unstemmed | 3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules |
| title_short | 3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules |
| title_sort | 3d structural prediction analysis and validation of sars cov 2 protein molecules |
| topic | algorithms Branch-and-Prune method COVID-19 pandemic Nuclear Magnetic Resonance protein folding SARS-CoV-2 |
| url | https://clei.org/cleiej/index.php/cleiej/article/view/540 |
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